Landscape of nuclear transport receptor cargo specificity.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29254951", "kind": "science-record", "revision": 6, "content_hash": "sha256:4fb0891ac5e205faa5f812f8ceac92d4681a3fa70f8163a72e9eb0762d8e9191", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:21:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Landscape of nuclear transport receptor cargo specificity.", "doi": "10.15252/msb.20177608", "pmid": "29254951", "authors": ["Marie-Therese Mackmull", "Bernd Klaus", "Ivonne Heinze", "Manopriya Chokkalingam", "Andreas Beyer", "Robert B Russell", "Alessandro Ori", "Martin Beck"], "journal": "Molecular systems biology", "year": 2017, "abstract": "Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo-NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.", "claims": [{"id": "claim-data-access", "statement": "The data set generated in this study is available in the following database:\n\nMass spectrometry proteomics data: PRIDE PXD007976 (https://www.ebi.ac.uk/pride/archive/projects/PXD007976) (Vizcaino et al, 2013).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29254951", "locator": "sections[22] \"Data availability\" paragraphs 1-3", "quote": "The data set generated in this study is available in the following database:\n\nMass spectrometry proteomics data: PRIDE PXD007976 (https://www.ebi.ac.uk/pride/archive/projects/PXD007976) (Vizcaino et al, 2013)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used BioID coupled to mass spectrometry with a statistical framework for estimating interaction specificity and false discovery rates to map NTR–cargo relationships in situ, and deposited the source data in ProteomeXchange under PXD007976.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29254951", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To systematically map cargo–NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID)."}, {"asset": "source:pmid:29254951", "locator": "sections[1] \"Introduction\" paragraph 7", "quote": "We implemented novel approaches to estimate the specificity of interactions and false discovery rate (FDR) in BioID experiments."}, {"asset": "source:pmid:29254951", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD007976."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used BioID coupled to mass spectrometry with a statistical framework for estimating interaction specificity and false discovery rates to map NTR–cargo relationships in situ, and deposited the source data in ProteomeXchange under PXD007976.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29254951"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD007976"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD007976"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29254951", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.15252/msb.20177608", "sha256": "sha256:cbf06513df61419501c7d4f76f64acfcd8d0e160a6dc5fc6800b59bff5136cf3", "bytes": 74366, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.15252/msb.20177608", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5740495", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD007976", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD007976", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD007976", "version": null, "note": "The data set generated in this study is available in the following database:\n\nMass spectrometry proteomics data: PRIDE PXD007976 (https://www.ebi.ac.uk/pride/archive/projects/PXD007976) (Vizcaino et al, 2013).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data set generated in this study is available in the following database:\n\nMass spectrometry proteomics data: PRIDE PXD007976 (https://www.ebi.ac.uk/pride/archive/projects/PXD007976) (Vizcaino et al, 2013).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Landscape of nuclear transport receptor cargo specificity", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29254951:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0c96d6520fb99198dc02870e79e4e308d4e9e8e80271f805422fead8bf9bbdec", "bytes": 3877, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#msb177608-tbl-0001", "version": null, "note": "Overview of enriched protein complexes and identified biotinylated subunits", "structure": {"pmcid": "PMC5740495", "section_index": 9, "section_title": "Discussion", "row_count": 55, "column_count": 5}, "table": {"label": "Table 1", "caption": "Overview of enriched protein complexes and identified biotinylated subunits", "rows": [["NTR", "Enriched protein complexes and proteins of similar biological function", "Number of identified subunits (ES > 25)", "Biotinylated subunit"], ["NTR‐BirA*", "BirA*‐NTR"], ["IMA1", "Condensin ll complex", "5 (5)", "4 (0)", "SMC4, hCAP‐D3"], ["H/ACA ribonucleoprotein complex", "5 (5)", "3 (0)", "DKC1"], ["DNA replication complex GINS", "3 (3)", "1 (0)", "–"], ["Little elongation complex", "4 (4)", "4 (3)", "ELL, ICE1"], ["Integrator complex", "8 (6)", "7 (0)", "INTS4, INTS10"], ["Exosome complex", "11 (10)", "11 (0)", "EXOSC9, EXOSC10, RRP44"], ["DNA‐directed RNA polymerase l", "9 (9)", "7 (5)", "–"], ["DNA‐directed RNA polymerase lll", "15 (14)", "11 (7)", "RPC3"], ["Chromodomain‐helicase‐DNA‐binding protein", "6 (5)", "6 (1)", "CHD4, CHD7, CHD8"], ["DNA mismatch repair protein", "5 (5)", "5 (2)", "MLH1, MSH6"], ["Mediator of RNA polymerase II transcription", "19 (17)", "13 (3)", "MED1, MED27"], ["MORC family CW‐type zinc finger protein", "3 (3)", "3 (1)", "–"], ["Negative elongation factor", "4 (4)", "4 (1)", "NELF‐A, NELF‐E"], ["Transcription initiation factor TFIID", "13 (13)", "11 (11)", "TAF1, TAF3, TAF7"], ["U6 snRNA‐associated Sm‐like protein", "7 (7)", "6 (6)", "–"], ["Putative polycomb group protein ASXL", "3 (3)", "2 (0)", "–"], ["IMA5", "Condensin ll complex", "4 (1)", "2 (0)", "SMC4"], ["H/ACA ribonucleoprotein complex", "5 (5)", "5 (4)", "DKC1"], ["Little elongation complex", "4 (3)", "4 (2)", "ELL"], ["Integrator complex", "9 (8)", "8 (5)", "INTS4, INTS10, INTS11"], ["Exosome complex", "10 (6)", "11 (1)", "EXOSC9, EXOSC10, RRP44"], ["DNA‐directed RNA polymerase l", "9 (7)", "7 (5)", "RPAC2"], ["DNA‐directed RNA polymerase lll", "13 (9)", "10 (5)", "RPAC2, RPC3"], ["Chromodomain‐helicase‐DNA‐binding protein", "6 (5)", "5 (2)", "CHDL1, CHD3, CHD7, CHD8"], ["DNA mismatch repair protein", "4 (3)", "5 (1)", "MLH1, MSH6"], ["IMA6", "H/ACA ribonucleoprotein complex", "5 (4)", "–", "DKC1"], ["Little elongation complex", "4 (3)", "–", "ICE1"], ["IPO4", "Anaphase‐promoting complex", "9 (3)", "9 (4)", "APC3"], ["AP2 adaptor complex", "5 (3)", "4 (1)", "–"], ["HAUS augmin‐like complex", "8 (8)", "8 (7)", "HAUS2*"], ["Eukaryotic translation initiation factor 3", "13 (9)", "13 (11)", "Subunit D, E, G, J"], ["Activating signal cointegrator (ASC‐1)", "4 (4)", "4 (4)", "TRIP4, ASCC1"], ["Histone chaperone ASF1", "2 (2)", "2 (2)", "–"], ["Transforming acidic coiled‐coil‐containing protein", "3 (3)", "3 (3)", "TACC1, TACC3"], ["IPO5", "Anaphase‐promoting complex", "8 (0)", "9 (9)", "–"], ["AP2 adaptor complex", "5 (0)", "4 (4)", "–"], ["HAUS augmin‐like complex", "8 (2)", "8 (7)", "–"], ["Eukaryotic translation initiation factor 3", "12 (6)", "13 (13)", "Subunit A, D, E, G, J"], ["WASH complex", "4 (2)", "4 (4)", "–"], ["IPO11", "Basic leucine zipper and W2 domain‐containing protein", "2 (2)", "–", "BZW1, BZW2"], ["IPO13", "Special AT‐rich sequence‐binding protein", "–", "2 (2)", "SATB1"], ["TNPO1", "Argonaute protein family", "–", "2 (2)", "–"], ["Nuclear receptor coactivator", "", "6 (5)", "SRC2*"], ["TNPO2", "Argonaute protein family", "3 (3)", "3 (3)", "–"], ["Nuclear receptor coactivator", "6 (6)", "6 (6)", "–"], ["CREB‐regulated transcription coactivator and binding protein", "4 (4)", "4 (4)", "CRTC1, CRTC2, CRTC3"], ["Far upstream element‐binding protein", "3 (2)", "3 (3)", "FUBP1, FUBP2, FUBP3"], ["CCAAT‐box‐binding transcription factor (CTF)", "3 (3)", "3 (2)", "–"], ["XPO1", "Little elongation complex", "4 (4)", "–", "–"], ["Exosome complex", "10 (2)", "", "EXOSC10"], ["XPO2", "DNA replication complex GINS", "3 (3)", "2 (1)", "–"], ["Heterogeneous nuclear ribonucleoprotein", "11 (0)", "21 (17)", "Protein A1, F, M, U, UL1"], ["XPO7", "COP9 signalosome", "–", "9 (9)", "CSN4"]], "row_count": 55, "column_count": 5, "numeric_cells": 109, "header_rows": 2, "locator": "section[9]/table-wrap[1]#msb177608-tbl-0001"}}], "gaps": ["asset:data:geo:PXD007976 not downloaded", "asset:data:geo:PXD007976 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-2", "family": null, "specific": null, "label": "Target-decoy strategy", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“Peptide and protein hits were filtered at a false discovery rate of 1% using a target‐decoy strategy (Elias & Gygi, 2007).”"}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD007976"], "resolved_accessions": ["PXD007976"], "statements": ["The data set generated in this study is available in the following database:\n\nMass spectrometry proteomics data: PRIDE PXD007976 (https://www.ebi.ac.uk/pride/archive/projects/PXD007976) (Vizcaino et al, 2013)."], "basis": "The paper names PXD007976 in PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pearson_r"], "assets": ["source:pmid:29254951", "data:geo:PXD007976", "asset:table:pmid:29254951:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD007976"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:04Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 141881, "completion_tokens": 3328, "cached_tokens": 36384}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:29254951", "type": "paper", "label": "pmid:29254951"}, {"id": "source:pmid:29254951", "type": "manuscript", "label": "PMID 29254951 full text"}, {"id": "data:geo:PXD007976", "type": "dataset", "label": "GEO PXD007976"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29254951", "type": "paper", "label": "pmid:29254951"}, {"id": "source:pmid:29254951", "type": "manuscript", "label": "PMID 29254951 full text"}, {"id": "data:geo:PXD007976", "type": "dataset", "label": "GEO PXD007976"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29254951", "type": "extraction", "used": ["source:pmid:29254951"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD007976", "type": "accession_resolution", "used": ["data:geo:PXD007976"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29254951", "parent_hash": "sha256:12d721c58e782dac7cb75a879f3d12d6632d2e1040a6c1362414df1cd048bbba", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD007976 licence not read", "asset:data:geo:PXD007976 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the enginee", "asm, but non‐straight forward to identify by mass spectrometry. We tagged NTRs with the engineered biotin l", "ic peptides from on‐bead digestion by tandem mass spectrometry in technical duplicates and used label‐free", "NTF2, NXT1, and NXT2 (Table EV1). Due to the proteomic nature of our methodology, we decided to pri"], "order_basis": "paper_text_order:687", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["vated fetal bovine serum (FBS). The parental cell line was grown with the addition of 100 μg/ml Zeocin (Invit", "n proteins in stable human embryonic kidney (HEK293) cell lines for 24 h (Fig 2A). In agreement"], "order_basis": "paper_text_order:2388", "id": "assay:2"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Pearson correlation"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}