[English] 日本語
Yorodumi
- PDB-5nvl: Crystal structure of the human 4EHP-GIGYF2 complex -

+
Open data


ID or keywords:

Loading...

-
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


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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more