[English] 日本語
Yorodumi
- PDB-2m3t: Solution-state NMR structure of wild-type human gamma(S)-crystallin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m3t
TitleSolution-state NMR structure of wild-type human gamma(S)-crystallin
ComponentsBeta-crystallin S
KeywordsSTRUCTURAL PROTEIN / gamma-S / eye lens / aggregation / crystallin / cataract / CRYGS
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsBrubaker, W.D. / Martin, R.W.
CitationJournal: Structure / Year: 2013
Title: Preferential and Specific Binding of Human alpha B-Crystallin to a Cataract-Related Variant of gamma S-Crystallin.
Authors: Kingsley, C.N. / Brubaker, W.D. / Markovic, S. / Diehl, A. / Brindley, A.J. / Oschkinat, H. / Martin, R.W.
History
DepositionJan 25, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

#1: Protein Beta-crystallin S / Gamma-S-crystallin / Gamma-crystallin S


Mass: 20959.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, GRYG8 / Variant: Wild-Type / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P22914

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1423D HN(CA)CB
1523D CBCA(CO)NH
1623D HNCO
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1923D 1H-15N NOESY
11023D 1H-13C NOESY aliphatic
11123D 1H-13C NOESY aromatic
21212D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
110 mM acetic acid, 2 mM 2,2',3,3'-D4 TSP, 0.05 % sodium azide, 7.5 % DIOTPC, 2.5 % DIOHPC, 2 mM [U-15N] (gamma)S-WT, 90% H2O/10% D2O90% H2O/10% D2O
210 mM acetic acid, 2 mM 2,2',3,3'-D4 TSP, 0.05 % sodium azide, 2.11 mM [U-13C; U-15N] (gamma)S-WT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMacetic acid-11
2 mMTSP-22,2',3,3'-D41
0.05 %sodium azide-31
7.5 %DIOTPC-41
2.5 %DIOHPC-51
2 mM(gamma)S-WT-6[U-15N]1
10 mMacetic acid-72
2 mMTSP-82,2',3,3'-D42
0.05 %sodium azide-92
2.11 mM(gamma)S-WT-10[U-13C; U-15N]2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
14.5ambient 295 K
24.5ambient 305 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
VNMRVariancollection
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 7444 / NOE intraresidue total count: 1547 / NOE long range total count: 3052 / NOE medium range total count: 1286 / NOE sequential total count: 1559
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 21

+
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