[English] 日本語
Yorodumi
- PDB-5v6b: Crystal structure of GIPC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v6b
TitleCrystal structure of GIPC1
ComponentsPDZ domain-containing protein GIPC1
KeywordsPROTEIN BINDING / binding partener
Function / homology
Function and homology information


FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / positive regulation of melanin biosynthetic process / vesicle membrane / glutamate secretion / cellular response to interleukin-7 / myosin binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / brush border ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / positive regulation of melanin biosynthetic process / vesicle membrane / glutamate secretion / cellular response to interleukin-7 / myosin binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / brush border / endocytic vesicle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein targeting / endothelial cell migration / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / dendritic shaft / PDZ domain binding / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / regulation of protein stability / synaptic vesicle / presynapse / actin binding / cell cortex / chemical synaptic transmission / cytoplasmic vesicle / postsynapse / dendritic spine / G protein-coupled receptor signaling pathway / signaling receptor binding / glutamatergic synapse / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
PDZ domain-containing protein GIPC1/2/3 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
PDZ domain-containing protein GIPC1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 16, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PDZ domain-containing protein GIPC1
B: PDZ domain-containing protein GIPC1


Theoretical massNumber of molelcules
Total (without water)61,7282
Polymers61,7282
Non-polymers00
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-39 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.396, 77.625, 80.346
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: 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: 30864.213 Da / Num. of mol.: 2 / Fragment: UNP residues 52-327
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Li2SO4, 0.1 M HEPES pH 7.5 and 25% (w/v) PEG3350

-
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: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44113 / % possible obs: 100 % / Redundancy: 4.1 % / Rpim(I) all: 0.034 / Net I/σ(I): 21.3
Reflection shellRpim(I) all: 0.319

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V6T

5v6t


Resolution: 1.9→40.173 Å / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 22.2
RfactorNum. reflection% reflection
Rfree0.1751 2019 4.97 %
Rwork0.1364 --
obs0.1403 40623 92.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 0 645 4728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064197
X-RAY DIFFRACTIONf_angle_d0.9275656
X-RAY DIFFRACTIONf_dihedral_angle_d13.3821594
X-RAY DIFFRACTIONf_chiral_restr0.034626
X-RAY DIFFRACTIONf_plane_restr0.004744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.94650.2479630.19361402X-RAY DIFFRACTION45
1.9465-1.99910.2404990.18731998X-RAY DIFFRACTION64
1.9991-2.0580.20631210.17332441X-RAY DIFFRACTION78
2.058-2.12440.21321390.17312816X-RAY DIFFRACTION91
2.1244-2.20030.20121720.16442959X-RAY DIFFRACTION94
2.2003-2.28840.20581440.15732998X-RAY DIFFRACTION95
2.2884-2.39250.19451560.15512953X-RAY DIFFRACTION95
2.3925-2.51860.17811510.15183013X-RAY DIFFRACTION95
2.5186-2.67640.16641530.15033006X-RAY DIFFRACTION95
2.6764-2.8830.17181540.14532983X-RAY DIFFRACTION95
2.883-3.1730.17721660.13642978X-RAY DIFFRACTION95
3.173-3.63190.14311540.11852994X-RAY DIFFRACTION95
3.6319-4.57470.14911590.10613021X-RAY DIFFRACTION95
4.5747-39.54760.17351460.11993080X-RAY DIFFRACTION95
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)
10.14760.06330.17020.69480.75791.35060.0489-0.08030.02950.0528-0.12180.1299-0.0417-0.32920.04290.06530.00080.00890.142-0.01590.1387-27.587813.0257-13.3092
22.75480.0625-1.02771.20330.09382.2714-0.06780.2213-0.149-0.1949-0.0133-0.14190.02630.12850.04420.11780.0447-0.00290.12690.00820.1371-12.9118-3.5265-51.5523
33.3487-0.32380.22881.48571.15582.9070.027-0.0003-0.0568-0.06940.0223-0.17480.01570.1507-0.02810.08370.0318-0.01050.08550.01680.1122-12.8204-3.765-49.0504
40.52150.02460.00280.37720.28842.35760.03960.1176-0.0447-0.16320.047-0.1252-0.20230.2327-0.03770.07110.0253-0.00080.1225-0.00160.1892-14.70040.0055-50.4754
51.96150.21731.57050.5420.75393.43370.03470.0354-0.034-0.0739-0.0248-0.3526-0.16390.23480.00260.0739-0.025-0.00720.11280.01780.2185-11.405922.6096-10.9571
63.43860.4662-2.8932.2439-1.11154.34390.2939-0.42190.20130.2463-0.2128-0.2093-0.44940.2929-0.03020.1979-0.11030.04220.2615-0.0690.3272-4.64733.5203-10.587
70.34020.1112-0.17260.81281.05492.60420.0572-0.0135-0.00610.0051-0.10630.06610.1447-0.26540.03150.0781-0.0041-0.0150.0818-0.00180.1126-27.22455.1521-27.6076
81.4209-0.15530.33831.04540.08491.8487-0.0552-0.36180.19040.48680.0719-0.18860.13690.00830.00480.24910.0026-0.0540.1862-0.02070.1413-14.916317.754810.97
92.2167-1.2506-1.98981.13731.05952.619-0.0992-0.14970.00170.23820.054-0.15490.36390.31940.03820.1470.0352-0.02890.13070.03850.1912-12.401-6.5833-27.6395
105.84840.68050.48084.2518-0.63686.6254-0.0111-0.3419-0.6418-0.0888-0.19430.12810.56510.14250.14270.30340.0748-0.09590.1625-0.0090.365-6.691-18.4202-27.9944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 240 )
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 291 )
6X-RAY DIFFRACTION6chain 'A' and (resid 292 through 327 )
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 130 )
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 240 )
9X-RAY DIFFRACTION9chain 'B' and (resid 241 through 291 )
10X-RAY DIFFRACTION10chain 'B' and (resid 292 through 327 )

+
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