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- PDB-7w3u: USP34 catalytic domain in complex with UbPA -

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Basic information

Entry
Database: PDB / ID: 7w3u
TitleUSP34 catalytic domain in complex with UbPA
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 34
KeywordsHYDROLASE / USP34 in complex
Function / homology
Function and homology information


protein K48-linked deubiquitination / protein deubiquitination / TCF dependent signaling in response to WNT / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity ...protein K48-linked deubiquitination / protein deubiquitination / TCF dependent signaling in response to WNT / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / nucleus / cytosol
Similarity search - Function
Domain of unknown function DUF3517 / Domain of unknown function (DUF3517) / 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 ...Domain of unknown function DUF3517 / Domain of unknown function (DUF3517) / 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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Ubiquitin B / Ubiquitin carboxyl-terminal hydrolase 34
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsXu, G.L. / Ming, Z.H.
Funding support2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052
National Natural Science Foundation of China (NSFC)81871938
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Insights into the Catalytic Mechanism and Ubiquitin Recognition of USP34.
Authors: Xu, G. / Su, H. / Lu, L. / Liu, X. / Zhao, L. / Tang, B. / Ming, Z.
History
DepositionNov 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Feb 7, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Apr 24, 2024Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 34
B: Ubiquitin carboxyl-terminal hydrolase 34
C: Ubiquitin carboxyl-terminal hydrolase 34
D: Polyubiquitin-B
E: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,62012
Polymers160,2536
Non-polymers3686
Water0
1
A: Ubiquitin carboxyl-terminal hydrolase 34
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5404
Polymers53,4182
Non-polymers1232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-2 kcal/mol
Surface area19180 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 34
E: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5404
Polymers53,4182
Non-polymers1232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-5 kcal/mol
Surface area18740 Å2
MethodPISA
3
C: Ubiquitin carboxyl-terminal hydrolase 34
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5404
Polymers53,4182
Non-polymers1232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-8 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.020, 71.330, 111.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 34 / Deubiquitinating enzyme 34 / Ubiquitin thioesterase 34 / Ubiquitin-specific-processing protease 34


Mass: 44897.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP34, KIAA0570, KIAA0729
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q70CQ2, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J3QS39
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE / Allylamine


Mass: 57.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7N
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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.13→23.596 Å / Num. obs: 27763 / % possible obs: 99.62 % / Redundancy: 15.21 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.5
Reflection shellResolution: 3.13→3.242 Å / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W3R

7w3r


Resolution: 3.13→23.596 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 3751 7.22 %
Rwork0.2166 48207 -
obs0.2187 27700 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.28 Å2 / Biso mean: 70 Å2 / Biso min: 48.29 Å2
Refinement stepCycle: final / Resolution: 3.13→23.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10105 0 15 0 10120
Biso mean--105.71 --
Num. residues----1239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.13-3.16950.37081410.35261804100
3.1695-3.21110.3751370.35271770100
3.2111-3.2550.36591450.3431822100
3.255-3.30140.30411380.31780100
3.3014-3.35050.37321400.31731753100
3.3505-3.40280.30791420.29521812100
3.4028-3.45840.3021330.27141745100
3.4584-3.51780.29661370.2631813100
3.5178-3.58160.3191410.26371815100
3.5816-3.65020.28431390.24971759100
3.6502-3.72440.2921370.24341819100
3.7244-3.80510.25381360.23541749100
3.8051-3.89320.27351430.2341819100
3.8932-3.99010.22851450.2126178299
3.9901-4.09750.26551390.19631766100
4.0975-4.21740.26511340.19511775100
4.2174-4.35270.2151400.18281789100
4.3527-4.50730.19461380.1731806100
4.5073-4.68640.20391380.17911786100
4.6864-4.89780.18541370.17571803100
4.8978-5.15350.18741370.1731778100
5.1535-5.47270.23161400.19541803100
5.4727-5.88910.28281370.21131780100
5.8891-6.47070.23761440.22691784100
6.4707-7.38180.24951390.21711782100
7.3818-9.20740.20941310.18231782100
9.2074-23.5960.20571430.1895173196
Refinement TLS params.Method: refined / Origin x: 25.9224 Å / Origin y: 48.5643 Å / Origin z: 17.549 Å
111213212223313233
T0.5663 Å20.0233 Å20.0454 Å2-0.4694 Å2-0.0834 Å2--0.6127 Å2
L0.6056 °20.1998 °2-0.0887 °2-1.0609 °2-0.4447 °2--1.761 °2
S-0.001 Å °0.1657 Å °-0.002 Å °-0.2655 Å °0.069 Å °-0.0951 Å °-0.0879 Å °0.1724 Å °-0.0625 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1892 - 2268
2X-RAY DIFFRACTION1allA2289
3X-RAY DIFFRACTION1allB1892 - 2267
4X-RAY DIFFRACTION1allB2289
5X-RAY DIFFRACTION1allC1892 - 2268
6X-RAY DIFFRACTION1allC2289
7X-RAY DIFFRACTION1allD1 - 75
8X-RAY DIFFRACTION1allD101
9X-RAY DIFFRACTION1allE1 - 75
10X-RAY DIFFRACTION1allE101
11X-RAY DIFFRACTION1allF1 - 75
12X-RAY DIFFRACTION1allF101

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