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- PDB-5v6r: Structure of Plexin D1 intracellular domain -

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Basic information

Entry
Database: PDB / ID: 5v6r
TitleStructure of Plexin D1 intracellular domain
ComponentsPlexin-D1
KeywordsPROTEIN BINDING / Rap GAP
Function / homology
Function and homology information


Other semaphorin interactions / synaptic target recognition / dichotomous subdivision of terminal units involved in salivary gland branching / RND2 GTPase cycle / semaphorin-plexin signaling pathway involved in axon guidance / cardiac septum development / semaphorin receptor complex / semaphorin receptor activity / coronary vasculature development / negative regulation of cell adhesion ...Other semaphorin interactions / synaptic target recognition / dichotomous subdivision of terminal units involved in salivary gland branching / RND2 GTPase cycle / semaphorin-plexin signaling pathway involved in axon guidance / cardiac septum development / semaphorin receptor complex / semaphorin receptor activity / coronary vasculature development / negative regulation of cell adhesion / aorta development / branching involved in blood vessel morphogenesis / positive regulation of axonogenesis / regulation of GTPase activity / outflow tract morphogenesis / lamellipodium membrane / semaphorin-plexin signaling pathway / endothelial cell migration / regulation of angiogenesis / regulation of cell migration / synapse assembly / kidney development / lamellipodium / cell body / positive regulation of protein binding / regulation of cell shape / angiogenesis / negative regulation of neuron apoptotic process / axon / protein domain specific binding / glutamatergic synapse / plasma membrane
Similarity search - Function
Plexin-D1, sema domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family ...Plexin-D1, sema domain / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShang, G. / Zhang, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088197 United States
Welch FoundationI-1702 United States
CitationJournal: Elife / Year: 2017
Title: Structure analyses reveal a regulated oligomerization mechanism of the PlexinD1/GIPC/myosin VI complex.
Authors: Shang, G. / Brautigam, C.A. / Chen, R. / Lu, D. / Torres-Vazquez, J. / Zhang, X.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plexin-D1
B: Plexin-D1


Theoretical massNumber of molelcules
Total (without water)135,7412
Polymers135,7412
Non-polymers00
Water1,76598
1
A: Plexin-D1


Theoretical massNumber of molelcules
Total (without water)67,8711
Polymers67,8711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plexin-D1


Theoretical massNumber of molelcules
Total (without water)67,8711
Polymers67,8711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.852, 164.544, 84.268
Angle α, β, γ (deg.)90.00, 99.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plexin-D1


Mass: 67870.641 Da / Num. of mol.: 2 / Fragment: UNP residues 1339-1925
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxnd1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UH93
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1 M imidazole (pH 7.8) and 15% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 51129 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rpim(I) all: 0.042 / Net I/σ(I): 29.9
Reflection shellRpim(I) all: 0.231

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IG3

3ig3


Resolution: 2.7→37.095 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 28.64
RfactorNum. reflection% reflection
Rfree0.2564 1759 3.73 %
Rwork0.215 --
obs0.2165 47172 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 0 98 8190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038266
X-RAY DIFFRACTIONf_angle_d0.61611191
X-RAY DIFFRACTIONf_dihedral_angle_d11.8473043
X-RAY DIFFRACTIONf_chiral_restr0.0221271
X-RAY DIFFRACTIONf_plane_restr0.0031415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.36911240.31823209X-RAY DIFFRACTION85
2.773-2.85460.31491360.28753463X-RAY DIFFRACTION92
2.8546-2.94670.30731370.27523593X-RAY DIFFRACTION94
2.9467-3.05190.28671390.27093604X-RAY DIFFRACTION95
3.0519-3.17410.31091400.26593597X-RAY DIFFRACTION94
3.1741-3.31840.28911380.25343561X-RAY DIFFRACTION94
3.3184-3.49330.3011380.23673556X-RAY DIFFRACTION93
3.4933-3.71190.2681370.22723547X-RAY DIFFRACTION93
3.7119-3.99820.24521360.223504X-RAY DIFFRACTION92
3.9982-4.40.21511350.19493488X-RAY DIFFRACTION91
4.4-5.03530.23831340.18453450X-RAY DIFFRACTION90
5.0353-6.33890.25671350.20793478X-RAY DIFFRACTION91
6.3389-37.09860.22411300.1733363X-RAY DIFFRACTION87
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)
16.24480.59332.71034.60422.92174.36370.18070.3938-0.2079-0.67490.1327-0.1698-0.4030.5071-0.33010.7725-0.11280.02020.70970.01190.3432-49.5378-31.5711-54.9669
25.8529-0.64851.2191.2303-0.34461.14410.13920.0294-0.59140.0185-0.02580.0378-0.0233-0.0516-0.08010.3653-0.0255-0.01820.41930.01390.3707-26.6428-39.5551-22.4054
38.5024-2.85650.53223.56270.34911.95750.25160.1366-1.52810.2725-0.422-0.20540.3360.41510.20510.83110.03580.1660.81380.29731.326823.4544-93.578825.6926
44.0803-1.10440.51391.6161-0.98222.06310.0010.0522-0.72140.07230.05370.04460.0208-0.1603-0.05010.4053-0.0211-0.05170.55230.11040.63881.3506-63.90689.5277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1552:1690
2X-RAY DIFFRACTION2chain A and not resi 1552:1690
3X-RAY DIFFRACTION3chain B and resi 1552:1690
4X-RAY DIFFRACTION4chain B and not resi 1552:1690

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