[English] 日本語
Yorodumi
- PDB-5c6d: Crystal structure of USP7 in complex with UHRF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c6d
TitleCrystal structure of USP7 in complex with UHRF1
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE/LIGASE / USP7 / UHRF1 / HYDROLASE-LIGASE complex
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / regulation of telomere capping / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / hemi-methylated DNA-binding / deubiquitinase activity / homologous recombination ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / regulation of telomere capping / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / hemi-methylated DNA-binding / deubiquitinase activity / homologous recombination / DNA alkylation repair / regulation of epithelial cell proliferation / methyl-CpG binding / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / heterochromatin / negative regulation of gluconeogenesis / heterochromatin formation / epigenetic regulation of gene expression / negative regulation of TORC1 signaling / methylated histone binding / positive regulation of protein metabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / regulation of signal transduction by p53 class mediator / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / nuclear matrix / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / histone binding / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nucleic acid binding / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. ...: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / 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. / PUA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Papain-like cysteine peptidase superfamily / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 7 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.292 Å
AuthorsZhang, Z.-M. / Song, J.
CitationJournal: Cell Rep / Year: 2015
Title: An Allosteric Interaction Links USP7 to Deubiquitination and Chromatin Targeting of UHRF1.
Authors: Zhang, Z.M. / Rothbart, S.B. / Allison, D.F. / Cai, Q. / Harrison, J.S. / Li, L. / Wang, Y. / Strahl, B.D. / Wang, G.G. / Song, J.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
C: E3 ubiquitin-protein ligase UHRF1
D: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)81,4864
Polymers81,4864
Non-polymers00
Water2,126118
1
A: Ubiquitin carboxyl-terminal hydrolase 7
C: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)40,7432
Polymers40,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-2 kcal/mol
Surface area17700 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
D: E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)40,7432
Polymers40,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-1 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.606, 62.430, 98.505
Angle α, β, γ (deg.)90.00, 90.42, 90.00
Int Tables number5
Space group name H-MC121

-
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: 37361.305 Da / Num. of mol.: 2 / Fragment: UNP residues 561-881
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / hNp95 / RING finger protein 106 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 3381.789 Da / Num. of mol.: 2 / Fragment: UNP residues 634-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100 mM CHES (pH 9.0), 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2014
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 36467 / % possible obs: 98.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.64
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLM

2ylm


Resolution: 2.292→49.251 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1989 5.46 %
Rwork0.1858 --
obs0.1884 36459 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.292→49.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 0 0 118 5165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085160
X-RAY DIFFRACTIONf_angle_d1.0437005
X-RAY DIFFRACTIONf_dihedral_angle_d13.7541885
X-RAY DIFFRACTIONf_chiral_restr0.039775
X-RAY DIFFRACTIONf_plane_restr0.005916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2919-2.34920.32341370.26092313X-RAY DIFFRACTION92
2.3492-2.41270.31491430.24812497X-RAY DIFFRACTION99
2.4127-2.48370.30931470.23892468X-RAY DIFFRACTION99
2.4837-2.56390.27671410.23192471X-RAY DIFFRACTION99
2.5639-2.65550.25911450.21592473X-RAY DIFFRACTION99
2.6555-2.76180.29091430.20812479X-RAY DIFFRACTION99
2.7618-2.88750.23831450.20362484X-RAY DIFFRACTION99
2.8875-3.03970.2951420.2052452X-RAY DIFFRACTION99
3.0397-3.23010.26661400.21422490X-RAY DIFFRACTION98
3.2301-3.47950.26191400.19512455X-RAY DIFFRACTION98
3.4795-3.82950.21311400.1792473X-RAY DIFFRACTION98
3.8295-4.38330.19851440.15762489X-RAY DIFFRACTION98
4.3833-5.52130.17431340.15532454X-RAY DIFFRACTION97
5.5213-49.26250.22531480.17632472X-RAY DIFFRACTION95
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)
13.2912-1.1569-1.29683.78310.05043.45370.38131.14270.4215-0.8724-0.5859-0.1063-0.3837-0.24870.19760.57910.2803-0.00390.66980.13610.4708-35.349610.998124.6342
24.9698-1.53730.56962.4276-0.08071.8356-0.03780.2535-0.57830.1572-0.15090.7616-0.1402-0.5610.19550.40620.07440.05530.3325-0.08810.5719-49.85536.946742.4126
37.5485-1.3358-0.43964.04373.6315.80120.00370.15190.444-0.2293-0.0466-0.5445-0.79030.24910.04560.5951-0.0592-0.03480.26180.09180.3917-21.736710.554464.7238
45.1518-1.3361-1.05523.5331.96265.0280.0702-0.04640.25110.1509-0.0136-0.1639-0.09530.1063-0.06960.33380.11360.03610.33280.10180.3824-16.69321.489631.0396
54.3106-0.1651-0.06162.06580.17033.473-0.02270.2099-0.8992-0.09-0.0538-0.1530.91340.60250.08090.58130.2650.0530.55440.02080.5788-9.9445-14.98819.1865
63.76-2.272.05063.498-1.08433.34410.4521.1983-0.0786-0.9269-0.5483-0.3520.61140.66180.12630.64240.25980.11760.95920.070.4503-10.5461-6.85546.6591
74.6786-1.1903-2.07753.60790.10743.5425-0.0743-0.9576-0.08320.26840.27660.0886-0.23360.0409-0.14590.67620.1424-0.06110.68930.08610.3238-25.709411.9642-9.3266
85.55585.0041-0.85775.34860.59835.71020.01740.12730.6740.5557-0.437-0.4872-0.29860.11460.4110.62430.06980.01630.31380.16850.6048-44.226126.617839.309
94.06732.9677-3.23456.13825.46671.99810.93960.90250.6971-0.7075-0.2798-0.5461-0.96670.6461-0.63610.66250.25180.13921.10490.05621.0024-1.84824.756418.7667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 561 through 664 )
2X-RAY DIFFRACTION2chain 'A' and (resid 665 through 800 )
3X-RAY DIFFRACTION3chain 'A' and (resid 801 through 881 )
4X-RAY DIFFRACTION4chain 'B' and (resid 560 through 669 )
5X-RAY DIFFRACTION5chain 'B' and (resid 670 through 739 )
6X-RAY DIFFRACTION6chain 'B' and (resid 740 through 800 )
7X-RAY DIFFRACTION7chain 'B' and (resid 801 through 881 )
8X-RAY DIFFRACTION8chain 'C' and (resid 652 through 664 )
9X-RAY DIFFRACTION9chain 'D' and (resid 656 through 662 )

+
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://pdbjlvh1.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