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- PDB-6nmg: Crystal Structure of Rat Ric-8A G alpha binding domain -

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Basic information

Entry
Database: PDB / ID: 6nmg
TitleCrystal Structure of Rat Ric-8A G alpha binding domain
ComponentsResistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor heterotrimeric G protein alpha subunit G alpha i(1)
Function / homology
Function and homology information


cell-cell adhesion involved in gastrulation / cell migration involved in gastrulation / basement membrane organization / vasculature development / G-protein alpha-subunit binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / visual learning / in utero embryonic development / plasma membrane / cytoplasm
Similarity search - Function
Synembryn / Guanine nucleotide exchange factor, Ric8 / Guanine nucleotide exchange factor synembryn / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZeng, B. / Mou, T.C. / Sprang, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM105993 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: Structure / Year: 2019
Title: Structure, Function, and Dynamics of the G alpha Binding Domain of Ric-8A.
Authors: Zeng, B. / Mou, T.C. / Doukov, T.I. / Steiner, A. / Yu, W. / Papasergi-Scott, M. / Tall, G.G. / Hagn, F. / Sprang, S.R.
History
DepositionJan 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
B: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7046
Polymers102,3202
Non-polymers3844
Water3,279182
1
A: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3523
Polymers51,1601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3523
Polymers51,1601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.045, 103.645, 141.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 51159.820 Da / Num. of mol.: 2
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25-30% PEG3350, 0.2 M lithium sulfate, 0.1 M Tris / PH range: 6-9

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.979
SYNCHROTRONNSLS-II 17-ID-221.77
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDNov 7, 2017
DECTRIS EIGER X 16M2PIXELOct 12, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.771
Reflection

Entry-ID: 6NMG / CC1/2: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2.2-31.055053799.46.432.80.040.1115.4
3.41-29.11410999.5785.983.30.0080.222118.3
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.2-2.284.52.249800.320.280.58199.2
3.41-3.72803.467.119800.980.0130.372100

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2975: ???)refinement
XDSdata reduction
pointlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→31.05 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 30.83
RfactorNum. reflection% reflection
Rfree0.2747 1505 2.98 %
Rwork0.2268 --
obs0.2283 50537 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→31.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6671 0 20 182 6873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046793
X-RAY DIFFRACTIONf_angle_d0.6189187
X-RAY DIFFRACTIONf_dihedral_angle_d12.9754184
X-RAY DIFFRACTIONf_chiral_restr0.0371079
X-RAY DIFFRACTIONf_plane_restr0.0041183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.41521340.38234375X-RAY DIFFRACTION99
2.271-2.35210.37571360.35354382X-RAY DIFFRACTION99
2.3521-2.44630.34481340.31824392X-RAY DIFFRACTION99
2.4463-2.55760.34231340.28874384X-RAY DIFFRACTION99
2.5576-2.69230.2851370.26654445X-RAY DIFFRACTION99
2.6923-2.86090.35311340.25534402X-RAY DIFFRACTION99
2.8609-3.08160.30461380.24194453X-RAY DIFFRACTION99
3.0816-3.39140.27141370.22574460X-RAY DIFFRACTION100
3.3914-3.88140.27361370.19274500X-RAY DIFFRACTION100
3.8814-4.88710.19821400.16764545X-RAY DIFFRACTION100
4.8871-31.29660.23371440.18634694X-RAY DIFFRACTION99

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