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- PDB-5nvl: Crystal structure of the human 4EHP-GIGYF2 complex -

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Basic information

Entry
Database: PDB / ID: 5nvl
TitleCrystal structure of the human 4EHP-GIGYF2 complex
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


musculoskeletal movement / post-transcriptional gene silencing / spinal cord motor neuron differentiation / proximal dendrite / 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 / RNA 7-methylguanosine cap binding ...musculoskeletal movement / post-transcriptional gene silencing / spinal cord motor neuron differentiation / proximal dendrite / 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 / RNA 7-methylguanosine cap binding / feeding behavior / proline-rich region binding / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / neuromuscular process controlling balance / negative regulation of translational initiation / homeostasis of number of cells within a tissue / translational initiation / mitotic G1 DNA damage checkpoint signaling / translation initiation factor activity / rescue of stalled ribosome / adult locomotory behavior / insulin-like growth factor receptor signaling pathway / post-embryonic development / P-body / multicellular organism growth / ISG15 antiviral mechanism / cytoplasmic stress granule / perikaryon / vesicle / molecular adaptor activity / negative regulation of translation / endosome / cadherin binding / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / protein-containing complex / RNA binding / membrane / cytosol / cytoplasm
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. / Translation Initiation factor eIF- 4e ...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
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: 2.3 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 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 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


Theoretical massNumber of molelcules
Total (without water)61,3364
Polymers61,3364
Non-polymers00
Water1,26170
1
A: Eukaryotic translation initiation factor 4E type 2
B: GRB10-interacting GYF protein 2


Theoretical massNumber of molelcules
Total (without water)30,6682
Polymers30,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area12030 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E type 2
D: GRB10-interacting GYF protein 2


Theoretical massNumber of molelcules
Total (without water)30,6682
Polymers30,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-24 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.550, 82.550, 148.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 5 residues of the coordinate sequence of chain A and the first residue of the coordinate sequence of chain C 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 GRB10-interacting GYF protein 2 / PERQ amino acid-rich with GYF domain-containing protein 2 / Trinucleotide repeat-containing gene 15 protein


Mass: 8689.040 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) / Variant (production host): STAR / References: UniProt: Q6Y7W6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.0 0.1 M magnesium chloride 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 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: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.3→45.9 Å / Num. obs: 23500 / % possible obs: 99.8 % / Redundancy: 11.2 % / Rsym value: 0.125 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 1690 / Rsym value: 0.938 / % possible all: 98.3

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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: 2JGB

2jgb


Resolution: 2.3→45.888 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.9
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 1168 4.97 %Random selection
Rwork0.2053 ---
obs0.2072 23497 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 0 70 3811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043832
X-RAY DIFFRACTIONf_angle_d0.545180
X-RAY DIFFRACTIONf_dihedral_angle_d12.8222305
X-RAY DIFFRACTIONf_chiral_restr0.041554
X-RAY DIFFRACTIONf_plane_restr0.003665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.38111310.29232688X-RAY DIFFRACTION99
2.4047-2.53150.29121200.2732777X-RAY DIFFRACTION100
2.5315-2.69010.32451550.25342734X-RAY DIFFRACTION100
2.6901-2.89770.31671490.24432737X-RAY DIFFRACTION100
2.8977-3.18930.27511490.22722785X-RAY DIFFRACTION100
3.1893-3.65060.24451460.20232792X-RAY DIFFRACTION100
3.6506-4.59870.17251550.17262831X-RAY DIFFRACTION100
4.5987-45.89690.23281630.18462985X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3068-0.66780.75093.9461-0.03663.5070.02980.31660.4838-0.2481-0.1691-0.3363-0.19790.0860.15720.3079-0.01830.03090.37620.00930.443554.981335.198357.1657
22.2517-1.13120.71263.33930.0652.10710.1309-0.06310.01120.0823-0.0851-0.13610.09830.012-0.06720.2854-0.02740.03680.4121-0.08170.419650.909829.386265.7074
33.397-0.0263-0.47133.7580.2282.9387-0.1111-0.2068-0.49850.2122-0.10840.38240.2518-0.07240.170.4151-0.03650.11090.3937-0.08720.510354.11120.335660.2501
44.43050.4806-0.33834.60051.53521.56970.1420.05250.0119-0.3556-0.08860.15920.0040.1165-0.05920.43460.0169-0.00080.4427-0.09470.277752.55415.945649.7032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 48 through 218)
2X-RAY DIFFRACTION2(chain 'B' and resid 37 through 105)
3X-RAY DIFFRACTION3(chain 'C' and resid 52 through 218)
4X-RAY DIFFRACTION4(chain 'D' and resid 37 through 103)

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