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- PDB-7ay0: Crystal structure of truncated USP1-UAF1 -

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Basic information

Entry
Database: PDB / ID: 7ay0
TitleCrystal structure of truncated USP1-UAF1
Components
  • Ubiquitin carboxyl-terminal hydrolase 1
  • WD repeat-containing protein 48
KeywordsHYDROLASE / deubiquitination / specificity / DNA repair / Fanconi Anemia
Function / homology
Function and homology information


regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / homeostasis of number of cells / protein deubiquitination ...regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / homeostasis of number of cells / protein deubiquitination / embryonic organ development / single fertilization / regulation of DNA repair / response to UV / positive regulation of double-strand break repair via homologous recombination / ubiquitin binding / positive regulation of epithelial cell proliferation / skeletal system development / positive regulation of receptor signaling pathway via JAK-STAT / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / regulation of protein stability / multicellular organism growth / late endosome / peptidase activity / single-stranded DNA binding / double-stranded DNA binding / spermatogenesis / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / cysteine-type endopeptidase activity / DNA repair / intracellular membrane-bounded organelle / DNA damage response / proteolysis / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase ...WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 1 / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsArkinson, C. / Rennie, M.L. / Walden, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2015-CoG-681582 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_12016/12 United Kingdom
Citation
Journal: Nat Struct Mol Biol / Year: 2021
Title: Structural basis of FANCD2 deubiquitination by USP1-UAF1.
Authors: Martin L Rennie / Connor Arkinson / Viduth K Chaugule / Rachel Toth / Helen Walden /
Abstract: Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1-UAF1 complex is the ...Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1-UAF1 complex is the monoubiquitinated FANCI-FANCD2 heterodimer, which is involved in the repair of DNA interstrand crosslinks via the Fanconi anemia pathway. Here we determine structures of human USP1-UAF1 with and without ubiquitin and bound to monoubiquitinated FANCI-FANCD2. The crystal structures of USP1-UAF1 reveal plasticity in USP1 and key differences to USP12-UAF1 and USP46-UAF1, two related proteases. A cryo-EM reconstruction of USP1-UAF1 in complex with monoubiquitinated FANCI-FANCD2 highlights a highly orchestrated deubiquitination process, with USP1-UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for the requirement of both proteins, despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1-UAF1 regulation and substrate recognition.
#1: Journal: Biorxiv / Year: 2020
Title: Structural basis of FANCD2 deubiquitination by USP1-UAF1
Authors: Rennie, M.L. / Arkinson, C. / Chaugule, V.K. / Toth, R. / Walden, H.
History
DepositionNov 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Apr 14, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 27, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 48
B: Ubiquitin carboxyl-terminal hydrolase 1
C: WD repeat-containing protein 48
D: Ubiquitin carboxyl-terminal hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,8206
Polymers216,6904
Non-polymers1312
Water00
1
A: WD repeat-containing protein 48
B: Ubiquitin carboxyl-terminal hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4103
Polymers108,3452
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: WD repeat-containing protein 48
D: Ubiquitin carboxyl-terminal hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4103
Polymers108,3452
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.570, 119.570, 195.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 13 through 329 or resid 345 through 479 or resid 502 through 559))
21(chain C and (resid 13 through 329 or resid 345 through 559))
12(chain B and (resid 84 through 116 or resid 144...
22(chain D and (resid 84 through 116 or resid 144...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGILEILE(chain A and (resid 13 through 329 or resid 345 through 479 or resid 502 through 559))AA13 - 32913 - 329
121PROPROVALVAL(chain A and (resid 13 through 329 or resid 345 through 479 or resid 502 through 559))AA345 - 479345 - 479
131LYSLYSMETMET(chain A and (resid 13 through 329 or resid 345 through 479 or resid 502 through 559))AA502 - 559502 - 559
211ARGARGILEILE(chain C and (resid 13 through 329 or resid 345 through 559))CC13 - 32913 - 329
221PROPROMETMET(chain C and (resid 13 through 329 or resid 345 through 559))CC345 - 559345 - 559
112ASNASNILEILE(chain B and (resid 84 through 116 or resid 144...BB84 - 11620 - 52
122GLUGLUPROPRO(chain B and (resid 84 through 116 or resid 144...BB144 - 16766 - 89
132THRTHRMETMET(chain B and (resid 84 through 116 or resid 144...BB176 - 19198 - 113
142ASPASPLYSLYS(chain B and (resid 84 through 116 or resid 144...BB199 - 219121 - 141
152VALVALGLUGLU(chain B and (resid 84 through 116 or resid 144...BB426 - 541168 - 283
162GLYGLYVALVAL(chain B and (resid 84 through 116 or resid 144...BB547 - 600289 - 342
172TRPTRPPROPRO(chain B and (resid 84 through 116 or resid 144...BB747 - 769359 - 381
182THRTHRLEULEU(chain B and (resid 84 through 116 or resid 144...BB774 - 785386 - 397
192ZNZNZNZN(chain B and (resid 84 through 116 or resid 144...BE1000
212ASNASNILEILE(chain D and (resid 84 through 116 or resid 144...DD84 - 11620 - 52
222GLUGLULYSLYS(chain D and (resid 84 through 116 or resid 144...DD144 - 21966 - 141
232VALVALGLUGLU(chain D and (resid 84 through 116 or resid 144...DD426 - 464168 - 206
242METMETLEULEU(chain D and (resid 84 through 116 or resid 144...DD482 - 785224 - 397
252ZNZNZNZN(chain D and (resid 84 through 116 or resid 144...DF1000

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.777939431227, -0.626484731248, 0.0482402617584), (0.624267481719, -0.779343112111, -0.0539854135208), (0.0714167530087, -0.0118825551635, 0.997375782878)9.09271152201, -87.7424812476, 30.2825225622
2given(-0.782156254805, -0.623044408296, 0.00687447170686), (0.619601924722, -0.778904464798, -0.0969602475178), (0.0657650967485, -0.0715786281625, 0.995264513604)7.51846811672, -89.3498048125, 26.4843352342

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Components

#1: Protein WD repeat-containing protein 48 / USP1-associated factor 1 / WD repeat endosomal protein / p80


Mass: 63224.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TAF3
#2: Protein Ubiquitin carboxyl-terminal hydrolase 1


Mass: 45120.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94782*PLUS, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 10% w/v PEG4000, 100 mM MES/Imidazole pH 6.0-6.5, 30 mM CaCl2, 30 mM MgCl2, 20-25% glycerol v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→84.55 Å / Num. obs: 25470 / % possible obs: 80.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 78.46 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.108 / Rrim(I) all: 0.258 / Net I/σ(I): 6.4
Reflection shellResolution: 3.602→3.754 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1264 / CC1/2: 0.565 / Rpim(I) all: 0.727 / Rrim(I) all: 1.698 / % possible all: 34.2

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVN (side chains removed), 5CVL

5cvn

5cvl


Resolution: 3.6→59.78 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1328 5.21 %
Rwork0.235 24139 -
obs0.2366 25467 80.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.6 Å2 / Biso mean: 86.5725 Å2 / Biso min: 32.43 Å2
Refinement stepCycle: final / Resolution: 3.6→59.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12747 0 2 0 12749
Biso mean--69.26 --
Num. residues----1610
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4790X-RAY DIFFRACTION10.7TORSIONAL
12C4790X-RAY DIFFRACTION10.7TORSIONAL
21B2416X-RAY DIFFRACTION10.7TORSIONAL
22D2416X-RAY DIFFRACTION10.7TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.750.3749520.3071144119634
3.75-3.920.2664650.28351383144842
3.92-4.120.326910.27461770186153
4.12-4.380.32311880.26133107329594
4.38-4.720.25281840.222733063490100
4.72-5.190.25451590.214833883547100
5.19-5.940.2752090.252433053514100
5.94-7.490.27531870.241633633550100
7.49-59.780.22081930.204633733566100
Refinement TLS params.Method: refined / Origin x: 29.5642 Å / Origin y: -35.2322 Å / Origin z: -27.7453 Å
111213212223313233
T0.3964 Å2-0.0848 Å2-0.0555 Å2-0.3472 Å20.1139 Å2--0.336 Å2
L0.6705 °2-0.3735 °2-0.2238 °2-1.128 °20.4517 °2--0.4068 °2
S0.032 Å °0.0772 Å °-0.0387 Å °-0.0905 Å °-0.1326 Å °-0.0154 Å °0.019 Å °-0.0637 Å °0.1107 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 559
2X-RAY DIFFRACTION1allB81 - 785
3X-RAY DIFFRACTION1allB1000
4X-RAY DIFFRACTION1allC13 - 559
5X-RAY DIFFRACTION1allD84 - 785
6X-RAY DIFFRACTION1allD1000

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