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- PDB-3l4c: Structural basis of membrane-targeting by Dock180 -

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Basic information

Entry
Database: PDB / ID: 3l4c
TitleStructural basis of membrane-targeting by Dock180
ComponentsDedicator of cytokinesis protein 1
KeywordsCELL ADHESION / CELL INVASION / APOPTOSIS / Dock180 / Dock1 / phosphoinositide specificity / Guanine Exchange Factor / Rho GTPase / cytoskeleton / cell migration / cell polarity / Cytoplasm / Guanine-nucleotide releasing factor / Membrane / Phagocytosis / Phosphoprotein / SH3 domain / SH3-binding
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / guanyl-nucleotide exchange factor complex / DCC mediated attractive signaling / phagocytosis, engulfment / small GTPase-mediated signal transduction / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of epithelial cell migration / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading ...guanyl-nucleotide exchange factor activity => GO:0005085 / guanyl-nucleotide exchange factor complex / DCC mediated attractive signaling / phagocytosis, engulfment / small GTPase-mediated signal transduction / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of epithelial cell migration / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / GTPase activator activity / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / VEGFA-VEGFR2 Pathway / cell migration / blood coagulation / Factors involved in megakaryocyte development and platelet production / nuclear speck / apoptotic process / signal transduction / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
: / Dedicator of cytokinesis protein 5 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C ...: / Dedicator of cytokinesis protein 5 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / C2 domain / C2 domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Dedicator of cytokinesis protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.37 Å
AuthorsPremkumar, L. / Bobkov, A.A. / Patel, M. / Jaroszewski, L. / Bankston, L.A. / Stec, B. / Vuori, K. / Cote, J.-F. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of membrane targeting by the Dock180 family of Rho family guanine exchange factors (Rho-GEFs).
Authors: Premkumar, L. / Bobkov, A.A. / Patel, M. / Jaroszewski, L. / Bankston, L.A. / Stec, B. / Vuori, K. / Cote, J.F. / Liddington, R.C.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 1
B: Dedicator of cytokinesis protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5004
Polymers49,3442
Non-polymers1562
Water1,26170
1
A: Dedicator of cytokinesis protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7502
Polymers24,6721
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dedicator of cytokinesis protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7502
Polymers24,6721
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.995, 63.529, 63.421
Angle α, β, γ (deg.)90.00, 109.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dedicator of cytokinesis protein 1 / 180 kDa protein downstream of CRK / DOCK180


Mass: 24671.770 Da / Num. of mol.: 2 / Fragment: Dock Homology Region-1, DHR-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14185
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.08 %
Crystal growTemperature: 293 K / Method: microbatch method under oil / pH: 8.8
Details: 30% (w/v) polyethylene glycol 10K, 0.2 M Na-acetate, 0.1 M Tris-HCl pH 8.8, microbatch method under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9116 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. all: 14465 / Num. obs: 14369 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 42.9 Å2 / Rsym value: 0.076 / Net I/σ(I): 22.6
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 1405 / Rsym value: 0.216 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC& CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 2bwq

2bwq


Resolution: 2.37→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 679 4.7 %random
Rwork0.216 ---
obs-13960 96.6 %-
Solvent computationBsol: 38.723 Å2
Displacement parametersBiso max: 100.1 Å2 / Biso mean: 42.902 Å2 / Biso min: 14.94 Å2
Baniso -1Baniso -2Baniso -3
1--19.494 Å20 Å2-7.069 Å2
2--15.897 Å20 Å2
3---3.597 Å2
Refinement stepCycle: LAST / Resolution: 2.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 2 70 2924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9291.5
X-RAY DIFFRACTIONc_scbond_it2.1482
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scangle_it3.2632.5
LS refinement shellResolution: 2.37→2.45 Å
RfactorNum. reflection% reflection
Rfree0.3491 52 -
Rwork0.2571 --
obs-1289 89 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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