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- PDB-1cip: GI-ALPHA-1 SUBUNIT OF GUANINE NUCLEOTIDE-BINDING PROTEIN COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1cip
TitleGI-ALPHA-1 SUBUNIT OF GUANINE NUCLEOTIDE-BINDING PROTEIN COMPLEXED WITH A GTP ANALOGUE
ComponentsPROTEIN (GUANINE NUCLEOTIDE-BINDING PROTEIN ALPHA-1 SUBUNIT)
KeywordsHYDROLASE / GTPASE / G PROTEIN
Function / homology
Function and homology information


Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / 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 / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsColeman, D. / Sprang, S.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Structure of Gialpha1.GppNHp, autoinhibition in a galpha protein-substrate complex.
Authors: Coleman, D.E. / Sprang, S.R.
History
DepositionApr 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GUANINE NUCLEOTIDE-BINDING PROTEIN ALPHA-1 SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8143
Polymers40,2681
Non-polymers5472
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.050, 80.050, 105.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein PROTEIN (GUANINE NUCLEOTIDE-BINDING PROTEIN ALPHA-1 SUBUNIT) / GIA1 / GUANINE NUCLEOTIDE-BINDING PROTEIN G(I) / ALPHA-1 SUBUNIT


Mass: 40267.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PQE6 / Production host: Escherichia coli (E. coli) / References: UniProt: P10824
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
Description: TWO DATA SETS WERE COMBINED TO OBTAIN FINAL SET. TWO CRYSTALS WERE USED FOR DATA COLLECTION. DATA FROM 15.0 -2.24A WAS COLLECTED AT CHESS A1.(CRYSTAL DIFFRACTED TO 1.7A). DATA FROM 2.24- ...Description: TWO DATA SETS WERE COMBINED TO OBTAIN FINAL SET. TWO CRYSTALS WERE USED FOR DATA COLLECTION. DATA FROM 15.0 -2.24A WAS COLLECTED AT CHESS A1.(CRYSTAL DIFFRACTED TO 1.7A). DATA FROM 2.24-1.50A WAS COLLECTED AT CHESS F1. SEE JBC (99) ARTICLE FOR DETAILS.
Crystal growpH: 7
Details: PROTEIN BOUND TO GPPNHP WAS CRYSTALLIZED IN 1.8-2.0M (NH4)2SO3, 100MM SODIUM ACETATE, H 6.0, 1MM MGSO4, 1MM GPPNHP, AND 5MM DTT. PRIOR TO DATA COLLECTION CRYSTALS WERE TRANSFERED TO 2.0M ...Details: PROTEIN BOUND TO GPPNHP WAS CRYSTALLIZED IN 1.8-2.0M (NH4)2SO3, 100MM SODIUM ACETATE, H 6.0, 1MM MGSO4, 1MM GPPNHP, AND 5MM DTT. PRIOR TO DATA COLLECTION CRYSTALS WERE TRANSFERED TO 2.0M LI2SO4, 1MM GPPNHP, 3MM DTT, 1MM MGSO4, 100MM BES, PH 7.0, AND 15% GLYCEROL. CRYSTALS WERE FLASH FROZEN IN LIQUID PROPANE.
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21.4 Mpotassium phosphate1drop
325 mMEPPS1drop
41 mM1dropMgSO4
62.5 mMdithiothreitol1drop
710 mMEDTA1drop
8100 mM1reservoirNaCl
91.45-1.65 Mpotassium phosphate1reservoir
5GppNHp1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS A110.91
SYNCHROTRONCHESS F120.918
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 1, 1998
ADSC QUANTUM 42CCDJun 1, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
20.9181
ReflectionResolution: 1.5→15 Å / Num. all: 57771 / Num. obs: 57771 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 3.92 % / Biso Wilson estimate: 15.94 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.5 / % possible all: 77.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 77.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GIA

1gia


Resolution: 1.5→15 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: RESIDUES 2 - 31, AND 348 - 354 ARE DISORDERED AND DID NOT APPEAR IN THE DENSITY. SIDE- CHAINS THAT ARE PARTIALLY DISORDERED HAVE THE OCCUPANCYS OF RELEVANT ATOMS SET TO 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2895 4.6 %RANDOM
Rwork0.213 ---
obs-57291 90.84 %-
Displacement parametersBiso mean: 18.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 33 157 2733
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_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.83
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.3681.5
X-RAY DIFFRACTIONx_mcangle_it2.1662
X-RAY DIFFRACTIONx_scbond_it2.6192
X-RAY DIFFRACTIONx_scangle_it4.172.5
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.242 324 5.25 %
Rwork0.246 6172 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARGNP.PROTOPGNP.PRO
X-RAY DIFFRACTION3PARWATER.PROTOPWATER.PRO
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.83
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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