[English] 日本語
Yorodumi
- PDB-5zi6: The RING domain structure of MEX-3C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zi6
TitleThe RING domain structure of MEX-3C
ComponentsRNA-binding E3 ubiquitin-protein ligase MEX3C
KeywordsLIGASE / E3 liagase / Ubiquitination / MEX-3C / RING domain
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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. ...: / : / : / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Zinc finger, C3HC4 type (RING finger) / 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
Similarity search - Domain/homology
RNA-binding E3 ubiquitin-protein ligase MEX3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMoududee, S.A. / Tang, Y.
CitationJournal: Protein Sci. / Year: 2018
Title: Structural and functional characterization of hMEX-3C Ring finger domain as an E3 ubiquitin ligase
Authors: Moududee, S.A. / Jiang, Y. / Gilbert, N. / Xie, G. / Xu, Z. / Wu, J. / Gong, Q. / Tang, Y. / Shi, Y.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RNA-binding E3 ubiquitin-protein ligase MEX3C
B: RNA-binding E3 ubiquitin-protein ligase MEX3C
C: RNA-binding E3 ubiquitin-protein ligase MEX3C
D: RNA-binding E3 ubiquitin-protein ligase MEX3C
E: RNA-binding E3 ubiquitin-protein ligase MEX3C
F: RNA-binding E3 ubiquitin-protein ligase MEX3C
G: RNA-binding E3 ubiquitin-protein ligase MEX3C
H: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,48824
Polymers48,4418
Non-polymers1,04716
Water18010
1
A: RNA-binding E3 ubiquitin-protein ligase MEX3C
B: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA-binding E3 ubiquitin-protein ligase MEX3C
D: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA-binding E3 ubiquitin-protein ligase MEX3C
F: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RNA-binding E3 ubiquitin-protein ligase MEX3C
H: RNA-binding E3 ubiquitin-protein ligase MEX3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3726
Polymers12,1102
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.135, 44.567, 67.157
Angle α, β, γ (deg.)92.430, 90.500, 91.390
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
21(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
31(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
41(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
51(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
61(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
71(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))
81(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSPHEPHE(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA608 - 6124 - 8
12ASNASNASNASN(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA61410
13VALVALLYSLYS(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA616 - 63912 - 35
14THRTHRSERSER(chain A and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))AA641 - 65937 - 55
21CYSCYSPHEPHE(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB608 - 6124 - 8
22ASNASNASNASN(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB61410
23VALVALLYSLYS(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB616 - 63912 - 35
24THRTHRSERSER(chain B and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))BB641 - 65937 - 55
31CYSCYSPHEPHE(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC608 - 6124 - 8
32ASNASNASNASN(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC61410
33VALVALLYSLYS(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC616 - 63912 - 35
34THRTHRSERSER(chain C and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))CC641 - 65937 - 55
41CYSCYSPHEPHE(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD608 - 6124 - 8
42ASNASNASNASN(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD61410
43VALVALLYSLYS(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD616 - 63912 - 35
44THRTHRSERSER(chain D and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))DD641 - 65937 - 55
51CYSCYSPHEPHE(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE608 - 6124 - 8
52ASNASNASNASN(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE61410
53VALVALLYSLYS(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE616 - 63912 - 35
54THRTHRSERSER(chain E and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))EE641 - 65937 - 55
61CYSCYSPHEPHE(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF608 - 6124 - 8
62ASNASNASNASN(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF61410
63VALVALLYSLYS(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF616 - 63912 - 35
64THRTHRSERSER(chain F and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))FF641 - 65937 - 55
71CYSCYSPHEPHE(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG608 - 6124 - 8
72ASNASNASNASN(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG61410
73VALVALLYSLYS(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG616 - 63912 - 35
74THRTHRSERSER(chain G and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))GG641 - 65937 - 55
81CYSCYSPHEPHE(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH608 - 6124 - 8
82ASNASNASNASN(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH61410
83VALVALLYSLYS(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH616 - 63912 - 35
84THRTHRSERSER(chain H and (resseq 608:612 or resseq 614 or resseq 616:639 or resseq 641:659))HH641 - 65937 - 55

-
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: 6055.123 Da / Num. of mol.: 8 / Fragment: UNP residues 605-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEX3C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5U5Q3, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 25%(w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 20938 / % possible obs: 94.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 42.83 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.053 / Rrim(I) all: 0.103 / Χ2: 0.635 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.10.8989730.6080.5621.0620.43290.1
2.24-2.283.30.75310310.7290.4630.8850.45393.3
2.28-2.323.40.70810750.8360.4320.8310.4294.6
2.32-2.373.50.58910360.8970.3530.6880.44295.2
2.37-2.423.60.50110510.9060.2990.5850.44495.2
2.42-2.483.60.48711000.90.2910.5680.45296.1
2.48-2.543.60.40610350.8950.2430.4730.43196
2.54-2.613.60.37310910.9160.2230.4360.45896
2.61-2.693.70.28210530.9530.1680.3290.46394.5
2.69-2.773.50.21910060.970.1330.2570.591.9
2.77-2.873.50.17610110.9780.1080.2080.52988.1
2.87-2.993.80.14410650.9880.0850.1680.55197.6
2.99-3.123.80.12410770.9890.0730.1440.55297
3.12-3.293.70.10110560.9910.060.1180.60396.1
3.29-3.493.70.08110970.9930.0480.0940.68397.2
3.49-3.763.70.06110540.9970.0360.0710.74994.4
3.76-4.143.50.0619840.9950.0370.0720.87388.1
4.14-4.743.80.04910450.9970.0290.0570.99496
4.74-5.973.80.05310730.9960.0310.0621.08396.2
5.97-403.70.05210250.9980.0310.061.46791.7

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→36.384 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.57 / Phase error: 27.19
RfactorNum. reflection% reflection
Rfree0.2434 959 4.58 %
Rwork0.2072 --
obs0.2088 20922 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.25 Å2 / Biso mean: 51.7163 Å2 / Biso min: 27.79 Å2
Refinement stepCycle: final / Resolution: 2.2→36.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 16 10 3346
Biso mean--43.58 39.47 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093376
X-RAY DIFFRACTIONf_angle_d1.2814576
X-RAY DIFFRACTIONf_chiral_restr0.072552
X-RAY DIFFRACTIONf_plane_restr0.008592
X-RAY DIFFRACTIONf_dihedral_angle_d15.9612096
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1719X-RAY DIFFRACTION11.768TORSIONAL
12B1719X-RAY DIFFRACTION11.768TORSIONAL
13C1719X-RAY DIFFRACTION11.768TORSIONAL
14D1719X-RAY DIFFRACTION11.768TORSIONAL
15E1719X-RAY DIFFRACTION11.768TORSIONAL
16F1719X-RAY DIFFRACTION11.768TORSIONAL
17G1719X-RAY DIFFRACTION11.768TORSIONAL
18H1719X-RAY DIFFRACTION11.768TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.29760.31881040.3051269588
2.2976-2.44150.31961400.301291595
2.4415-2.62990.30311750.2714290896
2.6299-2.89450.2971480.2437274992
2.8945-3.31310.25341460.2362296097
3.3131-4.17320.22811100.1925285292
4.1732-36.3840.19871360.1558288495

+
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