[English] 日本語
Yorodumi
- PDB-8th7: Crystal Structure of the G3BP1 NTF2-like domain bound to the Capr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8th7
TitleCrystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide
Components
  • Caprin-1
  • Ras GTPase-activating protein-binding protein 1
KeywordsPEPTIDE BINDING PROTEIN / NTF2L Caprin1
Function / homology
Function and homology information


regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / non-membrane-bounded organelle assembly / positive regulation of dendrite morphogenesis / intracellular non-membrane-bounded organelle / generation of neurons / cell leading edge ...regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / non-membrane-bounded organelle assembly / positive regulation of dendrite morphogenesis / intracellular non-membrane-bounded organelle / generation of neurons / cell leading edge / ribosomal small subunit binding / positive regulation of type I interferon production / signaling adaptor activity / stress granule assembly / DNA helicase activity / synapse assembly / molecular condensate scaffold activity / molecular function activator activity / P-body / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / lamellipodium / perikaryon / endonuclease activity / defense response to virus / DNA helicase / Ras protein signal transduction / RNA helicase activity / negative regulation of translation / RNA helicase / ribonucleoprotein complex / innate immune response / focal adhesion / mRNA binding / synapse / dendrite / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / 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 ...Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / 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 / Caprin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsHughes, M.P. / Taylor, J.P. / Yang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)R35NS097974 United States
CitationJournal: Cell Rep / Year: 2024
Title: Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity.
Authors: Yang, Z. / Johnson, B.A. / Meliopoulos, V.A. / Ju, X. / Zhang, P. / Hughes, M.P. / Wu, J. / Koreski, K.P. / Clary, J.E. / Chang, T.C. / Wu, G. / Hixon, J. / Duffner, J. / Wong, K. / Lemieux, ...Authors: Yang, Z. / Johnson, B.A. / Meliopoulos, V.A. / Ju, X. / Zhang, P. / Hughes, M.P. / Wu, J. / Koreski, K.P. / Clary, J.E. / Chang, T.C. / Wu, G. / Hixon, J. / Duffner, J. / Wong, K. / Lemieux, R. / Lokugamage, K.G. / Alvarado, R.E. / Crocquet-Valdes, P.A. / Walker, D.H. / Plante, K.S. / Plante, J.A. / Weaver, S.C. / Kim, H.J. / Meyers, R. / Schultz-Cherry, S. / Ding, Q. / Menachery, V.D. / Taylor, J.P.
History
DepositionJul 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Structure summary / Category: audit_author

-
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: Caprin-1
D: Caprin-1


Theoretical massNumber of molelcules
Total (without water)37,2164
Polymers37,2164
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-43 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 71.440, 51.950
Angle α, β, γ (deg.)90.00, 111.26, 90.00
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: 15986.153 Da / Num. of mol.: 2
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 / Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / ...Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / GPI-anchored membrane protein 1 / GPI-anchored protein p137 / GPI-p137 / p137GPI / Membrane component chromosome 11 surface marker 1 / RNA granule protein 105


Mass: 2621.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPRIN1, GPIAP1, GPIP137, M11S1, RNG105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14444
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M tri-ammonium citrate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
ReflectionResolution: 2.88→48.42 Å / Num. obs: 6159 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.938 / Net I/σ(I): 4.5
Reflection shellResolution: 2.88→2.955 Å / Num. unique obs: 966 / CC1/2: 0.837

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q9O

3q9o


Resolution: 2.88→48.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.87 / SU B: 23.778 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27652 341 5.2 %RANDOM
Rwork0.18965 ---
obs0.19448 6159 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20.06 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.88→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 0 12 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172222
X-RAY DIFFRACTIONr_angle_refined_deg1.61.643331
X-RAY DIFFRACTIONr_angle_other_deg1.2321.5825055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3625304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72422.34141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.85615373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6411515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.913.9721231
X-RAY DIFFRACTIONr_mcbond_other2.93.9711230
X-RAY DIFFRACTIONr_mcangle_it4.7285.9391530
X-RAY DIFFRACTIONr_mcangle_other4.7275.941531
X-RAY DIFFRACTIONr_scbond_it2.7634.081229
X-RAY DIFFRACTIONr_scbond_other2.7624.0811230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4486.0171802
X-RAY DIFFRACTIONr_long_range_B_refined7.07945.9632672
X-RAY DIFFRACTIONr_long_range_B_other7.07745.9622673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 23 -
Rwork0.282 456 -
obs--99.38 %

+
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://pdbjlvh1.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