[English] 日本語
Yorodumi
- PDB-1agr: COMPLEX OF ALF4-ACTIVATED GI-ALPHA-1 WITH RGS4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1agr
TitleCOMPLEX OF ALF4-ACTIVATED GI-ALPHA-1 WITH RGS4
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
  • RGS4
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/REGULATOR) / GI-ALPHA-1 / HYDROLASE / SIGNAL TRANSDUCTION / RGS4 / COMPLEX (SIGNAL TRANSDUCTION-REGULATOR) / GTP-BINDING / GTPASE ACTIVATING PROTEIN / COMPLEX (SIGNAL TRANSDUCTION-REGULATOR) complex
Function / homology
Function and homology information


negative regulation of glycine import across plasma membrane / negative regulation of dopamine receptor signaling pathway / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / negative regulation of potassium ion transmembrane transport / dorsal root ganglion development / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of G protein-coupled receptor signaling pathway / regulation of actin filament organization / regulation of potassium ion transmembrane transport ...negative regulation of glycine import across plasma membrane / negative regulation of dopamine receptor signaling pathway / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / negative regulation of potassium ion transmembrane transport / dorsal root ganglion development / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of G protein-coupled receptor signaling pathway / regulation of actin filament organization / regulation of potassium ion transmembrane transport / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of heart rate / positive regulation of excitatory postsynaptic potential / regulation of calcium ion transport / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / response to amphetamine / GTPase activator activity / response to cocaine / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / response to ethanol / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / protein kinase binding / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 4, RGS domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 ...Regulator of G-protein signalling 4, RGS domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / G-protein alpha subunit, group I / 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 / 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 / CITRIC ACID / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Regulator of G-protein signaling 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, DENSITY MODIFICATION / Resolution: 2.8 Å
AuthorsTesmer, J.J.G. / Sprang, S.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structure of RGS4 bound to AlF4--activated G(i alpha1): stabilization of the transition state for GTP hydrolysis.
Authors: Tesmer, J.J. / Berman, D.M. / Gilman, A.G. / Sprang, S.R.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 G(I)
D: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
E: RGS4
H: RGS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,63412
Polymers127,1094
Non-polymers1,5258
Water1,04558
1
A: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
E: RGS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3176
Polymers63,5552
Non-polymers7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
H: RGS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3176
Polymers63,5552
Non-polymers7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.000, 97.200, 110.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.964372, 0.208506, -0.162827), (0.207851, -0.97793, -0.021238), (-0.163661, -0.013363, -0.986426)
Vector: 7.7071, -25.6439, 61.2808)

-
Components

-
Protein , 2 types, 4 molecules ADEH

#1: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN G(I) / GI-ALPHA-1


Mass: 40267.836 Da / Num. of mol.: 2 / Fragment: ALPHA-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Organ: BRAIN / Plasmid: PQE6/GIA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10824
#2: Protein RGS4 / / REGULATOR OF G-PROTEIN SIGNALLING 4


Mass: 23286.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Organ: BRAIN / Plasmid: PQE60-H6RGS4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P49799

-
Non-polymers , 5 types, 66 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: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.3
Details: THE COMPLEX WAS CRYSTALLIZED IN HANGING DROPS USING PEG 10000 AS THE PRECIPITANT AND SODIUM CITRATE PH 5.3 AS THE BUFFER., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium citrate1reservoir
214.4 %(v/v)PEG100001reservoir
35 mMDTT1reservoir
40.140 mM1reservoirAlCl3
570 mM1reservoirNaF

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 43341 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rsym value: 0.12 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.55 / % possible all: 99.4
Reflection
*PLUS
Rmerge(I) obs: 0.12

-
Processing

Software
NameVersionClassification
AVGSYSmodel building
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
AVGSYSphasing
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, DENSITY MODIFICATION
Starting model: PDB ENTRY 1GFI

1gfi


Resolution: 2.8→5 Å / Rfactor Rfree error: 0.0048 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: ALL BUT LAST ROUND / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3644 10 %RANDOM
Rwork0.216 ---
obs0.216 35475 99 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7580 56 28 56 7720
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.60.5
X-RAY DIFFRACTIONx_mcangle_it5.81
X-RAY DIFFRACTIONx_scbond_it7.41
X-RAY DIFFRACTIONx_scangle_it10.91.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.05 Å / Weight position: 200
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.337 1331

+
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