[English] 日本語
Yorodumi
- PDB-5l0o: IQGAP1 calponin homology domain fragment (CHDF) mutant K161C unde... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l0o
TitleIQGAP1 calponin homology domain fragment (CHDF) mutant K161C under oxidizing conditions
ComponentsRas GTPase-activating-like protein IQGAP1
KeywordsSIGNALING PROTEIN / Calponin homology / disulfide-bonded dimer
Function / homology
Function and homology information


negative regulation of dephosphorylation / mitotic actomyosin contractile ring assembly actin filament organization / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions / neuron projection extension ...negative regulation of dephosphorylation / mitotic actomyosin contractile ring assembly actin filament organization / podocyte development / slit diaphragm / GTPase inhibitor activity / MAP-kinase scaffold activity / fibroblast migration / S100 protein binding / Nephrin family interactions / neuron projection extension / RHOV GTPase cycle / cortical actin cytoskeleton / RHOC GTPase cycle / RHOQ GTPase cycle / cellular response to platelet-derived growth factor stimulus / phosphatidylinositol-3,4,5-trisphosphate binding / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / CDC42 GTPase cycle / lateral plasma membrane / fibroblast growth factor receptor signaling pathway / RHOA GTPase cycle / positive regulation of protein kinase activity / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / ruffle / regulation of mitotic cell cycle / regulation of cytokine production / cellular response to epidermal growth factor stimulus / RAC1 GTPase cycle / cellular response to calcium ion / GTPase activator activity / protein serine/threonine kinase activator activity / secretory granule membrane / actin filament / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / small GTPase binding / cytoplasmic side of plasma membrane / cytoplasmic ribonucleoprotein granule / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / actin filament binding / cell migration / cell cortex / midbody / growth cone / basolateral plasma membrane / protein phosphatase binding / microtubule / positive regulation of MAPK cascade / molecular adaptor activity / calmodulin binding / neuron projection / cadherin binding / ribonucleoprotein complex / apical plasma membrane / protein domain specific binding / axon / focal adhesion / calcium ion binding / Neutrophil degranulation / protein kinase binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 ...RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ras GTPase-activating-like protein IQGAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLiu, J. / Worthylake, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084072 United States
CitationJournal: Biochemistry / Year: 2016
Title: The IQGAP1 N-Terminus Forms Dimers, and the Dimer Interface Is Required for Binding F-Actin and Calcium-Bound Calmodulin.
Authors: Liu, J. / Kurella, V.B. / LeCour, L. / Vanagunas, T. / Worthylake, D.K.
History
DepositionJul 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: 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
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras GTPase-activating-like protein IQGAP1
B: Ras GTPase-activating-like protein IQGAP1
C: Ras GTPase-activating-like protein IQGAP1
D: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)89,4464
Polymers89,4464
Non-polymers00
Water00
1
A: Ras GTPase-activating-like protein IQGAP1
B: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)44,7232
Polymers44,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-13 kcal/mol
Surface area16640 Å2
MethodPISA
2
C: Ras GTPase-activating-like protein IQGAP1
D: Ras GTPase-activating-like protein IQGAP1


Theoretical massNumber of molelcules
Total (without water)44,7232
Polymers44,7232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-12 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.752, 72.464, 73.272
Angle α, β, γ (deg.)77.15, 72.07, 86.80
Int Tables number1
Space group name H-MP1
DetailsDimer according to gel filtration, mutagenesis, shape complementary analysis

-
Components

#1: Protein
Ras GTPase-activating-like protein IQGAP1 / p195


Mass: 22361.402 Da / Num. of mol.: 4 / Mutation: K161C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP1, KIAA0051 / Production host: Escherichia coli (E. coli)
Strain (production host): in Rosetta Gami 2(DE3) pLysS cells (EMD4Biosciences)
References: UniProt: P46940
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 18% PEG 3350, 10% ethylene glycol, 10% glucose, 100mM -160mM potassium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→68.06 Å / Num. obs: 41528 / % possible obs: 98.4 % / Redundancy: 3.13 % / Rmerge(I) obs: 0.0847 / Net I/σ(I): 25.57
Reflection shellResolution: 2.36→2.46 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.3504 / Mean I/σ(I) obs: 2.14 / % possible all: 94.8

-
Processing

Software
NameClassification
CNSrefinement
SAINTdata reduction
XPREPdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I6X

3i6x


Resolution: 2.36→15 Å / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2056 4.9 %RANDOM
Rwork0.262 ---
obs0.262 38960 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.36→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 0 0 5436

+
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