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- PDB-1cul: COMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENY... -

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Entry
Database: PDB / ID: 1cul
TitleCOMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENYLYL CYCLASE: COMPLEX WITH 2',5'-DIDEOXY-ADENOSINE 3'-TRIPHOSPHATE AND MG
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(S)
  • TYPE II ADENYLYL CYCLASE
  • TYPE V ADENYLYL CYCLASE
KeywordsLyase/Lyase/Signaling protein / COMPLEX (LYASE-HYDROLASE) / HYDROLASE / SIGNAL TRANSDUCING PROTEIN / CYCLASE / EFFECTOR ENZYME / LYASE-HYDROLASE COMPLEX / Lyase-Lyase-Signaling protein complex
Function / homology
Function and homology information


Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / mu-type opioid receptor binding / regulation of insulin secretion involved in cellular response to glucose stimulus / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / mu-type opioid receptor binding / regulation of insulin secretion involved in cellular response to glucose stimulus / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / beta-2 adrenergic receptor binding / cAMP-mediated signaling / adenylate cyclase binding / D1 dopamine receptor binding / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to forskolin / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase activator activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cilium / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of GTPase activity / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / manganese ion binding / positive regulation of cytosolic calcium ion concentration / intracellular signal transduction / membrane raft / GTPase activity / dendrite / GTP binding / magnesium ion binding / protein-containing complex / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / Nucleotide cyclase, GGDEF domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. ...Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / Nucleotide cyclase, GGDEF domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / 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 / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',5'-DIDEOXY-ADENOSINE 3'-MONOPHOSPHATE / TRIPHOSPHATE / FORSKOLIN / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase type 2 / Adenylate cyclase type 5
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Rattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsTesmer, J.J.G. / Dessauer, C.A. / Sunahara, R.K. / Johnson, R.A. / Gilman, A.G. / Sprang, S.R.
CitationJournal: Biochemistry / Year: 2000
Title: Molecular basis for P-site inhibition of adenylyl cyclase.
Authors: Tesmer, J.J. / Dessauer, C.W. / Sunahara, R.K. / Murray, L.D. / Johnson, R.A. / Gilman, A.G. / Sprang, S.R.
History
DepositionAug 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE V ADENYLYL CYCLASE
B: TYPE II ADENYLYL CYCLASE
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,12314
Polymers92,0663
Non-polymers2,05711
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-78 kcal/mol
Surface area30790 Å2
MethodPISA
2
A: TYPE V ADENYLYL CYCLASE
B: TYPE II ADENYLYL CYCLASE
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(S)
hetero molecules

A: TYPE V ADENYLYL CYCLASE
B: TYPE II ADENYLYL CYCLASE
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,24628
Polymers184,1326
Non-polymers4,11422
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20420 Å2
ΔGint-173 kcal/mol
Surface area60390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.2, 133.6, 70.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-398-

CL

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein TYPE V ADENYLYL CYCLASE / E.C.4.6.1.1 / ATP PYROPHOSPHATE-LYASE


Mass: 24495.361 Da / Num. of mol.: 1 / Fragment: C1A DOMAIN / Mutation: V476M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Organ: HEART / Plasmid: PQE60-H6-VC1(580) / Production host: Escherichia coli (E. coli) / References: UniProt: P30803, adenylate cyclase
#2: Protein TYPE II ADENYLYL CYCLASE / E.C.4.6.1.1 / ATP PYROPHOSPHATE-LYASE / ADENYLYL CYCLASE


Mass: 23230.422 Da / Num. of mol.: 1 / Fragment: C2A DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PQE60-ARGC-IIC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P26769, adenylate cyclase
#3: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN G(S) / ADENYLATE CYCLASE-STIMULATING G ALPHA PROTEIN


Mass: 44340.145 Da / Num. of mol.: 1 / Fragment: GS(ALPHA) / Mutation: TRYPSINIZED, SHORT FORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: UDDER / Plasmid: PQE60-GSALPHA-H / Production host: Escherichia coli (E. coli) / References: UniProt: P04896

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Non-polymers , 8 types, 94 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FOK / FORSKOLIN / Forskolin


Mass: 410.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34O7
#6: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-103 / 2',5'-DIDEOXY-ADENOSINE 3'-MONOPHOSPHATE


Mass: 315.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O5P
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PROTEIN MIXED 1:1 WITH WELL SOLUTION OF 7.2-7.5% PEG 8000, 500MM NACL AND 100 MM MES BUFFER pH 5.4-5.6. VAPOR DIFFUSION, HANGING DROP at 293 K
Crystal grow
*PLUS
Details: PROTEIN MIXED 1:1 WITH WELL SOLUTION / PH range low: 5.6 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
27.2-7.5 %PEG80001reservoir
3500 mM1reservoirNaCl
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.921
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 36169 / Num. obs: 36169 / % possible obs: 82.4 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 5.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.206 / Num. unique all: 2267 / % possible all: 35.9
Reflection shell
*PLUS
% possible obs: 35.9 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3176 10 %RANDOM
Rwork0.216 ---
all0.221 32910 --
obs0.221 32910 74.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.511 Å20 Å20 Å2
2---19.131 Å20 Å2
3---42.851 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 124 83 5847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_bond_d0.007
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48.4 Å2

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