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- PDB-6nmj: Crystal Structure of Rat Ric-8A G alpha binding domain, "Paratone... -

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Basic information

Entry
Database: PDB / ID: 6nmj
TitleCrystal Structure of Rat Ric-8A G alpha binding domain, "Paratone-N Immersed"
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 Gα Binding Domain of Ric-8A.
Authors: Baisen Zeng / Tung-Chung Mou / Tzanko I Doukov / Andrea Steiner / Wenxi Yu / Makaia Papasergi-Scott / Gregory G Tall / Franz Hagn / Stephen R Sprang /
Abstract: Ric-8A is a 530-amino acid cytoplasmic molecular chaperone and guanine nucleotide exchange factor (GEF) for i, q, and 12/13 classes of heterortrimeric G protein alpha subunits (Gα). We report the 2. ...Ric-8A is a 530-amino acid cytoplasmic molecular chaperone and guanine nucleotide exchange factor (GEF) for i, q, and 12/13 classes of heterortrimeric G protein alpha subunits (Gα). We report the 2.2-Å crystal structure of the Ric-8A Gα-binding domain with GEF activity, residues 1-452, and is phosphorylated at Ser435 and Thr440. Residues 1-429 adopt a superhelical fold comprised of Armadillo (ARM) and HEAT repeats, and the C terminus is disordered. One of the phosphorylated residues potentially binds to a basic cluster in an ARM motif. Amino acid sequence conservation and published hydrogen-deuterium exchange data indicate repeats 3 through 6 to be a putative Gα-binding surface. Normal mode modeling of small-angle X-ray scattering data indicates that phosphorylation induces relative rotation between repeats 1-4, 5-6, and 7-9. 2D H-N-TROSY spectra of [H,N]-labeled Gαi1 in the presence of R452 reveals chemical shift perturbations of the C terminus and Gαi1 residues involved in nucleotide binding.
History
DepositionJan 11, 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 1.3Oct 11, 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

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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)


Theoretical massNumber of molelcules
Total (without water)102,3202
Polymers102,3202
Non-polymers00
Water1,72996
1
A: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)


Theoretical massNumber of molelcules
Total (without water)51,1601
Polymers51,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)


Theoretical massNumber of molelcules
Total (without water)51,1601
Polymers51,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.298, 100.114, 129.959
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 / Mutation: F232Y
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.01 Å3/Da / Density % sol: 38.87 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25-30% PEG3350, 0.2 M lithium sulfate, 0.1 M Tris / PH range: 6-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→39.65 Å / Num. obs: 37176 / % possible obs: 99.11 % / Redundancy: 26.3 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.09 / Net I/σ(I): 30.72
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 26.9 % / Mean I/σ(I) obs: 4.55 / Num. unique obs: 3675 / CC1/2: 0.95 / Rpim(I) all: 0.2 / Rrim(I) all: 1.04 / % possible all: 99.19

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NMG

6nmg


Resolution: 2.3→39.655 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1171 3.15 %
Rwork0.2077 --
obs0.2094 37129 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6445 0 0 96 6541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036546
X-RAY DIFFRACTIONf_angle_d0.578849
X-RAY DIFFRACTIONf_dihedral_angle_d11.2754041
X-RAY DIFFRACTIONf_chiral_restr0.0361051
X-RAY DIFFRACTIONf_plane_restr0.0041134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.33591440.24674419X-RAY DIFFRACTION99
2.4047-2.53150.30871430.24334403X-RAY DIFFRACTION98
2.5315-2.690.24871450.23074462X-RAY DIFFRACTION100
2.69-2.89770.27191460.2314464X-RAY DIFFRACTION100
2.8977-3.18920.27551460.23444480X-RAY DIFFRACTION99
3.1892-3.65040.2931450.21264470X-RAY DIFFRACTION99
3.6504-4.5980.21981480.18174555X-RAY DIFFRACTION99
4.598-39.66080.24791540.19454705X-RAY DIFFRACTION99

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