[English] 日本語
Yorodumi
- PDB-2kb0: Cdc42(T35A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kb0
TitleCdc42(T35A)
ComponentsCell division control protein 42 homolog
KeywordsSIGNALING PROTEIN / globular / folded / Switch 1 / mutation / Ras / Alternative splicing / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation
Function / homology
Function and homology information


GBD domain binding / positive regulation of pinocytosis / COG complex / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / embryonic heart tube development ...GBD domain binding / positive regulation of pinocytosis / COG complex / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / embryonic heart tube development / endothelin receptor signaling pathway / Inactivation of CDC42 and RAC1 / positive regulation of pseudopodium assembly / host-mediated perturbation of viral process / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / establishment of Golgi localization / dendritic spine morphogenesis / establishment of epithelial cell apical/basal polarity / cell junction assembly / GTP-dependent protein binding / heart process / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate KTN1 / DCC mediated attractive signaling / positive regulation of filopodium assembly / CD28 dependent Vav1 pathway / regulation of postsynapse organization / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / Myogenesis / establishment of cell polarity / small GTPase-mediated signal transduction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / RHOQ GTPase cycle / Golgi organization / RHOU GTPase cycle / macrophage differentiation / establishment or maintenance of cell polarity / CDC42 GTPase cycle / RHO GTPases activate PAKs / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / negative regulation of protein-containing complex assembly / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / RAC1 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / integrin-mediated signaling pathway / actin filament organization / regulation of actin cytoskeleton organization / small monomeric GTPase / FCGR3A-mediated phagocytosis / filopodium / EGFR downregulation / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / mitotic spindle / endocytosis / MAPK6/MAPK4 signaling / cytoplasmic ribonucleoprotein granule / apical part of cell / microtubule cytoskeleton / cell-cell junction / actin cytoskeleton organization / G beta:gamma signalling through CDC42 / ubiquitin protein ligase activity / positive regulation of cell growth / Factors involved in megakaryocyte development and platelet production / midbody / G protein activity / postsynapse / neuron projection / positive regulation of cell migration / Golgi membrane / focal adhesion / centrosome / neuronal cell body / GTPase activity / dendrite / protein kinase binding / endoplasmic reticulum membrane / GTP binding / glutamatergic synapse / signal transduction
Similarity search - Function
Cdc42 / Small GTPase Rho / Small GTPase Rho domain profile. / 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 ...Cdc42 / Small GTPase Rho / Small GTPase Rho domain profile. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsAdams, P.D. / Oswald, R.E. / McFeeters, R.
CitationJournal: To be Published
Title: Cdc42(T35A)
Authors: Adams, P. / Oswald, R. / McFeeters, R.
History
DepositionNov 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)19,7451
Polymers19,7451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 18structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 19744.678 Da / Num. of mol.: 1 / Mutation: T35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D (H)CCH-TOCSY

-
Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] Cdc42(T35A), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.4 mM / Component: Cdc42(T35A) / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian AMX / Manufacturer: Varian / Model: AMX / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: nih-xplor used to calculate structures
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 18 / Conformers submitted total number: 12

+
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