[English] 日本語
Yorodumi
- PDB-5cjp: The Structural Basis for Cdc42-Induced Dimerization of IQGAPs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cjp
TitleThe Structural Basis for Cdc42-Induced Dimerization of IQGAPs
Components
  • Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
  • Ras GTPase-activating-like protein IQGAP2
KeywordsPROTEIN BINDING / IQGAP2 GAP related domain X-ray GTPase interactions Complex Cdc42
Function / homology
Function and homology information


: / intracellular protein localization => GO:0008104 / modification of synaptic structure / : / mitotic actomyosin contractile ring assembly actin filament organization / Cdc42 protein signal transduction / establishment or maintenance of apical/basal cell polarity / regulation of protein binding / GBD domain binding / submandibular salivary gland formation ...: / intracellular protein localization => GO:0008104 / modification of synaptic structure / : / mitotic actomyosin contractile ring assembly actin filament organization / Cdc42 protein signal transduction / establishment or maintenance of apical/basal cell polarity / regulation of protein binding / GBD domain binding / submandibular salivary gland formation / Arp2/3 complex binding / Golgi transport complex / positive regulation of pinocytosis / Arp2/3 complex-mediated actin nucleation / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / GTPase inhibitor activity / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of lamellipodium assembly / regulation of stress fiber assembly / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / thrombin-activated receptor signaling pathway / heart contraction / establishment or maintenance of cell polarity / establishment of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / phosphatidylinositol-3,4,5-trisphosphate binding / microvillus / RHOU GTPase cycle / macrophage differentiation / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / secretory granule membrane / secretory granule / small monomeric GTPase / actin filament organization / positive regulation of DNA replication / integrin-mediated signaling pathway / cell projection / filopodium / regulation of actin cytoskeleton organization
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Cdc42 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. / GTPase-activator protein for Ras-like GTPases ...RasGAP protein, C-terminal / RasGAP C-terminus / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Cdc42 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Small GTPase Rho / Small GTPase Rho domain profile. / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / WW domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a / Cell division control protein 42 homolog / Ras GTPase-activating-like protein IQGAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsWorthylake, D.K. / Boyapati, V.K. / LeCour Jr, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01BM084072 United States
CitationJournal: Structure / Year: 2016
Title: The Structural Basis for Cdc42-Induced Dimerization of IQGAPs.
Authors: LeCour, L. / Boyapati, V.K. / Liu, J. / Li, Z. / Sacks, D.B. / Worthylake, D.K.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
B: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
C: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
D: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
E: Ras GTPase-activating-like protein IQGAP2
F: Ras GTPase-activating-like protein IQGAP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,34114
Polymers167,1516
Non-polymers2,1908
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22830 Å2
ΔGint-111 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.633, 120.169, 157.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a


Mass: 19758.748 Da / Num. of mol.: 4 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42, hCG_1981007 / Plasmid: pPRO EX HTb
Details (production host): plasmid encodes a TEV protease cleavable 6xHis tag which leaves a Gly-Ala cloning artifact preceding the initiator methionine
Cell line (production host): RIL / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: A0A024RAE4, UniProt: P60953*PLUS
#2: Protein Ras GTPase-activating-like protein IQGAP2


Mass: 44058.094 Da / Num. of mol.: 2 / Fragment: unp reesidues 875-1258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP2 / Plasmid: pET Trx
Details (production host): kanamycin, encodes E. coli thioredoxin and a TEV protease-cleavable 6xHis tag N-terminal to the IQGAP2 GAP-related domain
Cell line (production host): RIL / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q13576
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28.5% (v/v) polyethylene glycol (PEG) MW 400, 100mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5 and 40mM MgCl2.
PH range: 6.5-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 12, 2014
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.57→20 Å / Num. obs: 61742 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/av σ(I): 2.9 / Net I/σ(I): 10.5
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
PDB_EXTRACTdata extraction
MOLREPphasing
Omodel building
SCALAdata scaling
RefinementResolution: 2.6→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2873 2993 5 %
Rwork0.2474 56575 -
obs-59568 99.8 %
Solvent computationBsol: 33.9884 Å2
Displacement parametersBiso max: 198.96 Å2 / Biso mean: 72.6528 Å2 / Biso min: 19.35 Å2
Baniso -1Baniso -2Baniso -3
1--9.939 Å20 Å20 Å2
2---2.859 Å20 Å2
3---12.797 Å2
Refinement stepCycle: final / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 251 0 11765
Biso mean--47.49 --
Num. residues----1452
Refine LS restraintsType: c_angle_d / Dev ideal: 1.314

+
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