[English] 日本語
Yorodumi
- PDB-5upl: CDC42 binds PAK4 via an extended GTPase-effector inteface - 2 pep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5upl
TitleCDC42 binds PAK4 via an extended GTPase-effector inteface - 2 peptide: PAK4FL, CDC42 - UNREFINED
Components
  • Cell division control protein 42 homolog
  • Serine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / GTPase / Kinase / CRIB
Function / homology
Function and homology information


GBD domain binding / positive regulation of pinocytosis / COG complex / endothelin receptor signaling pathway involved in heart process / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / dendritic cell migration / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis ...GBD domain binding / positive regulation of pinocytosis / COG complex / endothelin receptor signaling pathway involved in heart process / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / dendritic cell migration / neuron fate determination / 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 / dendritic spine development / Inactivation of CDC42 and RAC1 / cadherin binding involved in cell-cell adhesion / positive regulation of pseudopodium assembly / cardiac conduction system development / host-mediated perturbation of viral process / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / establishment of Golgi localization / embryonic heart tube development / positive regulation of focal adhesion disassembly / dendritic spine morphogenesis / filopodium assembly / cell junction assembly / establishment of epithelial cell apical/basal polarity / adherens junction organization / GTP-dependent protein binding / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / Activation of RAC1 / RHO GTPases activate KTN1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / Myogenesis / nuclear migration / regulation of mitotic nuclear division / small GTPase-mediated signal transduction / heart contraction / spindle midzone / positive regulation of cytokinesis / establishment of cell polarity / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHOU GTPase cycle / establishment or maintenance of cell polarity / macrophage differentiation / RHO GTPases activate PAKs / CDC42 GTPase cycle / regulation of MAPK cascade / RHOG GTPase cycle / RHOH GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / negative regulation of endothelial cell apoptotic process / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / RAC1 GTPase cycle / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / integrin-mediated signaling pathway / cellular response to starvation / actin filament organization / regulation of actin cytoskeleton organization / small monomeric GTPase / FCGR3A-mediated phagocytosis / filopodium / adherens junction / regulation of cell growth / EGFR downregulation / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / MAPK6/MAPK4 signaling / endocytosis / positive regulation of angiogenesis / apical part of cell / cytoplasmic ribonucleoprotein granule / cell-cell junction / mitotic spindle / G beta:gamma signalling through CDC42 / intracellular protein localization
Similarity search - Function
Cdc42 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Small GTPase Rho / Small GTPase Rho domain profile. ...Cdc42 / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 4 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsHa, B.H. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: CDC42 binds PAK4 via an extended GTPase-effector interface.
Authors: Ha, B.H. / Boggon, T.J.
History
DepositionFeb 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
B: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)71,8162
Polymers71,8162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-1 kcal/mol
Surface area22640 Å2
Unit cell
Length a, b, c (Å)141.652, 141.652, 62.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 51099.684 Da / Num. of mol.: 1 / Fragment: UNP residues 2-426 / Mutation: S474SEP
Source method: isolated from a genetically manipulated source
Details: Ser474 is phosphorylated (SEP) / Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Variant: isoform2 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILP
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 20716.744 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILP / References: UniProt: P60953
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 50mM Na2SO4, 6% PEG6000 / PH range: 8.0-9.0 / Temp details: R/T

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3→43.637 Å / Num. obs: 14433 / % possible obs: 99.9 % / Redundancy: 18 % / CC1/2: 0.588 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.034 / Rsym value: 0.117 / Χ2: 1.187 / Net I/σ(I): 20.3
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 1.6 / CC1/2: 0.588 / Rpim(I) all: 0.707 / Χ2: 1.608 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fie

4fie


Resolution: 3.003→43.637 Å / SU ML: 0.57 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3102 726 5.04 %
Rwork0.2568 --
obs0.2593 14394 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.003→43.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 0 0 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233718
X-RAY DIFFRACTIONf_angle_d1.6175054
X-RAY DIFFRACTIONf_dihedral_angle_d21.1891390
X-RAY DIFFRACTIONf_chiral_restr0.088586
X-RAY DIFFRACTIONf_plane_restr0.009648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0035-3.23530.48461290.36972725X-RAY DIFFRACTION100
3.2353-3.56070.3541670.2812684X-RAY DIFFRACTION100
3.5607-4.07570.3091550.26612718X-RAY DIFFRACTION100
4.0757-5.13360.31731260.23362751X-RAY DIFFRACTION100
5.1336-43.64130.27221490.24462790X-RAY DIFFRACTION100

+
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