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- PDB-3d3m: The Crystal Structure of the C-terminal region of Death Associate... -

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Basic information

Entry
Database: PDB / ID: 3d3m
TitleThe Crystal Structure of the C-terminal region of Death Associated Protein 5(DAP5)
ComponentsEukaryotic translation initiation factor 4 gamma 2Eukaryotic translation initiation factor 4 gamma 1
KeywordsTRANSLATION / HEAT repeat domain / Structural Genomics / PSI / Protein Structure Initiative / Israel Structural Proteomics Center / ISPC / Acetylation / Initiation factor / Phosphoprotein / Protein biosynthesis / Repressor / Translation regulation
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 / Resolution: 1.9 Å
AuthorsDym, O. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The crystal structure of the C-terminal DAP5/p97 domain sheds light on the molecular basis for its processing by caspase cleavage.
Authors: Liberman, N. / Dym, O. / Unger, T. / Albeck, S. / Peleg, Y. / Jacobovitch, Y. / Branzburg, A. / Eisenstein, M. / Marash, L. / Kimchi, A.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)39,3152
Polymers39,3152
Non-polymers00
Water1,17165
1
A: Eukaryotic translation initiation factor 4 gamma 2


Theoretical massNumber of molelcules
Total (without water)19,6581
Polymers19,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 4 gamma 2


Theoretical massNumber of molelcules
Total (without water)19,6581
Polymers19,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.059, 45.734, 63.357
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19657.566 Da / Num. of mol.: 2 / Fragment: C terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4G2, DAP5, OK/SW-cl.75 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P78344
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6
Details: 100mM MMT (D,L Maleic acid, MES and Tris) pH=6, and 20% PEG 1,500, Microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97873, 0.91840
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978731
20.91841
ReflectionResolution: 1.9→25 Å / Num. obs: 27035 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.065 / Net I/σ(I): 47.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2682 / Rsym value: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.776 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1357 5 %RANDOM
Rwork0.211 ---
obs0.214 27016 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.35 Å2
2--1.25 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 0 65 2714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222720
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.9633677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83625.781128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24115510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.204152
X-RAY DIFFRACTIONr_chiral_restr0.1780.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212012
X-RAY DIFFRACTIONr_mcbond_it1.4321.51595
X-RAY DIFFRACTIONr_mcangle_it2.46522591
X-RAY DIFFRACTIONr_scbond_it3.93931125
X-RAY DIFFRACTIONr_scangle_it6.124.51086
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 96 -
Rwork0.247 1867 -
all-1963 -
obs--99.7 %

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