[English] 日本語
Yorodumi
- PDB-1d7q: HUMAN TRANSLATION INITIATION FACTOR EIF1A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d7q
TitleHUMAN TRANSLATION INITIATION FACTOR EIF1A
Components
  • PROTEIN (N-TERMINAL HISTIDINE TAG)
  • TRANSLATION INITIATION FACTOR 1A
KeywordsGENE REGULATION / OB-FOLD / BETA-BARREL / RNA-BINDING PROTEIN
Function / homology
Function and homology information


multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / translational initiation / translation initiation factor activity / ribosome assembly / tRNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 1A, X-chromosomal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING, MOLECULAR DYNAMICS FROM AN EXTENDED CONFORMATION WITH RANDOM PHI, PSI ANGLES.
AuthorsBattiste, J.L. / Pestova, T.V. / Hellen, C.U.T. / Wagner, G.
Citation
Journal: Mol.Cell / Year: 2000
Title: The eIF1A solution structure reveals a large RNA-binding surface important for scanning function.
Authors: Battiste, J.L. / Pestova, T.V. / Hellen, C.U. / Wagner, G.
#1: Journal: Nature / Year: 1998
Title: Eukaryotic Ribosomes Require Initiation Factors 1 and 1A to Locate Initiation Codons
Authors: Pestova, T.V. / Borukhov, S.I. / Hellen, C.U.T.
History
DepositionOct 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: PROTEIN (N-TERMINAL HISTIDINE TAG)
A: TRANSLATION INITIATION FACTOR 1A


Theoretical massNumber of molelcules
Total (without water)18,0812
Polymers18,0812
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)20 / 50structures with the least restraint violations
RepresentativeModel #8lowest energy

-
Components

#1: Protein/peptide PROTEIN (N-TERMINAL HISTIDINE TAG) / EIF-1A


Mass: 1723.917 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HISTIDINE TAG IS ENGINEERED INTO THE VECTOR THAT IS EXPRESSED WITH THE PROTEIN
#2: Protein TRANSLATION INITIATION FACTOR 1A


Mass: 16357.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE31 / Production host: Escherichia coli (E. coli) / References: UniProt: P47813

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
2223D 15N-SEPARATED NOESY
3332D NOESY
NMR detailsText: THE PROTEIN WAS ASSIGNED FROM THE TRIPLE RESONANCE EXPERIMENTS HNCA, HN(CO)CA, HNCO, HN(CA)CO, CBCA(CO)NH, HBHA(CBCACO)NH, H(CCCO)NH, (H)C(CCO)NH, AND HCCH- TOCSY. VAL AND LEU METHYL GROUPS ...Text: THE PROTEIN WAS ASSIGNED FROM THE TRIPLE RESONANCE EXPERIMENTS HNCA, HN(CO)CA, HNCO, HN(CA)CO, CBCA(CO)NH, HBHA(CBCACO)NH, H(CCCO)NH, (H)C(CCO)NH, AND HCCH- TOCSY. VAL AND LEU METHYL GROUPS WERE STEREOSPECIFICALLY ASSIGNED FROM ANALYSIS OF MULTIPLET COUPLINGS IN AN HSQC OF 10% 13C-LABELED PROTEIN. BACKBONE DIHEDRAL ANGLES WERE ESTIMATED USING THE PROGRAM TALOS AND BACKBONE HETERONUCLEAR CHEMICAL SHIFTS.

-
Sample preparation

Details
Solution-IDContents
10.8MM U-13C,15N EIF1A, 10MM PHOSPHATE BUFFER, PH 7.5, 500MM NACL, 1MM DTT, 0.1MM EDTA
20.5MM U-15N EIF1A, 10MM PHOSPHATE BUFFER, PH 7.5, 500MM NACL, 1MM DTT, 0.1MM EDTA
31.2MM EIF1A, 10MM PHOSPHATE BUFFER, PH 7.5, 500MM NACL, 1MM DTT, 0.1MM EDTA
40.4MM 15N-LYSINE EIF1A, 10MM PHOSPHATE BUFFER, PH 7.5, 500MM NACL, 1MM DTT, 0.1MM EDTA
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1500mM 7.5 1 atm298 K
2500mM 7.5 1 atm298 K
3500mM 7.5 1 atm298 K
4500mM 7.5 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002
Varian UNITYVarianUNITY5003

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1VARIANcollection
Felix98BIOSYMprocessing
XEASY1.2C. BARTELS, T. XIA, M. BILLETER, P. GUNTERT, AND K. WUTHRICHdata analysis
X-PLOR3.851A.T. BRUNGERstructure solution
TALOS1G. CORNILESCU, F. DELAGLIO, AND A. BAXdata analysis
X-PLOR3.851A.T. BRUNGERrefinement
RefinementMethod: STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING, MOLECULAR DYNAMICS FROM AN EXTENDED CONFORMATION WITH RANDOM PHI, PSI ANGLES.
Software ordinal: 1
Details: CALCULATIONS WERE RESTRAINED WITH THE FOLLOWING NMR DATA. NOE DISTANCE RESTRAINTS INTRA-RESIDUE 607 INTER-RESIDUE SEQUENTIAL (IJ=1) 266 INTER-RESIDUE MEDIUM (IJ 4) 342 HYDROGENS BONDS: ...Details: CALCULATIONS WERE RESTRAINED WITH THE FOLLOWING NMR DATA. NOE DISTANCE RESTRAINTS INTRA-RESIDUE 607 INTER-RESIDUE SEQUENTIAL (IJ=1) 266 INTER-RESIDUE MEDIUM (IJ <= 4) 105 INTER-RESIDUE LONG (IJ > 4) 342 HYDROGENS BONDS: PROTEIN BACKBONE 40 DIHEDRAL ANGLES: PHI 65 PSI 65 NO NOE VIOLATIONS >0.3 A IN FINAL STRUCTURES. RMS DEVIATIONS OF THE ENSEMBLE SUPERPOSITION TO THE AVERAGE STRUCTURE ARE: BACKBONE 39-131 0.57 A SECONDARY STRUCTURE 0.23 A HEAVY ATOMS 39-131 1.17 A SECONDARY STRUCTURE 0.72 A BOND LENGTHS 0.0016 A BOND ANGLES 0.345 DEGREE IMPROPER ANGLES 0.259 DEGREE. NOTE THAT RESIDUES 1-38 AND 132-143 HAD NO LONG RANGE NOES AND ARE DISORDERED IN THE CALCULATED STRUCTURES.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

+
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