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- PDB-4zgn: Structure Cdc123 complexed with the C-terminal domain of eIF2gamma -

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Basic information

Entry
Database: PDB / ID: 4zgn
TitleStructure Cdc123 complexed with the C-terminal domain of eIF2gamma
Components
  • Cell division cycle protein 123
  • Eukaryotic translation initiation factor 2 subunit gamma
KeywordsCELL CYCLE / ATP-grasp fold / eIF2 assembly
Function / homology
Function and homology information


eukaryotic translation initiation factor 2 complex assembly / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / selenocysteine metabolic process / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase ...eukaryotic translation initiation factor 2 complex assembly / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / selenocysteine metabolic process / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / protein folding chaperone / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome / GTPase activity / GTP binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Cell division cycle protein 123 / D123 / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...Cell division cycle protein 123 / D123 / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 2 subunit gamma / Translation initiation factor eIF2 assembly protein
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPanvert, M. / Dubiez, E. / Arnold, L. / Perez, J. / Seufert, W. / Mechulam, Y. / Schmitt, E.
Funding support France, 2items
OrganizationGrant numberCountry
CNRSUMR7654 France
Ecole polytec France
CitationJournal: Structure / Year: 2015
Title: Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features.
Authors: Panvert, M. / Dubiez, E. / Arnold, L. / Perez, J. / Mechulam, Y. / Seufert, W. / Schmitt, E.
History
DepositionApr 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle protein 123
B: Eukaryotic translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6194
Polymers52,0872
Non-polymers5312
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-18 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.260, 116.640, 132.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cell division cycle protein 123


Mass: 38979.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cdc123, SPAP27G11.03 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P7N5
#2: Protein Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 13108.387 Da / Num. of mol.: 1 / Fragment: residues 410-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCD11, TIF213, YER025W / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P32481
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25%PEG3350, 0.2MLiSO4, 0.1M TrispH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. obs: 13237 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 100.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGO and 2AHO

4zgo

2aho


Resolution: 2.9→45 Å / Cor.coef. Fo:Fc: 0.9191 / Cor.coef. Fo:Fc free: 0.8798 / SU R Cruickshank DPI: 1.337 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.203 / SU Rfree Blow DPI: 0.362 / SU Rfree Cruickshank DPI: 0.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 653 4.99 %RANDOM
Rwork0.1951 ---
obs0.1983 13078 99.79 %-
Displacement parametersBiso mean: 101.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.7468 Å20 Å20 Å2
2---28.1739 Å20 Å2
3---29.9206 Å2
Refine analyzeLuzzati coordinate error obs: 0.512 Å
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3093 0 32 5 3130
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093198HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184339HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1117SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes457HARMONIC5
X-RAY DIFFRACTIONt_it3198HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3557SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.13 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3174 132 4.99 %
Rwork0.2426 2513 -
all0.246 2645 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.93620.3670.04231.2039-0.23697.3494-0.008-0.23620.4706-0.07710.0861-0.0095-0.9465-0.2677-0.0781-0.2140.12890.0629-0.29880.0145-0.066521.4361136.516139.086
24.6262-0.15750.42782.8971-0.52076.61910.0916-0.65270.05780.83430.12530.08970.6841-0.5346-0.217-0.0453-0.0093-0.02250.00810.0963-0.276922.7278115.623164.512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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