[English] 日本語
Yorodumi
- PDB-5www: Crystal structure of the KH1 domain of human RNA-binding E3 ubiqu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5www
TitleCrystal structure of the KH1 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA
Components
  • RNA (5'-R(*GP*UP*UP*UP*AP*G)-3')
  • RNA-binding E3 ubiquitin-protein ligase MEX3C
KeywordsRNA BINDING PROTEIN/RNA / KH1 / MEX-3C / RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


chondrocyte hypertrophy / regulation of fat cell differentiation / energy homeostasis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / Zinc finger, C3HC4 type (RING finger) / K Homology domain, type 1 superfamily ...: / : / : / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / Zinc finger, C3HC4 type (RING finger) / K Homology domain, type 1 superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / K Homology domain / K homology RNA-binding domain / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA-binding E3 ubiquitin-protein ligase MEX3C
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsYang, L. / Wang, C. / Li, F. / Gong, Q.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity
Authors: Yang, L. / Wang, C. / Li, F. / Zhang, J. / Nayab, A. / Wu, J. / Shi, Y. / Gong, Q.
History
DepositionJan 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: RNA-binding E3 ubiquitin-protein ligase MEX3C
B: RNA (5'-R(*GP*UP*UP*UP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,4052
Polymers12,4052
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-8 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.366, 76.366, 36.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-466-

HOH

-
Components

#1: Protein RNA-binding E3 ubiquitin-protein ligase MEX3C / RING finger and KH domain-containing protein 2 / RING finger protein 194 / RING-type E3 ubiquitin ...RING finger and KH domain-containing protein 2 / RING finger protein 194 / RING-type E3 ubiquitin transferase MEX3C


Mass: 10512.194 Da / Num. of mol.: 1 / Fragment: KH1 domain, UNP residues 221-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEX3C, RKHD2, RNF194, BM-013 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5U5Q3, RING-type E3 ubiquitin transferase
#2: RNA chain RNA (5'-R(*GP*UP*UP*UP*AP*G)-3')


Mass: 1893.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5% v/v Tacsimate pH 7.0, 0.1M HEPES pH 7.0, 10% w/v polyethylene glycol monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 11406 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 22.96 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.053 / Rrim(I) all: 0.168 / Χ2: 1.051 / Net I/σ(I): 3.6 / Num. measured all: 115295
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8610.30.70511300.8650.2290.7420.49398.9
1.86-1.949.80.52711080.9010.1770.5560.5299.2
1.94-2.039.50.38811360.9450.1320.410.57299.5
2.03-2.1310.60.31311270.9660.10.3290.674100
2.13-2.2710.70.24711340.9730.0780.2590.79899.6
2.27-2.4410.50.21411400.9770.0690.2250.90699.6
2.44-2.69100.1911370.9780.0630.21.01299.8
2.69-3.089.50.15711500.9820.0540.1661.36599.8
3.08-3.8810.60.13511490.9890.0440.1421.97499.9
3.88-409.60.12111950.9890.0420.1282.14599.4

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
MOSFLMdata reduction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DGR

2dgr


Resolution: 1.798→38.183 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 564 4.95 %
Rwork0.172 10838 -
obs0.1738 11402 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.34 Å2 / Biso mean: 26.3348 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 1.798→38.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 125 0 93 953
Biso mean---36.16 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006917
X-RAY DIFFRACTIONf_angle_d0.7781270
X-RAY DIFFRACTIONf_chiral_restr0.049148
X-RAY DIFFRACTIONf_plane_restr0.007144
X-RAY DIFFRACTIONf_dihedral_angle_d15.672562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7979-1.97890.23921340.19352661279599
1.9789-2.26520.23591490.173726872836100
2.2652-2.85380.21611380.181527142852100
2.8538-38.19160.19251430.163427762919100

+
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