[English] 日本語
Yorodumi
- PDB-5hqg: WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hqg
TitleWD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2)
ComponentsE3 ubiquitin-protein ligase RFWD2
KeywordsHYDROLASE / WD40 domain E3 ligase
Function / homology
Function and homology information


Cul4A-RING E3 ubiquitin ligase complex / response to ionizing radiation / Autodegradation of the E3 ubiquitin ligase COP1 / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination ...Cul4A-RING E3 ubiquitin ligase complex / response to ionizing radiation / Autodegradation of the E3 ubiquitin ligase COP1 / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear speck / Golgi membrane / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase COP1 / Zinc finger, C3HC4 type (RING finger) / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type ...E3 ubiquitin-protein ligase COP1 / Zinc finger, C3HC4 type (RING finger) / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase COP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUljon, S. / Blacklow, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)K08 CA166227 United States
CitationJournal: Structure / Year: 2016
Title: Structural Basis for Substrate Selectivity of the E3 Ligase COP1.
Authors: Uljon, S. / Xu, X. / Durzynska, I. / Stein, S. / Adelmant, G. / Marto, J.A. / Pear, W.S. / Blacklow, S.C.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RFWD2


Theoretical massNumber of molelcules
Total (without water)40,9531
Polymers40,9531
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.914, 68.914, 133.922
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-870-

HOH

21A-891-

HOH

-
Components

#1: Protein E3 ubiquitin-protein ligase RFWD2 / Constitutive photomorphogenesis protein 1 homolog / hCOP1 / RING finger and WD repeat domain ...Constitutive photomorphogenesis protein 1 homolog / hCOP1 / RING finger and WD repeat domain protein 2 / RING finger protein 200


Mass: 40952.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFWD2, COP1, RNF200 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8NHY2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.24 Å3/Da / Density % sol: 45.13 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium nitrate 0.5M 10% PEG 3350 / PH range: 5.5-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→34.5 Å / Num. obs: 25511 / % possible obs: 100 % / Redundancy: 4.9 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9
Reflection shellResolution: 2→2.075 Å / Redundancy: 5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.29 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H14

2h14


Resolution: 2→34.5 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35 / Details: mol rep then autobuild then phenix refine
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 2575 10.09 %Random selection
Rwork0.2105 ---
obs0.2137 25511 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 104 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022548
X-RAY DIFFRACTIONf_angle_d0.5733460
X-RAY DIFFRACTIONf_dihedral_angle_d13.9591496
X-RAY DIFFRACTIONf_chiral_restr0.045388
X-RAY DIFFRACTIONf_plane_restr0.002436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.33011520.2821240X-RAY DIFFRACTION100
2.0385-2.08010.27871540.26891230X-RAY DIFFRACTION99
2.0801-2.12530.32641090.24811279X-RAY DIFFRACTION100
2.1253-2.17480.28351260.25731274X-RAY DIFFRACTION100
2.1748-2.22910.31321450.26261235X-RAY DIFFRACTION100
2.2291-2.28940.35641660.31221228X-RAY DIFFRACTION98
2.2894-2.35670.26411330.24921257X-RAY DIFFRACTION100
2.3567-2.43280.30471550.24591255X-RAY DIFFRACTION100
2.4328-2.51970.27841160.25421269X-RAY DIFFRACTION100
2.5197-2.62060.2631300.25451288X-RAY DIFFRACTION100
2.6206-2.73980.25661420.25521286X-RAY DIFFRACTION100
2.7398-2.88420.29941040.23121300X-RAY DIFFRACTION100
2.8842-3.06480.26911390.22541276X-RAY DIFFRACTION100
3.0648-3.30130.28691680.22951260X-RAY DIFFRACTION100
3.3013-3.63320.23891370.21299X-RAY DIFFRACTION100
3.6332-4.15830.20811580.17931276X-RAY DIFFRACTION100
4.1583-5.23640.16411650.1511310X-RAY DIFFRACTION100
5.2364-35.75280.23641760.19191374X-RAY DIFFRACTION100
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)
11.09710.4085-0.1650.1512-0.06060.0240.1798-0.8857-0.03190.12380.16340.35780.1933-0.61550.89420.3629-0.1676-0.14171.13020.26460.7685-19.47581.860211.054
23.8548-0.4399-0.2790.79910.2474.5372-0.0132-0.63150.40560.1480.15790.1023-0.4924-0.9247-0.09890.3221-0.031-0.03870.63020.00330.47091.674387.354320.0464
32.024-0.16592.10851.2641-0.27613.68980.3268-0.1438-0.1551-0.31820.0920.1030.9011-0.24610.2390.5788-0.2162-0.07770.32760.08060.38746.417373.43279.7217
42.5404-0.26990.37641.98150.24941.78550.0185-0.62330.0284-0.18710.24980.35250.1075-1.0442-0.01230.3778-0.158-0.07240.68910.12330.4452-9.091585.09187.8115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 391 through 412 )
2X-RAY DIFFRACTION2chain 'A' and (resid 413 through 453 )
3X-RAY DIFFRACTION3chain 'A' and (resid 454 through 636 )
4X-RAY DIFFRACTION4chain 'A' and (resid 637 through 731 )

+
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