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- PDB-1d7q: HUMAN TRANSLATION INITIATION FACTOR EIF1A -

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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 / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression ...multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / ribosome assembly / translational initiation / tRNA binding / RNA binding / cytosol / cytoplasm
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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.

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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 7.51 atm298 K
2500mM 7.51 atm298 K
3500mM 7.51 atm298 K
4500mM 7.51 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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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

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