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- PDB-1hu3: MIDDLE DOMAIN OF HUMAN EIF4GII -

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Basic information

Entry
Database: PDB / ID: 1hu3
TitleMIDDLE DOMAIN OF HUMAN EIF4GII
ComponentsEIF4GII
KeywordsTRANSLATION / eIF4G / HEAT repeat
Function / homology
Function and homology information


RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / intracellular membraneless organelle / spermatid development / translation initiation factor activity / positive regulation of translation / translational initiation / ISG15 antiviral mechanism ...RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / intracellular membraneless organelle / spermatid development / translation initiation factor activity / positive regulation of translation / translational initiation / ISG15 antiviral mechanism / mRNA binding / RNA binding / cytosol
Similarity search - Function
Initiation factor 4G / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. ...Initiation factor 4G / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4 gamma 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.37 Å
AuthorsMarcotrigiano, J. / Lomakin, I. / Pestova, T.V. / Hellen, C.U.T. / Sonenberg, N. / Burley, S.K.
CitationJournal: Mol.Cell / Year: 2001
Title: A conserved HEAT domain within eIF4G directs assembly of the translation initiation machinery.
Authors: Marcotrigiano, J. / Lomakin, I.B. / Sonenberg, N. / Pestova, T.V. / Hellen, C.U. / Burley, S.K.
History
DepositionJan 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: EIF4GII


Theoretical massNumber of molelcules
Total (without water)30,8261
Polymers30,8261
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.8, 118.8, 58.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein EIF4GII / EUKARYOTIC INITIATION FACTOR 4GII


Mass: 30826.410 Da / Num. of mol.: 1 / Fragment: RESIDUES 745-1003
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43432
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M acetate (4.6), 0.1M ammonium acetate, 20-22% PEG4000, and 5mM tris(carboxyethyl)phosphine, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Macetate1reservoir
20.1 Mammonium acetate1reservoir
320-22 %(w/v)PEG40001reservoir
45 mMtris(carboxyethyl)phospine1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97928 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 28, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.37→20 Å / Num. all: 170724 / Num. obs: 12425 / % possible obs: 97.5 % / Observed criterion σ(I): 4 / Redundancy: 4 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.195 / % possible all: 85
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 170724
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.37→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2181 10 %RANDOM
Rwork0.249 ---
obs-24808 --
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 0 69 1658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shellResolution: 2.37→2.39 Å
RfactorNum. reflection
Rfree0.328 38
Rwork0.317 287
obs-1022
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.328 / Rfactor Rwork: 0.317

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