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- PDB-4iul: MIF4G domain of DAP5 -

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Basic information

Entry
Database: PDB / ID: 4iul
TitleMIF4G domain of DAP5
ComponentsEukaryotic translation initiation factor 4 gamma 2Eukaryotic translation initiation factor 4 gamma 1
KeywordsTRANSLATION / HEAT repeats / protein-protein interaction / eIF4A
Function / homology
Function and homology information


macromolecule biosynthetic process / cell death / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / positive regulation of dendritic spine development / positive regulation of axon extension / translational initiation / translation initiation factor activity / negative regulation of autophagy ...macromolecule biosynthetic process / cell death / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / positive regulation of dendritic spine development / positive regulation of axon extension / translational initiation / translation initiation factor activity / negative regulation of autophagy / positive regulation of translation / adherens junction / ISG15 antiviral mechanism / heart development / positive regulation of cell growth / regulation of cell cycle / cadherin binding / axon / mRNA binding / RNA binding / membrane / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFrank, F. / Virgili, G. / Feoktistova, K. / Sawicki, M. / Sonenberg, N. / Fraser, C. / Nagar, B.
CitationJournal: Structure / Year: 2013
Title: Structural Analysis of the DAP5 MIF4G Domain and Its Interaction with eIF4A.
Authors: Virgili, G. / Frank, F. / Feoktistova, K. / Sawicki, M. / Sonenberg, N. / Fraser, C.S. / Nagar, B.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / 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_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 4 gamma 2
B: Eukaryotic translation initiation factor 4 gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9627
Polymers61,4822
Non-polymers4805
Water4,035224
1
A: Eukaryotic translation initiation factor 4 gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9333
Polymers30,7411
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4 gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0294
Polymers30,7411
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-8 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.696, 56.696, 74.374
Angle α, β, γ (deg.)90.00, 112.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Eukaryotic translation initiation factor 4 gamma 2 / Eukaryotic translation initiation factor 4 gamma 1 / eIF-4-gamma 2 / eIF-4G 2 / eIF4G 2 / Death-associated protein 5 / DAP-5 / p97


Mass: 30740.855 Da / Num. of mol.: 2 / Fragment: MIF4G domain, UNP residues 61-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAP5, EIF4G2, OK/SW-cl.75 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P78344
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M ammonium sulfate and 18 20% (w/v) polyethylene glycol 5000 monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 30, 2009
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 28073 / Num. obs: 28017 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / % possible all: 87.5

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Processing

Software
NameClassification
HKL-2000data collection
CCP4model building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HU3

1hu3


Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 2495 Random
Rwork0.221 --
all0.224 29003 -
obs0.224 27401 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 25 224 4059

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