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- PDB-3vmf: Archaeal protein -

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Basic information

Entry
Database: PDB / ID: 3vmf
TitleArchaeal protein
Components
  • Elongation factor 1-alpha
  • Peptide chain release factor subunit 1
KeywordsTRANSLATION / translation termination
Function / homology
Function and homology information


translation release factor activity, codon specific / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Peptide chain release factor aRF1 / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Translation elongation factor EF1A, eukaryotic/archaeal / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 ...Peptide chain release factor aRF1 / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Translation elongation factor EF1A, eukaryotic/archaeal / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / 60s Ribosomal Protein L30; Chain: A; / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / 50S ribosomal protein L30e-like / Small GTP-binding protein domain / Nucleotidyltransferase; domain 5 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Peptide chain release factor subunit 1 / Elongation factor 1-alpha
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKobayashi, K. / Saito, K. / Ishitani, R. / Ito, K. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural basis for translation termination by archaeal RF1 and GTP-bound EF1alpha complex
Authors: Kobayashi, K. / Saito, K. / Ishitani, R. / Ito, K. / Nureki, O.
History
DepositionDec 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1-alpha
B: Peptide chain release factor subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6665
Polymers91,0232
Non-polymers6443
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-47 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.567, 55.169, 90.689
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Elongation factor 1-alpha / EF-1-alpha / Elongation factor Tu / EF-Tu


Mass: 49016.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: tuf, APE_1844 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus / References: UniProt: Q9YAV0
#2: Protein Peptide chain release factor subunit 1 / Translation termination factor aRF1


Mass: 42005.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: prf1, APE_1988.1 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus / References: UniProt: Q9YAF1

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Non-polymers , 4 types, 165 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23% PEG 3350, 200mM Ammonium sulfate, 10mM L-proline, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 38192 / Num. obs: 38192 / % possible obs: 98.9 % / Redundancy: 5.7 % / Rsym value: 0.063 / Net I/σ(I): 37.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.82 / Num. unique all: 1866 / Rsym value: 0.282 / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGJ, 3AGK

3agj
PDB Unreleased entry

3agk


Resolution: 2.3→46.498 Å / SU ML: 0.77 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1906 5.02 %Random
Rwork0.2013 ---
obs0.2042 37988 98.88 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.334 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.771 Å20 Å20.0466 Å2
2--6.5219 Å20 Å2
3----10.293 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5961 0 38 162 6161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096116
X-RAY DIFFRACTIONf_angle_d1.2028294
X-RAY DIFFRACTIONf_dihedral_angle_d18.3642270
X-RAY DIFFRACTIONf_chiral_restr0.083955
X-RAY DIFFRACTIONf_plane_restr0.0051056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.35750.31381350.2663251597
2.3575-2.42130.35061280.2513254098
2.4213-2.49250.31831380.2543252298
2.4925-2.57290.35571410.2517255299
2.5729-2.66490.36021260.2412255098
2.6649-2.77160.29861380.242256799
2.7716-2.89770.27531450.2378254499
2.8977-3.05050.34831250.2361258099
3.0505-3.24150.2751170.2182260099
3.2415-3.49170.25821230.20952594100
3.4917-3.8430.26431450.18732599100
3.843-4.39870.21871390.16852616100
4.3987-5.54040.2111510.16222629100
5.5404-46.50790.23621550.1912267499

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