[English] 日本語
Yorodumi
- PDB-1shz: Crystal Structure of the p115RhoGEF rgRGS Domain in A Complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1shz
TitleCrystal Structure of the p115RhoGEF rgRGS Domain in A Complex with Galpha(13):Galpha(i1) Chimera
Components
  • Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
  • Rho guanine nucleotide exchange factor 1
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / PROTEIN COMPLEX
Function / homology
Function and homology information


D5 dopamine receptor binding / CDC42 GTPase cycle / regulation of fibroblast migration / Thromboxane signalling through TP receptor / NRAGE signals death through JNK / RAC1 GTPase cycle / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / G alpha (12/13) signalling events ...D5 dopamine receptor binding / CDC42 GTPase cycle / regulation of fibroblast migration / Thromboxane signalling through TP receptor / NRAGE signals death through JNK / RAC1 GTPase cycle / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / G alpha (12/13) signalling events / negative regulation of vascular associated smooth muscle cell migration / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / branching involved in blood vessel morphogenesis / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / negative regulation of vascular associated smooth muscle cell proliferation / Rho protein signal transduction / positive regulation of protein localization to cell cortex / RHOA GTPase cycle / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / brush border membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / regulation of blood pressure / GDP binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / melanosome / cell cortex / midbody / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / angiogenesis / in utero embryonic development / cell differentiation / intracellular signal transduction / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p115RhoGEF, RGS domain / G-protein alpha subunit, group 12/13 / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / ARHGEF1-like, PH domain / PH domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like ...p115RhoGEF, RGS domain / G-protein alpha subunit, group 12/13 / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / ARHGEF1-like, PH domain / PH domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / RGS, subdomain 2 / RGS domain superfamily / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / G-protein alpha subunit, group I / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Guanine nucleotide-binding protein subunit alpha-13 / Rho guanine nucleotide exchange factor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChen, Z. / Singer, W.D. / Sternweis, P.C. / Sprang, S.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structure of the p115RhoGEF rgRGS domain-Galpha13/i1 chimera complex suggests convergent evolution of a GTPase activator.
Authors: Chen, Z. / Singer, W.D. / Sternweis, P.C. / Sprang, S.R.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / 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_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
C: Rho guanine nucleotide exchange factor 1
D: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
F: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,11510
Polymers131,9744
Non-polymers1,1416
Water1,51384
1
A: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
C: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5585
Polymers65,9872
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-32 kcal/mol
Surface area25860 Å2
MethodPISA
2
D: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
F: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5585
Polymers65,9872
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-31 kcal/mol
Surface area25210 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-74 kcal/mol
Surface area47340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.747, 105.274, 71.748
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe deposited PDB file contains a pair of homodimers of the complexes. However, the biological unit is identical to the monomeric form of the complex

-
Components

-
Protein , 2 types, 4 molecules ADCF

#1: Protein Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera


Mass: 39640.191 Da / Num. of mol.: 2
Fragment: residues 21-47, 185-210, 213-230, 240-353 of Galpha(i1) and residues 64-207, 234-235, 254-262 of Galpha(13)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Genus: Mus, Rattus / Species: , / Strain: , / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P10824, UniProt: P27601
#2: Protein Rho guanine nucleotide exchange factor 1 / p115-RhoGEF / p115RhoGEF / 115 kDa guanine nucleotide exchange factor / Sub1.5


Mass: 26346.879 Da / Num. of mol.: 2
Fragment: N-terminal RhoGEF RGS (rgRGS) domain of p115RhoGEF (residues 7-239)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTrcC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92888

-
Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.14 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium Sulfate, Tris, Ethylene glycol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2003 / Details: MIRRORS
RadiationMonochromator: Double crystal, Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 33997 / Num. obs: 31348 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.188 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2286 / Rsym value: 0.585 / % possible all: 67.4

-
Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGR, CHAIN A

1agr


Resolution: 2.85→46.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1865632.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2203 7 %RANDOM
Rwork0.229 ---
obs0.229 31348 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.4754 Å2 / ksol: 0.30693 e/Å3
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.95 Å20 Å29.92 Å2
2---2.89 Å20 Å2
3----12.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.85→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8450 0 68 84 8602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it3.721.5
X-RAY DIFFRACTIONc_mcangle_it5.742
X-RAY DIFFRACTIONc_scbond_it5.972
X-RAY DIFFRACTIONc_scangle_it8.412.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 251 6.5 %
Rwork0.333 3632 -
obs-3632 67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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