[English] 日本語
Yorodumi
- PDB-2f1y: Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f1y
TitleCrystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide
ComponentsHAUSP/USP7
KeywordsHYDROLASE / HAUSP / USP7 / MDM2 / UBP / TRAF_like domain / MDM2 recognition / substrate binding
Function / homology
Function and homology information


regulation of telomere capping / histone H2B deubiquitinase activity / histone H2A deubiquitinase activity / regulation of establishment of protein localization to telomere / cellular response to vitamin B1 / response to formaldehyde / monoubiquitinated protein deubiquitination / response to water-immersion restraint stress / cellular response to UV-C / response to ether ...regulation of telomere capping / histone H2B deubiquitinase activity / histone H2A deubiquitinase activity / regulation of establishment of protein localization to telomere / cellular response to vitamin B1 / response to formaldehyde / monoubiquitinated protein deubiquitination / response to water-immersion restraint stress / cellular response to UV-C / response to ether / peptidase complex / regulation of retrograde transport, endosome to Golgi / fibroblast activation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Trafficking of AMPA receptors / DNA alkylation repair / deubiquitinase activity / receptor serine/threonine kinase binding / protein K48-linked deubiquitination / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SUMO transferase activity / cellular response to alkaloid / K48-linked deubiquitinase activity / response to steroid hormone / regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of protein processing / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / AKT phosphorylates targets in the cytosol / response to iron ion / NEDD8 ligase activity / symbiont-mediated disruption of host cell PML body / regulation of protein catabolic process / positive regulation of muscle cell differentiation / cellular response to peptide hormone stimulus / cellular response to antibiotic / regulation of postsynaptic neurotransmitter receptor internalization / ligase activity / SUMOylation of ubiquitinylation proteins / negative regulation of gene expression via chromosomal CpG island methylation / protein K63-linked deubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / negative regulation of signal transduction by p53 class mediator / cellular response to estrogen stimulus / negative regulation of gluconeogenesis / protein localization to nucleus / protein sumoylation / : / response to magnesium ion / protein deubiquitination / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / protein autoubiquitination / positive regulation of mitotic cell cycle / NPAS4 regulates expression of target genes / positive regulation of protein export from nucleus / ubiquitin ligase complex / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / regulation of signal transduction by p53 class mediator / Regulation of PTEN localization / response to cocaine / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / DNA damage response, signal transduction by p53 class mediator / negative regulation of neuron projection development / antiviral innate immune response / ubiquitin binding / establishment of protein localization / regulation of protein stability / Stabilization of p53 / protein destabilization / cellular response to gamma radiation / response to toxic substance / Regulation of RUNX3 expression and activity / PML body / Oncogene Induced Senescence / RING-type E3 ubiquitin transferase / Regulation of TP53 Activity through Methylation / cellular response to growth factor stimulus / Degradation of CDH1 / cellular response to hydrogen peroxide / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / protein polyubiquitination / disordered domain specific binding / p53 binding / ubiquitin-protein transferase activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / endocytic vesicle membrane / Signaling by ALK fusions and activated point mutants / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of TP53 Degradation / ubiquitin protein ligase activity / protein-containing complex assembly / 5S rRNA binding
Similarity search - Function
MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass ...MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / p53 negative regulator Mdm2/Mdm4 / TRAF-like / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 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. / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2 / Ubiquitin C-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHu, M. / Gu, L. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Plos Biol. / Year: 2006
Title: Structural Basis of Competitive Recognition of p53 and MDM2 by HAUSP/USP7: Implications for the Regulation of the p53-MDM2 Pathway.
Authors: Hu, M. / Gu, L. / Li, M. / Jeffrey, P.D. / Gu, W. / Shi, Y.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HAUSP/USP7


Theoretical massNumber of molelcules
Total (without water)18,5561
Polymers18,5561
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.526, 37.526, 177.296
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein HAUSP/USP7


Mass: 18555.512 Da / Num. of mol.: 1
Fragment: HAUSP N-terminal domain with MDM2 peptide fused to its C-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, UniProt: Q00987
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% PEG4000, 300 mM calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005
RadiationMonochromator: focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→99 Å / Num. all: 31380 / Num. obs: 30752 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.78 Å / % possible all: 92.7

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2F1W

2f1w


Resolution: 1.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.237 1416 random
Rwork0.218 --
all0.22 30706 -
obs0.22 28992 -
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 183 1301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_bond_d0.005

+
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