[English] 日本語
Yorodumi
- PDB-1nf3: Structure of Cdc42 in a complex with the GTPase-binding domain of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nf3
TitleStructure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6
Components
  • G25K GTP-binding protein, placental isoform
  • PAR-6B
KeywordsSIGNALING PROTEIN / semi-CRIB motif / Switch I and II / PDZ domain / GTPase binding domain
Function / homology
Function and homology information


Tight junction interactions / RHOV GTPase cycle / 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 ...Tight junction interactions / RHOV GTPase cycle / 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 / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / embryonic heart tube development / 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 / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / regulation of mitotic nuclear division / Myogenesis / heart contraction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / establishment of cell polarity / Golgi organization / RHOQ GTPase cycle / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / bicellular tight junction / 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 / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament organization / small monomeric GTPase / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / 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 / endocytosis / G beta:gamma signalling through CDC42 / apical part of cell / mitotic spindle / ubiquitin protein ligase activity / cell-cell junction / intracellular protein localization / G protein activity / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization / positive regulation of cell growth / protein-containing complex assembly / midbody / cell cortex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
Partitioning defective protein 6, PB1 domain / : / Cdc42 / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Small GTPase Rho / Small GTPase Rho domain profile. ...Partitioning defective protein 6, PB1 domain / : / Cdc42 / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Small GTPase Rho / Small GTPase Rho domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / PDZ superfamily / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / Partitioning defective 6 homolog beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGarrard, S.M. / Capaldo, C.T. / Gao, L. / Rosen, M.K. / Macara, I.G. / Tomchick, D.R.
Citation
Journal: Embo J. / Year: 2003
Title: Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6
Authors: Garrard, S.M. / Capaldo, C.T. / Gao, L. / Rosen, M.K. / Macara, I.G. / Tomchick, D.R.
#1: Journal: Curr.Biol. / Year: 2002
Title: Assembly of epithelial tight junctions is negatively regulated by Par6
Authors: Gao, L. / Joberty, G. / Macara, I.G.
#2: Journal: Nat.Cell Biol. / Year: 2000
Title: The cell-polarity protein Par6 links Par3 and atypical protein kinase C to Cdc42
Authors: Joberty, G. / Petersen, C. / Gao, L. / Macara, I.G.
#3: Journal: Nat.Cell Biol. / Year: 2000
Title: A mammalian Par-3-Par-6 complex implicated in Cdc42/Rac1 and aPKC signalling and cell polarity
Authors: Lin, D. / Edwards, A.S. / Fawcett, J.P. / Mbamalu, G. / Scott, J.D. / Pawson, T.
#4: Journal: Curr.Biol. / Year: 2000
Title: A human homolog of the C. elegans polarity determinant Par-6 links Rac and Cdc42 to PKCzeta signaling and cell transformation
Authors: Qiu, R.G. / Abo, A. / Steven Martin, G.
#5: Journal: DEVELOPMENT / Year: 1996
Title: Par-6, a gene involved in the establishment of asymmetry in early C. elegans embryos, mediates the asymmetric localization of Par-3
Authors: Watts, J.L. / Etemad-Moghadam, B. / Guo, S. / Boyd, L. / Draper, B.W. / Mello, C.C. / Priess, J.R. / Kemphues, K.J.
History
DepositionDec 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G25K GTP-binding protein, placental isoform
B: G25K GTP-binding protein, placental isoform
C: PAR-6B
D: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5788
Polymers71,4854
Non-polymers1,0934
Water7,620423
1
A: G25K GTP-binding protein, placental isoform
C: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2894
Polymers35,7422
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-29 kcal/mol
Surface area16400 Å2
MethodPISA
2
B: G25K GTP-binding protein, placental isoform
D: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2894
Polymers35,7422
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-29 kcal/mol
Surface area16200 Å2
MethodPISA
3
A: G25K GTP-binding protein, placental isoform
C: PAR-6B
hetero molecules

B: G25K GTP-binding protein, placental isoform
D: PAR-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5788
Polymers71,4854
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area7170 Å2
ΔGint-61 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.744, 53.787, 79.521
Angle α, β, γ (deg.)81.55, 76.59, 90.04
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein G25K GTP-binding protein, placental isoform / GP / CDC42 homolog


Mass: 21566.949 Da / Num. of mol.: 2 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60953
#2: Protein PAR-6B


Mass: 14175.417 Da / Num. of mol.: 2 / Fragment: GTPase-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Par6B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JK83
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 24% PEG 4000, 100mM sodium citrate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris1droppH8.5
31 mM1dropMgCl2
40.100 mMGMPPNP1drop
510 mMbeta-mercaptoethanol1drop
624 %PEG40001reservoir
7100 mMsodium citrate1reservoirpH6.4
80.2 Mammonium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 8, 2002 / Details: double crystal monochromator
RadiationMonochromator: graphite double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→40.5 Å / Num. all: 38985 / Num. obs: 38985 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 80223
Reflection shell
*PLUS
% possible obs: 87.1 % / Rmerge(I) obs: 0.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NGR

2ngr


Resolution: 2.1→29.17 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1733 5 %RANDOM
Rwork0.219 ---
all0.219 34917 --
obs0.219 34917 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2756 Å2 / ksol: 0.35546 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.63 Å2-3.7 Å2
2---5.93 Å2-0.45 Å2
3---4.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å-
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å-
Refinement stepCycle: LAST / Resolution: 2.1→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 66 423 5395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 165 4.9 %
Rwork0.265 3173 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMLIGANDS.TOP
X-RAY DIFFRACTION4LIGANDS.PARAMION.TOP
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

+
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