[English] 日本語
Yorodumi
- PDB-7xhg: Crystal structure of the NTF2L domain of human G3BP1 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xhg
TitleCrystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide
Components
  • Caprin-1(369-378)
  • Ras GTPase-activating protein-binding protein 1
KeywordsRNA BINDING PROTEIN / Complex / Stress granules / Lipid-lipid phase separation
Function / homology
Function and homology information


positive regulation of stress granule assembly / DNA/RNA helicase activity / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon ...positive regulation of stress granule assembly / DNA/RNA helicase activity / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon / endonuclease activity / defense response to virus / Ras protein signal transduction / DNA helicase / RNA helicase activity / RNA helicase / ribonucleoprotein complex / focal adhesion / mRNA binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsDan, S. / Weimin, G.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Yin and yang regulation of stress granules by Caprin-1.
Authors: Song, D. / Kuang, L. / Yang, L. / Wang, L. / Li, H. / Li, X. / Zhu, Z. / Shi, C. / Zhu, H. / Gong, W.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
C: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
F: Caprin-1(369-378)
G: Caprin-1(369-378)
E: Caprin-1(369-378)


Theoretical massNumber of molelcules
Total (without water)67,2787
Polymers67,2787
Non-polymers00
Water73941
1
A: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
E: Caprin-1(369-378)


Theoretical massNumber of molelcules
Total (without water)33,0263
Polymers33,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-26 kcal/mol
Surface area12820 Å2
MethodPISA
2
B: Ras GTPase-activating protein-binding protein 1
C: Ras GTPase-activating protein-binding protein 1
F: Caprin-1(369-378)
G: Caprin-1(369-378)


Theoretical massNumber of molelcules
Total (without water)34,2534
Polymers34,2534
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-35 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.669, 171.761, 42.968
Angle α, β, γ (deg.)90.000, 99.820, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ras GTPase-activating protein-binding protein 1 / G3BP-1 / ATP-dependent DNA helicase VIII / hDH VIII / GAP SH3 domain-binding protein 1


Mass: 15899.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP1, G3BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Protein/peptide Caprin-1(369-378)


Mass: 1227.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30 % w/v Polyethylene glycol 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.45→85.88 Å / Num. obs: 21506 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Net I/σ(I): 28.2
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1065 / CC1/2: 0.818 / Rpim(I) all: 0.333 / Rrim(I) all: 0.629

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fcj

4fcj


Resolution: 2.46→85.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.939 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.706 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 1073 5 %RANDOM
Rwork0.206 ---
obs0.2095 20403 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 39.622 Å2 / Biso min: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å2-0 Å21.11 Å2
2---2.01 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 2.46→85.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 0 41 4471
Biso mean---32.69 -
Num. residues----553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194567
X-RAY DIFFRACTIONr_bond_other_d0.0020.024237
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9186187
X-RAY DIFFRACTIONr_angle_other_deg0.97439641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45523.78246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24515723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8241531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025367
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021220
LS refinement shellResolution: 2.46→2.519 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.356 58 -
Rwork0.298 1409 -
obs--92.97 %

+
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