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- PDB-1rz4: Crystal Structure of Human eIF3k -

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Basic information

Entry
Database: PDB / ID: 1rz4
TitleCrystal Structure of Human eIF3k
ComponentsEukaryotic translation initiation factor 3 subunit 11
KeywordsBIOSYNTHETIC PROTEIN / HEAT analogous motif / winged-helix
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / 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 ...eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / 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 / translational initiation / ribosome binding / RNA binding / membrane / nucleus / cytosol
Similarity search - Function
ARM repeat; domain 1 / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...ARM repeat; domain 1 / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWei, Z. / Zhang, P. / Zhou, Z. / Gong, W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of human eIF3k, the first structure of eIF3 subunits
Authors: Wei, Z. / Zhang, P. / Zhou, Z. / Cheng, Z. / Wan, M. / Gong, W.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 3 subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5322
Polymers26,4361
Non-polymers961
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Eukaryotic translation initiation factor 3 subunit 11
hetero molecules

A: Eukaryotic translation initiation factor 3 subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0644
Polymers52,8722
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2890 Å2
ΔGint-43 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.074, 44.671, 55.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit 11 / eukaryotic initiation factor 3 subunit k / eIF3k


Mass: 26436.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ5
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M ammonium sulfate, 0.1M Hepes, 0.1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.222 1276 RANDOM
Rwork0.187 --
all0.208 12366 -
obs0.208 12366 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 5 149 1867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.102
X-RAY DIFFRACTIONc_bond_d0.005

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