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- PDB-5nvm: Crystal structure of the human 4EHP-GIGYF2 complex lacking the au... -

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Basic information

Entry
Database: PDB / ID: 5nvm
TitleCrystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences
Components
  • Eukaryotic translation initiation factor 4E type 2
  • GRB10-interacting GYF protein 2
KeywordsTRANSLATION / translational regulation / cap-binding protein / 4EHP-binding protein / GRB10-interacting GYF protein 2
Function / homology
Function and homology information


post-transcriptional gene silencing / musculoskeletal movement / spinal cord motor neuron differentiation / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / proximal dendrite / RNA 7-methylguanosine cap binding ...post-transcriptional gene silencing / musculoskeletal movement / spinal cord motor neuron differentiation / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / proximal dendrite / RNA 7-methylguanosine cap binding / proline-rich region binding / feeding behavior / negative regulation of type I interferon-mediated signaling pathway / neuromuscular process controlling balance / mRNA destabilization / mitotic G1 DNA damage checkpoint signaling / translation initiation factor activity / negative regulation of translational initiation / rescue of stalled ribosome / homeostasis of number of cells within a tissue / insulin-like growth factor receptor signaling pathway / adult locomotory behavior / post-embryonic development / translational initiation / P-body / ISG15 antiviral mechanism / multicellular organism growth / cytoplasmic stress granule / perikaryon / vesicle / molecular adaptor activity / endosome / negative regulation of translation / cadherin binding / ubiquitin protein ligase binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / RNA binding / membrane / cytoplasm / cytosol
Similarity search - Function
: / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. ...: / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Eukaryotic translation initiation factor 4E type 2 / GRB10-interacting GYF protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPeter, D. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2017
Title: GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression.
Authors: Peter, D. / Weber, R. / Sandmeir, F. / Wohlbold, L. / Helms, S. / Bawankar, P. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 2
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3768
Polymers53,9964
Non-polymers3804
Water2,342130
1
A: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1884
Polymers26,9982
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-29 kcal/mol
Surface area11760 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1884
Polymers26,9982
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-28 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.210, 98.590, 39.280
Angle α, β, γ (deg.)90.00, 99.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Eukaryotic translation initiation factor 4E type 2 / eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic ...eIF4E type 2 / Eukaryotic translation initiation factor 4E homologous protein / Eukaryotic translation initiation factor 4E-like 3 / eIF4E-like protein 4E-LP / mRNA cap-binding protein 4EHP / h4EHP / mRNA cap-binding protein type 3


Mass: 21979.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first six residues of the coordinate sequence belong to the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E2, EIF4EL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O60573
#2: Protein/peptide GRB10-interacting GYF protein 2 / PERQ amino acid-rich with GYF domain-containing protein 2 / Trinucleotide repeat-containing gene 15 protein


Mass: 5018.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIGYF2, KIAA0642, PERQ2, TNRC15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6Y7W6
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6 0.6 M diammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.613 Å / Num. obs: 38577 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rsym value: 0.066 / Net I/σ(I): 12
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.09 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NVL

5nvl


Resolution: 2→44.613 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 1931 5.01 %Random selection
Rwork0.1984 ---
obs0.2001 38550 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 20 130 3520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073490
X-RAY DIFFRACTIONf_angle_d0.774720
X-RAY DIFFRACTIONf_dihedral_angle_d15.0422076
X-RAY DIFFRACTIONf_chiral_restr0.049490
X-RAY DIFFRACTIONf_plane_restr0.005603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35471520.29232560X-RAY DIFFRACTION100
2.05-2.10540.30451410.2762578X-RAY DIFFRACTION100
2.1054-2.16740.31351360.2652642X-RAY DIFFRACTION100
2.1674-2.23730.25171380.25822573X-RAY DIFFRACTION100
2.2373-2.31730.28841390.23972657X-RAY DIFFRACTION100
2.3173-2.410.2429940.23732626X-RAY DIFFRACTION100
2.41-2.51970.25381550.23542591X-RAY DIFFRACTION100
2.5197-2.65250.29031250.23272630X-RAY DIFFRACTION100
2.6525-2.81870.26671490.22662602X-RAY DIFFRACTION100
2.8187-3.03630.27341350.2292626X-RAY DIFFRACTION100
3.0363-3.34180.25531350.21652624X-RAY DIFFRACTION100
3.3418-3.82510.2331380.18852600X-RAY DIFFRACTION100
3.8251-4.81830.18971670.162621X-RAY DIFFRACTION100
4.8183-44.62390.18931270.16312689X-RAY DIFFRACTION100

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