[English] 日本語
Yorodumi
- PDB-2odb: The crystal structure of human cdc42 in complex with the CRIB dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2odb
TitleThe crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Components
  • Human Cell Division Cycle 42 (CDC42)
  • Serine/threonine-protein kinase PAK 6
KeywordsPROTEIN BINDING / small GTPase / CRIB / kinase / protein-protein complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination ...GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / neuron projection arborization / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / RHOD GTPase cycle / embryonic heart tube development / Activation of RAC1 / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / neuron projection extension / regulation of mitotic nuclear division / nuclear migration / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / positive regulation of cytokinesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / macrophage differentiation / 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 / cytoskeleton organization / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament organization / cellular response to starvation / small monomeric GTPase / integrin-mediated signaling pathway / learning / filopodium / regulation of actin cytoskeleton organization / locomotory behavior / FCGR3A-mediated phagocytosis / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / fibrillar center / memory / endocytosis / G beta:gamma signalling through CDC42 / mitotic spindle / ubiquitin protein ligase activity / cell junction / apical part of cell
Similarity search - Function
Serine/threonine-protein kinase PAK 6 / 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 ...Serine/threonine-protein kinase PAK 6 / 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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Cell division control protein 42 homolog / Serine/threonine-protein kinase PAK 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUgochukwu, E. / Yang, X. / Elkins, J. / Soundararajan, M. / Pike, A.C.W. / Eswaran, J. / Burgess, N. / Debreczeni, J.E. / Sundstrom, M. / Arrowsmith, C. ...Ugochukwu, E. / Yang, X. / Elkins, J. / Soundararajan, M. / Pike, A.C.W. / Eswaran, J. / Burgess, N. / Debreczeni, J.E. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Gileadi, O. / von Delft, F. / Knapp, S. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Authors: Yang, X. / Ugochukwu, E. / Elkins, J. / Soundararajan, M. / Eswaran, J. / Pike, A.C.W. / Burgess, N. / Debreczeni, J.E. / Gileadi, O. / Knapp, S. / Doyle, D.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequence of human CDC42 isoform 1 is not available in uniprot database at the time of processing.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3068
Polymers25,4372
Non-polymers8696
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-69 kcal/mol
Surface area10740 Å2
MethodPISA
2
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,61316
Polymers50,8744
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-2/31
Buried area8820 Å2
ΔGint-183 kcal/mol
Surface area19930 Å2
MethodPISA
3
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,61316
Polymers50,8744
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area9490 Å2
ΔGint-168 kcal/mol
Surface area19270 Å2
MethodPISA
4
A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules

A: Human Cell Division Cycle 42 (CDC42)
B: Serine/threonine-protein kinase PAK 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,61316
Polymers50,8744
Non-polymers1,73812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area9840 Å2
ΔGint-152 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.366, 162.366, 45.968
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
11B-201-

SO4

DetailsOne monomer of each protein in the asymmetric unit

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Human Cell Division Cycle 42 (CDC42)


Mass: 21370.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P60953
#2: Protein/peptide Serine/threonine-protein kinase PAK 6 / p21-activated kinase 6 / PAK-6


Mass: 4066.510 Da / Num. of mol.: 1 / Fragment: PAK6 CRIB domain / Source method: obtained synthetically / References: UniProt: Q9NQU5

-
Non-polymers , 5 types, 50 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M acetate, 2M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97956
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 2.4→40.59 Å / Num. obs: 14484 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 / Rsym value: 0.071
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.502 / Rsym value: 0.502 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GRN

1grn


Resolution: 2.4→40.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.923 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23184 732 5.1 %RANDOM
Rwork0.2034 ---
all0.20484 13737 --
obs0.20484 13737 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.158 Å2
Baniso -1Baniso -2Baniso -3
1--4.96 Å2-2.48 Å20 Å2
2---4.96 Å20 Å2
3---7.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 49 44 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221711
X-RAY DIFFRACTIONr_bond_other_d0.0010.021099
X-RAY DIFFRACTIONr_angle_refined_deg1.46622348
X-RAY DIFFRACTIONr_angle_other_deg0.9232713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34125.22467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.291154
X-RAY DIFFRACTIONr_chiral_restr0.0780.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
X-RAY DIFFRACTIONr_nbd_refined0.2010.2283
X-RAY DIFFRACTIONr_nbd_other0.1820.21064
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2817
X-RAY DIFFRACTIONr_nbtor_other0.0860.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4961.51109
X-RAY DIFFRACTIONr_mcbond_other0.0831.5417
X-RAY DIFFRACTIONr_mcangle_it0.79221736
X-RAY DIFFRACTIONr_scbond_it1.2843716
X-RAY DIFFRACTIONr_scangle_it1.9654.5612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 48 -
Rwork0.297 984 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.981.05480.26363.4947-0.04772.10670.1415-0.27291.00780.5026-0.14870.4553-0.19940.00920.0072-0.0814-0.07540.1025-0.2307-0.08330.138913.9842-63.2942-3.8227
27.8741.7819-0.83822.1767-0.68440.22720.06960.4965-0.5417-0.0323-0.0084-0.49110.12990.2255-0.0612-0.0889-0.035-0.0129-0.0786-0.0153-0.208814.0796-77.4512-15.826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1783 - 179
2X-RAY DIFFRACTION2BB11 - 451 - 35

+
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