[English] 日本語
Yorodumi
- PDB-6tyl: Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tyl
TitleCrystal structure of mammalian Ric-8A:Galpha(i):nanobody complex
Components
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
  • Nanobody A
  • Nanobody B
  • Nanobody C
  • Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
KeywordsSIGNALING PROTEIN / Ric-8A / G protein / GEF
Function / homology
Function and homology information


cell-cell adhesion involved in gastrulation / cell migration involved in gastrulation / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / basement membrane organization / negative regulation of synaptic transmission / vasculature development / GTPase activating protein binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 ...cell-cell adhesion involved in gastrulation / cell migration involved in gastrulation / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / basement membrane organization / negative regulation of synaptic transmission / vasculature development / GTPase activating protein binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / neurotransmitter receptor localization to postsynaptic specialization membrane / response to light stimulus / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / gastrulation / cellular response to forskolin / protein folding chaperone / regulation of mitotic spindle organization / GTPase activator activity / guanyl-nucleotide exchange factor activity / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / visual learning / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / GDP binding / heterotrimeric G-protein complex / G protein activity / midbody / cell cortex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / in utero embryonic development / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / glutamatergic synapse / magnesium ion binding / protein-containing complex / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Synembryn / Guanine nucleotide exchange factor, Ric8 / Guanine nucleotide exchange factor synembryn / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. ...Synembryn / Guanine nucleotide exchange factor, Ric8 / Guanine nucleotide exchange factor synembryn / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chaperone Ric-8A / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMou, T.C. / McClelland, L. / Yates-Hansen, C. / Sprang, S.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105993 United States
National Science Foundation (United States)1738547 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Gαi1.
Authors: Levi J McClelland / Kaiming Zhang / Tung-Chung Mou / Jake Johnston / Cindee Yates-Hansen / Shanshan Li / Celestine J Thomas / Tzanko I Doukov / Sarah Triest / Alexandre Wohlkonig / Gregory G ...Authors: Levi J McClelland / Kaiming Zhang / Tung-Chung Mou / Jake Johnston / Cindee Yates-Hansen / Shanshan Li / Celestine J Thomas / Tzanko I Doukov / Sarah Triest / Alexandre Wohlkonig / Gregory G Tall / Jan Steyaert / Wah Chiu / Stephen R Sprang /
Abstract: Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Gα) and serves as an essential Gα chaperone. Mechanisms by which Ric-8A ...Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Gα) and serves as an essential Gα chaperone. Mechanisms by which Ric-8A catalyzes these activities, which are stimulated by Casein Kinase II phosphorylation, are unknown. We report the structure of the nanobody-stabilized complex of nucleotide-free Gα bound to phosphorylated Ric-8A at near atomic resolution by cryo-electron microscopy and X-ray crystallography. The mechanism of Ric-8A GEF activity differs considerably from that employed by G protein-coupled receptors at the plasma membrane. Ric-8A engages a specific conformation of Gα at multiple interfaces to form a complex that is stabilized by phosphorylation within a Ric-8A segment that connects two Gα binding sites. The C-terminus of Gα is ejected from its beta sheet core, thereby dismantling the GDP binding site. Ric-8A binds to the exposed Gα beta sheet and switch II to stabilize the nucleotide-free state of Gα.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
C: Nanobody A
H: Nanobody A
E: Nanobody B
J: Nanobody B
D: Nanobody C
I: Nanobody C
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
G: Guanine nucleotide-binding protein G(i) subunit alpha-1
F: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)


Theoretical massNumber of molelcules
Total (without water)277,97610
Polymers277,97610
Non-polymers00
Water00
1
A: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
C: Nanobody A
E: Nanobody B
D: Nanobody C
B: Guanine nucleotide-binding protein G(i) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)138,9885
Polymers138,9885
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Nanobody A
J: Nanobody B
I: Nanobody C
G: Guanine nucleotide-binding protein G(i) subunit alpha-1
F: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)


Theoretical massNumber of molelcules
Total (without water)138,9885
Polymers138,9885
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.048, 144.726, 114.420
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans) / Ric8a protein / Synembryn-A


Mass: 55836.926 Da / Num. of mol.: 2 / Mutation: Y232F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ric8a, rCG_48458 / Production host: Escherichia coli (E. coli) / References: UniProt: B1H241
#2: Antibody Nanobody A


Mass: 13609.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody Nanobody B


Mass: 14247.603 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Antibody Nanobody C


Mass: 14894.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40399.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai1, Gnai-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10824
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 1.2-1.4M Sodium Malonate / PH range: 6-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→39.58 Å / Num. obs: 20707 / % possible obs: 90.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 91.88 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.11 / Rrim(I) all: 0.21 / Net I/σ(I): 3.7
Reflection shellResolution: 3.3→3.9 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1035 / CC1/2: 0.7 / Rpim(I) all: 0.38 / Rrim(I) all: 0.7

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NMG

6nmg


Resolution: 3.3→39.53 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.287 -5 %
Rwork0.248 --
obs-20707 90.1 %
Displacement parametersBiso mean: 109.9 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15938 0 0 0 15938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216223
X-RAY DIFFRACTIONf_angle_d0.54821930
X-RAY DIFFRACTIONf_dihedral_angle_d17.8129825
X-RAY DIFFRACTIONf_chiral_restr0.0382461
X-RAY DIFFRACTIONf_plane_restr0.0042841
Refinement TLS params.Method: refined / Origin x: 25.8389 Å / Origin y: -18.0538 Å / Origin z: 27.0874 Å
111213212223313233
T0.5501 Å2-0.1561 Å2-0.0023 Å2-0.5406 Å2-0.0783 Å2--0.4201 Å2
L0.6963 °2-0.0485 °2-0.0697 °2-1.1735 °2-0.1776 °2--0.941 °2
S0.12 Å °-0.0093 Å °-0.0531 Å °-0.0238 Å °-0.1963 Å °0.2957 Å °0.1999 Å °0.0576 Å °0.0799 Å °
Refinement TLS groupSelection details: all

+
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