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Yorodumi- PDB-2xns: Crystal Structure Of Human G alpha i1 Bound To A Designed Helical... -
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-Basic information
Entry | Database: PDB / ID: 2xns | ||||||
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Title | Crystal Structure Of Human G alpha i1 Bound To A Designed Helical Peptide Derived From The Goloco Motif Of RGS14 | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / ADP-RIBOSYLATION / ARGININE FINGER / GTP-BINDING / LIPOPROTEIN / NUCLEOTIDE-BINDING / PALMITATE / SIGNALING PROTEIN / TRANSDUCER / PROTEIN-PROTEIN INTERFACE DESIGN | ||||||
Function / homology | Function and homology information zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / positive regulation of neurogenesis / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway ...zygote asymmetric cell division / negative regulation of synaptic plasticity / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / GDP-dissociation inhibitor activity / nucleocytoplasmic transport / positive regulation of neurogenesis / spindle organization / negative regulation of G protein-coupled receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / G-protein alpha-subunit binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / long-term memory / regulation of mitotic spindle organization / negative regulation of MAP kinase activity / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity / learning / Regulation of insulin secretion / chromosome segregation / G protein-coupled receptor binding / long-term synaptic potentiation / G-protein beta/gamma-subunit complex binding / visual learning / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / PML body / negative regulation of ERK1 and ERK2 cascade / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / spindle pole / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / spindle / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / mitotic cell cycle / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / microtubule binding / Extra-nuclear estrogen signaling / response to oxidative stress / microtubule / dendritic spine / postsynaptic density / nuclear body / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / glutamatergic synapse / dendrite / nucleolus / GTP binding / protein kinase binding / magnesium ion binding / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å | ||||||
Authors | Bosch, D. / Sammond, D.W. / Butterfoss, G.L. / Machius, M. / Siderovski, D.P. / Kuhlman, B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Computational Design of the Sequence and Structure of a Protein-Binding Peptide. Authors: Sammond, D.W. / Bosch, D.E. / Butterfoss, G.L. / Purbeck, C. / Machius, M. / Siderovski, D.P. / Kuhlman, B. #1: Journal: J.Mol.Biol. / Year: 2007 Title: Structure-Based Protocol for Identifying Mutations that Enhance Protein-Protein Binding Affinities. Authors: Sammond, D.W. / Eletr, Z.M. / Purbeck, C. / Kimple, R.J. / Siderovski, D.P. / Kuhlman, B. #2: Journal: Nature / Year: 2002 Title: Structural Determinants for Goloco-Induced Inhibition of Nucleotide Release by Galpha Subunits. Authors: Kimple, R.J. / Kimple, M.E. / Betts, L. / Sondek, J. / Siderovski, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xns.cif.gz | 308.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xns.ent.gz | 256.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xns_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2xns_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xns_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 2xns_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xns ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xns | HTTPS FTP |
-Related structure data
Related structure data | 2om2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 37374.555 Da / Num. of mol.: 2 / Fragment: RESIDUES 30-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLICGNAI1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P63096, EC: 3.6.5.1 #2: Protein/peptide | Mass: 4695.173 Da / Num. of mol.: 2 / Fragment: RESIDUES 497-517 / Source method: obtained synthetically Details: DESIGNED HELICAL PEPTIDE DERIVED FROM REGULATOR OF G- PROTEIN SIGNALING 14 GOLOCO MOTIF PEPTIDE Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43566 |
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-Non-polymers , 4 types, 16 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 28-29 OF CHAINS A, B ARE CLONING LINKERS. PEPTIDE RESIDUES 496-516 FOR CHAINS C AND D, ...RESIDUES 28-29 OF CHAINS A, B ARE CLONING LINKERS. PEPTIDE RESIDUES 496-516 FOR CHAINS C AND D, CORRESPOND |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 9.3 Å3/Da / Density % sol: 86.78 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: HEXAGONAL CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION USING 1 MICROLITER PREMIXED GALPHA I1 AND GOLOCO PEPTIDE (1:1.5 MOLAR RATIO) AT 12 MG/ML IN BUFFER (10 MM TRIS PH 7.5, 1 MM ...Details: HEXAGONAL CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION USING 1 MICROLITER PREMIXED GALPHA I1 AND GOLOCO PEPTIDE (1:1.5 MOLAR RATIO) AT 12 MG/ML IN BUFFER (10 MM TRIS PH 7.5, 1 MM MAGNESIUM CHLORIDE, 10 MICROMOLAR GDP, 5 MM DTT) AND 1 MICROLITER CRYSTALLIZATION SOLUTION (800 MM AMMONIUM SULFATE, 200 MM K/NA TARTRATE, 100 MM SODIUM CITRATE PH 5.5). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.41→40 Å / Num. obs: 42418 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 99.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 3.41→3.42 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OM2 Resolution: 3.41→39.99 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / SU B: 30.905 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.41→39.99 Å
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