[English] 日本語
Yorodumi
- PDB-2vwf: Grb2 SH3C (2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vwf
TitleGrb2 SH3C (2)
Components
  • GRB2-ASSOCIATED-BINDING PROTEIN 2
  • GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
KeywordsPROTEIN BINDING / POLYMORPHISM / PHOSPHOPROTEIN / GOLGI APPARATUS / GRB2 / ALTERNATIVE SPLICING / HOST-VIRUS INTERACTION / SH3C / SIGNALING / SH2 DOMAIN / SH3 DOMAIN / PROTEIN-BINDING
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / positive regulation of mast cell degranulation / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / positive regulation of mast cell degranulation / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling / phosphatidylinositol-3,4-bisphosphate binding / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / MET activates RAP1 and RAC1 / vesicle membrane / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of actin filament polymerization / endodermal cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / PI3K events in ERBB2 signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / signal transduction in response to DNA damage / fibroblast growth factor receptor signaling pathway / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signalling to RAS / GAB1 signalosome / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / InlB-mediated entry of Listeria monocytogenes into host cell / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / ephrin receptor binding / Signaling by FGFR2 in disease / phosphotyrosine residue binding / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / cellular response to ionizing radiation / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / osteoclast differentiation / Constitutive Signaling by Overexpressed ERBB2 / T cell activation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Negative regulation of FGFR2 signaling
Similarity search - Function
GRB2-associated-binding protein 1-4-like / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain ...GRB2-associated-binding protein 1-4-like / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2 / GRB2-associated-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsHarkiolaki, M. / Tsirka, T. / Feller, S.M.
CitationJournal: Structure / Year: 2009
Title: Distinct Binding Modes of Two Epitopes in Gab2 that Interact with the Sh3C Domain of Grb2.
Authors: Harkiolaki, M. / Tsirka, T. / Lewitzky, M. / Simister, P.C. / Joshi, D. / Bird, L.E. / Jones, E.Y. / O'Reilly, N. / Feller, S.M.
History
DepositionJun 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GRB2-ASSOCIATED-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)8,3882
Polymers8,3882
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8.2 kcal/mol
Surface area5450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)41.166, 41.166, 107.915
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

-
Components

#1: Protein GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 / ADAPTER PROTEIN GRB2 / SH2/SH3 ADAPTER GRB2 / PROTEIN ASH / GRB2 SH3C


Mass: 6612.233 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 159-214 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GP- OVERHANG DUE TO INFUSION VECTOR USED
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: OPIN J / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62993
#2: Protein/peptide GRB2-ASSOCIATED-BINDING PROTEIN 2 / GROWTH FACTOR RECEPTOR BOUND PROTEIN 2-ASSOCIATED PROTEIN 2 / GRB2-ASSOCIATED BINDER 2 / PP100 / GAB2


Mass: 1776.090 Da / Num. of mol.: 1 / Fragment: SH3 BINDING REGION, RESIDUES 508-522 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9UQC2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 212 TO ALA
Sequence detailsN-TERMINAL GP SEQUENCE IS DUE TO THE VECTOR USED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.58 Å3/Da / Density % sol: 22.1 % / Description: NONE
Crystal growpH: 7
Details: 2M TRI-AMMONIUM CITRATE, 0.1M BIS-TRIS PROPANE PH7, pH 7.0

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 8066 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 19.5 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 26.7
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVK

2vvk


Resolution: 1.58→35.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.814 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21907 369 4.6 %RANDOM
Rwork0.18812 ---
obs0.18951 7645 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.58→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 0 0 42 612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022592
X-RAY DIFFRACTIONr_bond_other_d0.0070.02409
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.922806
X-RAY DIFFRACTIONr_angle_other_deg0.9673985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.584570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7392435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1711586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.963155
X-RAY DIFFRACTIONr_chiral_restr0.0960.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_nbd_refined0.1980.294
X-RAY DIFFRACTIONr_nbd_other0.2110.2411
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2285
X-RAY DIFFRACTIONr_nbtor_other0.0920.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2941.5443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5312570
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3613282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3614.5235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 25
Rwork0.253 543

+
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