[English] 日本語
Yorodumi
- PDB-5v6t: The Plexin D1 intracellular region in complex with GIPC1 -

+
Open data


ID or keywords:

Loading...

-
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 / Other semaphorin interactions / TGFBR3 regulates TGF-beta signaling / 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 / Other semaphorin interactions / TGFBR3 regulates TGF-beta signaling / 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 cytokinesis / positive regulation of transforming growth factor beta receptor signaling pathway / 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 synaptic plasticity / regulation of protein stability / Schaffer collateral - CA1 synapse / 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 / signaling receptor binding / protein domain specific binding / axon / glutamatergic synapse / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Plexin-D1, sema domain / : / : / GIPC1-3 GH2 domain / GIPC1-3 GH1 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 ...Plexin-D1, sema domain / : / : / GIPC1-3 GH2 domain / GIPC1-3 GH1 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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