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- PDB-5v6t: The Plexin D1 intracellular region in complex with GIPC1 -

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Basic information

Entry
Database: PDB / ID: 5v6t
TitleThe Plexin D1 intracellular region in complex with GIPC1
Components
  • PDZ domain-containing protein GIPC1
  • Plexin-D1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


TGFBR3 regulates FGF2 signaling / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGFBR3 regulates TGF-beta signaling / Other semaphorin interactions / dichotomous subdivision of terminal units involved in salivary gland branching / RND2 GTPase cycle / cardiac septum development / positive regulation of melanin biosynthetic process / synaptic target recognition ...TGFBR3 regulates FGF2 signaling / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGFBR3 regulates TGF-beta signaling / Other semaphorin interactions / dichotomous subdivision of terminal units involved in salivary gland branching / RND2 GTPase cycle / cardiac septum development / positive regulation of melanin biosynthetic process / synaptic target recognition / semaphorin receptor activity / coronary vasculature development / cellular response to interleukin-7 / glutamate secretion / vesicle membrane / aorta development / branching involved in blood vessel morphogenesis / myosin binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / outflow tract morphogenesis / semaphorin-plexin signaling pathway / lamellipodium membrane / regulation of angiogenesis / endothelial cell migration / protein targeting / synapse assembly / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / regulation of cell migration / dendritic shaft / kidney development / regulation of protein stability / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / synaptic vesicle / actin binding / cell body / cell cortex / angiogenesis / chemical synaptic transmission / dendritic spine / negative regulation of neuron apoptotic process / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / signaling receptor binding / glutamatergic synapse / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Plexin-D1, sema domain / : / PDZ domain-containing protein GIPC1/2/3 / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain ...Plexin-D1, sema domain / : / PDZ domain-containing protein GIPC1/2/3 / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding 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 / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / PDZ domain / Pdz3 Domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / Immunoglobulin E-set / Roll / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Plexin-D1 / PDZ domain-containing protein GIPC1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.189 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 14, 2017Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value
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

Downloads & links

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Assembly

Deposited unit
A: Plexin-D1
B: PDZ domain-containing protein GIPC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0849
Polymers99,4122
Non-polymers6727
Water34219
1
A: Plexin-D1
B: PDZ domain-containing protein GIPC1
hetero molecules

A: Plexin-D1
B: PDZ domain-containing protein GIPC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,16818
Polymers198,8234
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
2
A: Plexin-D1
hetero molecules

A: Plexin-D1
hetero molecules

B: PDZ domain-containing protein GIPC1
hetero molecules

B: PDZ domain-containing protein GIPC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,16818
Polymers198,8234
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_774-y+2,-x+2,-z-1/61
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area10110 Å2
ΔGint-187 kcal/mol
Surface area67720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.777, 99.777, 531.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Plexin-D1


Mass: 67870.641 Da / Num. of mol.: 1 / 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: Protein PDZ domain-containing protein GIPC1 / GAIP C-terminus-interacting protein / RGS-GAIP-interacting protein / RGS19-interacting protein 1 / ...GAIP C-terminus-interacting protein / RGS-GAIP-interacting protein / RGS19-interacting protein 1 / SemaF cytoplasmic domain-associated protein 1 / SEMCAP-1 / Synectin


Mass: 31541.020 Da / Num. of mol.: 1 / Fragment: UNP residues 52-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gipc1, Gipc, Rgs19ip1, Semcap1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z0G0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.84 Å3/Da / Density % sol: 68.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 2 M (NH4)2SO4

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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: 3.2→50 Å / Num. obs: 27629 / % possible obs: 100 % / Redundancy: 12 % / Rpim(I) all: 0.041 / Net I/σ(I): 17.5
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.361 / % possible all: 100

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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: 5V6R

5v6r


Resolution: 3.189→49.033 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 1850 6.91 %
Rwork0.1793 --
obs0.1819 26781 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.189→49.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5416 0 35 19 5470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055554
X-RAY DIFFRACTIONf_angle_d0.8337507
X-RAY DIFFRACTIONf_dihedral_angle_d13.2712059
X-RAY DIFFRACTIONf_chiral_restr0.029841
X-RAY DIFFRACTIONf_plane_restr0.003950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1894-3.27560.3242900.29331295X-RAY DIFFRACTION68
3.2756-3.3720.30691370.2541857X-RAY DIFFRACTION96
3.372-3.48080.29531420.22321902X-RAY DIFFRACTION100
3.4808-3.60510.23581430.2031929X-RAY DIFFRACTION100
3.6051-3.74940.23461420.18421923X-RAY DIFFRACTION100
3.7494-3.920.22631430.18481929X-RAY DIFFRACTION100
3.92-4.12660.2141450.17081949X-RAY DIFFRACTION100
4.1266-4.3850.18391450.14741935X-RAY DIFFRACTION100
4.385-4.72330.15141470.13091965X-RAY DIFFRACTION100
4.7233-5.19810.15491480.14361978X-RAY DIFFRACTION100
5.1981-5.94920.24311490.17432010X-RAY DIFFRACTION100
5.9492-7.49110.24071540.1962042X-RAY DIFFRACTION100
7.4911-49.03920.20341650.17552217X-RAY DIFFRACTION100
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)
11.75580.7949-0.42551.088-0.26150.7976-0.0342-0.0832-0.0995-0.11010.01340.10780.16960.03630.0230.30460.0318-0.06740.2828-0.05180.307-2.630534.5803-12.7719
20.65010.7457-0.9285.0502-3.36012.68690.1465-0.10730.2560.17860.26360.4623-0.18830.0042-0.430.5526-0.1461-0.06120.4255-0.20320.5504-34.76819.2598-34.8571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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