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- PDB-1cs4: COMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENY... -

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Entry
Database: PDB / ID: 1cs4
TitleCOMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN ADENYLYL CYCLASE: COMPLEX WITH 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE, PYROPHOSPHATE AND MG
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(S)
  • TYPE II ADENYLATE CYCLASE
  • TYPE V ADENYLATE 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 / regulation of insulin secretion involved in cellular response to glucose stimulus / mu-type opioid receptor binding / cAMP biosynthetic process / corticotropin-releasing hormone receptor 1 binding ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / regulation of insulin secretion involved in cellular response to glucose stimulus / mu-type opioid receptor binding / cAMP biosynthetic process / corticotropin-releasing hormone receptor 1 binding / G alpha (z) signalling events / adenylate cyclase activity / beta-2 adrenergic receptor binding / adenylate cyclase binding / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / cellular response to forskolin / adenylate cyclase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cilium / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / manganese ion binding / positive regulation of cytosolic calcium ion concentration / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / 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'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE / FORSKOLIN / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / PYROPHOSPHATE 2- / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsTesmer, J.J.G. / Dessauer, C.A. / Sunahara, R.K. / Johnson, R.A. / Gilman, A.G. / Sprang, S.R.
Citation
Journal: 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.
#1: Journal: Science / Year: 1997
Title: Crystal Structure of the Catalytic Domains of Adenylyl Cyclase in a Complex with Gs(Alpha)-GTP(Gamma)S
Authors: Tesmer, J.J.G. / Sunahara, R.K. / Gilman, A.G. / Sprang, S.R.
History
DepositionAug 16, 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_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.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.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_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_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 ADENYLATE CYCLASE
B: TYPE II ADENYLATE CYCLASE
C: GUANINE NUCLEOTIDE-BINDING PROTEIN G(S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,94512
Polymers95,0133
Non-polymers1,9319
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-62 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.5, 134.5, 71.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-1035-

HOH

DetailsBiological assembly is a heterotrimer as it exists in the asymmetric unit. But then, you never know for sure.

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 25526.514 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) / Keywords: N-TERMINAL HEXAHISTADINE TAG / References: UniProt: P30803, adenylate cyclase
#2: Protein TYPE II ADENYLATE CYCLASE / E.C.4.6.1.1 / ATP PYROPHOSPHATE-LYASE / ADENYLYL CYCLASE


Mass: 23717.033 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: 45769.527 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 (domestic cattle) / Organ: NOSTRIL / Plasmid: PQE60-GSALPHA-H / Production host: Escherichia coli (E. coli) / References: UniProt: P04896

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Non-polymers , 8 types, 86 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FOK / FORSKOLIN


Mass: 410.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34O7
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#8: Chemical ChemComp-101 / 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN MIXED 1:1 WITH WELL SOLUTION OF 7.2-7.5% PEG 8000, 500MM NACL AND 100 MM MES BUFFER, VAPOR DIFFUSION, HANGING DROP at 293 K
Crystal grow
*PLUS
Method: vapor diffusion / 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: 2.5→30 Å / Num. obs: 39407 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 53.6 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.815 / Num. unique all: 5757 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3639 10 %RANDOM
Rwork0.216 ---
all0.221 40011 --
obs0.221 36050 90.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.73 Å20 Å20 Å2
2---23.79 Å20 Å2
3---36.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5647 0 119 77 5843
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: 50.9 Å2

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