[English] 日本語
Yorodumi
- PDB-4wph: Crystal structure of USP7 ubiquitin-like domains in compact confo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wph
TitleCrystal structure of USP7 ubiquitin-like domains in compact conformation
Components
  • ICP0
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / deubiquitinating (DUB) enzyme / ubiquitin-like (Ubl) domains / ICP0 binding site / HAUSP
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / host cell PML body / release from viral latency / regulation of telomere capping / viral tegument / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / DNA alkylation repair / deubiquitinase activity ...symbiont-mediated perturbation of host exit from mitosis / host cell PML body / release from viral latency / regulation of telomere capping / viral tegument / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / DNA alkylation repair / deubiquitinase activity / response to type I interferon / K48-linked deubiquitinase activity / regulation of tumor necrosis factor-mediated signaling pathway / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gluconeogenesis / protein deubiquitination / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / regulation of signal transduction by p53 class mediator / Regulation of PTEN localization / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of protein stability / PML body / RING-type E3 ubiquitin transferase / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / protein polyubiquitination / positive regulation of protein catabolic process / p53 binding / ubiquitin-protein transferase activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / ubiquitin protein ligase activity / rhythmic process / chromosome / ubiquitin-dependent protein catabolic process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / nuclear body / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / Ub-specific processing proteases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cysteine-type endopeptidase activity / host cell nucleus / protein-containing complex / proteolysis / DNA binding / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ICP0 / Ubiquitin C-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Herpes simplex virus
MethodX-RAY DIFFRACTION / Resolution: 2.92 Å
AuthorsPfoh, R. / Lacdao, I. / Saridakis, V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106583 Canada
CitationJournal: Plos Pathog. / Year: 2015
Title: Crystal Structure of USP7 Ubiquitin-like Domains with an ICP0 Peptide Reveals a Novel Mechanism Used by Viral and Cellular Proteins to Target USP7.
Authors: Pfoh, R. / Lacdao, I.K. / Georges, A.A. / Capar, A. / Zheng, H. / Frappier, L. / Saridakis, V.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
C: ICP0
D: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4508
Polymers90,3084
Non-polymers1424
Water70339
1
A: Ubiquitin carboxyl-terminal hydrolase 7
D: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2605
Polymers45,1542
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-19 kcal/mol
Surface area20490 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
C: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1903
Polymers45,1542
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.336, 92.336, 190.283
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 543 - 880 / Label seq-ID: 30 - 367

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 43838.535 Da / Num. of mol.: 2 / Fragment: ubiquitin-like domain (UNP residues 535-888)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)mgk / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide ICP0


Mass: 1315.594 Da / Num. of mol.: 2 / Fragment: USP7 binding sequence / Source method: obtained synthetically / Source: (synth.) Herpes simplex virus (type 1 / strain 17) / References: UniProt: P08393*PLUS
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3000, sodium citrate, L-proline

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.92→30.6 Å / Num. obs: 21012 / % possible obs: 99.5 % / Redundancy: 1.86 % / Net I/σ(I): 22.19
Reflection shellResolution: 2.92→3.02 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.92→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.2153 / FOM work R set: 0.8089 / SU B: 39.065 / SU ML: 0.319 / SU R Cruickshank DPI: 0.373 / SU Rfree: 0.4123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 1039 5 %RANDOM
Rwork0.2328 19939 --
obs0.2342 19939 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 209.61 Å2 / Biso mean: 76.499 Å2 / Biso min: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.41 Å20 Å2
2---0.41 Å20 Å2
3---1.34 Å2
Refinement stepCycle: final / Resolution: 2.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5519 0 4 39 5562
Biso mean--84.19 48.5 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195653
X-RAY DIFFRACTIONr_bond_other_d0.0030.025376
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9717627
X-RAY DIFFRACTIONr_angle_other_deg0.856312372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08624.371286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.954151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3091542
X-RAY DIFFRACTIONr_chiral_restr0.0670.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216362
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021300
Refine LS restraints NCS

Ens-ID: 1 / Number: 18948 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.92→2.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 70 -
Rwork0.424 1447 -
all-1517 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04750.06920.0990.79030.0650.5052-0.0271-0.04610.0203-0.1228-0.0411-0.1482-0.04550.08870.06820.29990.22240.10790.31260.04830.089325.726-0.392-25.229
20.60130.06380.17120.3621-0.0930.08620.1261-0.098-0.0311-0.0489-0.1196-0.00850.03510.0032-0.00640.42920.2990.10010.35130.11110.03821.898-26.118-8.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A540 - 2120
2X-RAY DIFFRACTION1D618 - 626
3X-RAY DIFFRACTION2B543 - 2117
4X-RAY DIFFRACTION2C617 - 626

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more