[English] 日本語
Yorodumi
- PDB-7bvw: Crystal structure of the RING-H2 domain of Arabidopsis RMR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bvw
TitleCrystal structure of the RING-H2 domain of Arabidopsis RMR1
ComponentsAT5G66160 protein
KeywordsTRANSPORT PROTEIN / C3H2C3 / ring finger / E3 ligase
Function / homologyRing finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / membrane => GO:0016020 / Zinc finger, RING/FYVE/PHD-type / AT5G66160 protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, S. / Wong, K.B.
CitationJournal: To Be Published
Title: The RING-finger of AtRMR1 (Arabidopsis receptor-homology-transmembrane-RING-H2 sorting receptor 1) is an E3 ligase that mediate its trafficking
Authors: Chen, S. / Zeng, Y.L. / Wong, H.Y. / Yang, L. / Luo, F. / Jiang, L.W. / Wong, K.B.
History
DepositionApr 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: AT5G66160 protein
B: AT5G66160 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7918
Polymers18,4412
Non-polymers3506
Water1,31573
1
A: AT5G66160 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4174
Polymers9,2211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5090 Å2
MethodPISA
2
B: AT5G66160 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3744
Polymers9,2211
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.431, 23.648, 75.699
Angle α, β, γ (deg.)90.000, 94.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

-
Components

#1: Protein AT5G66160 protein / Really-Interesting-New-Gene (RING) domain


Mass: 9220.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g66160 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: C0Z2X4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 20% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→37.72 Å / Num. obs: 7849 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Net I/σ(I): 9 / Num. measured all: 27884
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.213 / Num. unique obs: 650 / CC1/2: 0.95 / Rpim(I) all: 0.135 / Rrim(I) all: 0.253 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V3K

4v3k


Resolution: 2.1→32.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.2219 422 5.38 %
Rwork0.1791 --
obs0.1815 7846 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.05 Å2 / Biso mean: 27.392 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 2.1→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 6 73 1263
Biso mean--24.23 32.65 -
Num. residues----154
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.40.2721440.1955241197
2.4-3.030.24781140.2042249498
Refinement TLS params.Method: refined / Origin x: 1.4047 Å / Origin y: 5.8871 Å / Origin z: 94.4639 Å
111213212223313233
T0.1217 Å2-0.0052 Å20.0021 Å2-0.1062 Å2-0.0178 Å2--0.2148 Å2
L3.8357 °21.6406 °20.4386 °2-1.5369 °20.0277 °2--0.3544 °2
S0.0314 Å °-0.0805 Å °-0.0116 Å °0.0639 Å °-0.0459 Å °0.0266 Å °-0.029 Å °0.0012 Å °0.0052 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA205 - 402
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB205 - 279
4X-RAY DIFFRACTION1allB401 - 501
5X-RAY DIFFRACTION1allS1 - 76

+
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