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- PDB-6mhf: Galphai3 co-crystallized with GIV/Girdin -

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Basic information

Entry
Database: PDB / ID: 6mhf
TitleGalphai3 co-crystallized with GIV/Girdin
Components
  • GirdinCCDC88A
  • Guanine nucleotide-binding protein G(k) subunit alpha
KeywordsSIGNALING PROTEIN / exchange / modulator / GPCR / inhibitory
Function / homology
Function and homology information


COPI-coated Golgi to ER transport vesicle / maintenance of protein location in plasma membrane / zymogen granule / G-protein gamma-subunit binding / Extra-nuclear estrogen signaling / negative regulation of secretion / Adenylate cyclase inhibitory pathway / protein kinase B binding / positive regulation of NAD(P)H oxidase activity / vesicle fusion ...COPI-coated Golgi to ER transport vesicle / maintenance of protein location in plasma membrane / zymogen granule / G-protein gamma-subunit binding / Extra-nuclear estrogen signaling / negative regulation of secretion / Adenylate cyclase inhibitory pathway / protein kinase B binding / positive regulation of NAD(P)H oxidase activity / vesicle fusion / positive regulation of protein localization to cilium / cytoskeleton-dependent intracellular transport / positive regulation of cilium assembly / membrane organization / vascular endothelial growth factor receptor 2 binding / dynein light intermediate chain binding / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / GTP metabolic process / GDP-dissociation inhibitor activity / GTPase activating protein binding / lamellipodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / dopamine receptor signaling pathway / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / regulation of neuron projection development / TOR signaling / activation of protein kinase activity / regulation of DNA replication / negative regulation of apoptotic signaling pathway / positive regulation of macroautophagy / G-protein alpha-subunit binding / G protein-coupled serotonin receptor binding / cytoplasmic microtubule organization / positive regulation of stress fiber assembly / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / centriole / phosphatidylinositol binding / SH2 domain binding / activation of protein kinase B activity / guanyl-nucleotide exchange factor activity / protein kinase C binding / positive regulation of superoxide anion generation / ciliary basal body / G protein-coupled receptor binding / regulation of actin cytoskeleton organization / regulation of protein phosphorylation / brain development / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / insulin receptor binding / GDP binding / heterotrimeric G-protein complex / cell migration / lamellipodium / nervous system development / actin binding / regulation of cell population proliferation / midbody / cytoplasmic vesicle / microtubule binding / DNA replication / cell cycle / membrane raft / cell division / protein domain specific binding / Golgi membrane / GTPase activity / centrosome / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Girdin / HOOK, N-terminal / HOOK domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / G-protein alpha subunit, group I / G-alpha domain profile. ...Girdin / HOOK, N-terminal / HOOK domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-3 / Girdin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRees, S.D. / Kalogriopoulos, N.A. / Ngo, T. / Kopcho, N. / Ilatovskiy, A. / Sun, N. / Komives, E. / Chang, G. / Ghosh, P. / Kufareva, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF/IOS-1444435 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural basis for GPCR-independent activation of heterotrimeric Gi proteins.
Authors: Kalogriopoulos, N.A. / Rees, S.D. / Ngo, T. / Kopcho, N.J. / Ilatovskiy, A.V. / Sun, N. / Komives, E.A. / Chang, G. / Ghosh, P. / Kufareva, I.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(k) subunit alpha
C: Girdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9144
Polymers43,3792
Non-polymers5352
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-31 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.780, 83.780, 141.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Guanine nucleotide-binding protein G(k) subunit alpha / G(i) alpha-3


Mass: 40066.418 Da / Num. of mol.: 1 / Fragment: residues 26-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai3, Gnai-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08753
#2: Protein/peptide Girdin / CCDC88A / Akt phosphorylation enhancer / APE / Coiled-coil domain-containing protein 88A / G alpha- ...Akt phosphorylation enhancer / APE / Coiled-coil domain-containing protein 88A / G alpha-interacting vesicle-associated protein / GIV / Girders of actin filament / Hook-related protein 1 / HkRP1


Mass: 3312.657 Da / Num. of mol.: 1 / Fragment: residues 1671-1701 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q3V6T2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2→72.08 Å / Num. obs: 63761 / % possible obs: 93.9 % / Redundancy: 4 % / Biso Wilson estimate: 32.04 Å2 / Net I/σ(I): 29.5
Reflection shellResolution: 2→2.08 Å / Num. unique obs: 34165

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
BOSdata collection
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G5R

4g5r


Resolution: 2→54.03 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.9134
RfactorNum. reflection% reflection
Rfree0.2391 3227 5.06 %
Rwork0.2061 --
obs0.2078 63761 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.19 Å2
Refinement stepCycle: LAST / Resolution: 2→54.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 34 222 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232847
X-RAY DIFFRACTIONf_angle_d0.52593842
X-RAY DIFFRACTIONf_chiral_restr0.0401429
X-RAY DIFFRACTIONf_plane_restr0.0023488
X-RAY DIFFRACTIONf_dihedral_angle_d12.94331708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.377960.33092734X-RAY DIFFRACTION99.72
2.03-2.060.34661430.32032625X-RAY DIFFRACTION99.68
2.06-2.10.35631650.30042690X-RAY DIFFRACTION99.51
2.1-2.130.28731590.28662629X-RAY DIFFRACTION99.75
2.13-2.170.27821320.27872686X-RAY DIFFRACTION99.44
2.17-2.210.3531490.26712663X-RAY DIFFRACTION99.33
2.21-2.260.31671100.25962691X-RAY DIFFRACTION99.43
2.26-2.310.2711530.25372660X-RAY DIFFRACTION99.4
2.31-2.360.21481430.24112629X-RAY DIFFRACTION99.21
2.36-2.420.26081620.23482678X-RAY DIFFRACTION99.4
2.42-2.480.30481330.22512642X-RAY DIFFRACTION99
2.48-2.560.27541310.21712666X-RAY DIFFRACTION99.08
2.56-2.640.24191490.21862661X-RAY DIFFRACTION99.05
2.64-2.730.23881810.21462610X-RAY DIFFRACTION98.76
2.73-2.840.25151450.21072619X-RAY DIFFRACTION98.78
2.84-2.970.2181310.21222689X-RAY DIFFRACTION98.64
2.97-3.130.23531340.20292610X-RAY DIFFRACTION97.83
3.13-3.330.25891210.22604X-RAY DIFFRACTION96.56
3.33-3.580.22991540.19212556X-RAY DIFFRACTION96.03
3.58-3.940.19711210.16842579X-RAY DIFFRACTION95.51
3.94-4.510.19081440.15352574X-RAY DIFFRACTION96.28
4.51-5.690.18561250.15792524X-RAY DIFFRACTION93.8
5.69-54.030.23131460.20512515X-RAY DIFFRACTION94.13

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