[English] 日本語
Yorodumi
- PDB-2n51: NMR structure of the C-terminal region of human eukaryotic elonga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n51
TitleNMR structure of the C-terminal region of human eukaryotic elongation factor 1B
ComponentsElongation factor 1-delta
KeywordsTRANSLATION / GUANINE NUCLEOTIDE EXCHANGE FACTOR
Function / homology
Function and homology information


Eukaryotic Translation Elongation / cytoplasmic translational elongation / eukaryotic translation elongation factor 1 complex / translation factor activity, RNA binding / translational elongation / translation elongation factor activity / heat shock protein binding / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / fibrillar center ...Eukaryotic Translation Elongation / cytoplasmic translational elongation / eukaryotic translation elongation factor 1 complex / translation factor activity, RNA binding / translational elongation / translation elongation factor activity / heat shock protein binding / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / fibrillar center / cellular response to heat / DNA-binding transcription factor binding / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain ...Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / : / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1B/ribosomal protein S6
Similarity search - Domain/homology
Elongation factor 1-delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics simulated annealing
Model detailslowest energy, model1
AuthorsWu, H. / Feng, Y.
CitationJournal: J.Biomol.Nmr / Year: 2016
Title: The C-terminal region of human eukaryotic elongation factor 1B delta.
Authors: Wu, H. / Wang, C. / Gong, W. / Wang, J. / Xuan, J. / Perrett, S. / Feng, Y.
History
DepositionJul 2, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongation factor 1-delta


Theoretical massNumber of molelcules
Total (without water)14,8941
Polymers14,8941
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Elongation factor 1-delta / EF-1-delta / Antigen NY-CO-4


Mass: 14893.642 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 153-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1D, EF1D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29692

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HN(CA)CO
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D HBHANH
11013D (H)CCH-TOCSY
11113D CCH-TOCSY
11213D CCH-COSY
11313D 1H-15N NOESY
11413D 1H-13C NOESY aliphatic
11513D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 0.8 mM [U-13C; U-15N] entity-1, 20 mM TRIS-2, 200 mM sodium chloride-3, 0.01 % w/v DSS-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity-1[U-13C; U-15N]1
20 mMTRIS-21
200 mMsodium chloride-31
0.01 w/vDSS-41
Sample conditionsIonic strength: 220 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
SANEDuggan, Legge, Dyson & Wrightdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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