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- PDB-4clt: Crystal structure of human soluble Adenylyl Cyclase with adenosin... -

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Basic information

Entry
Database: PDB / ID: 4clt
TitleCrystal structure of human soluble Adenylyl Cyclase with adenosine-3', 5'-cyclic-monophosphate and pyrophosphate
ComponentsADENYLATE CYCLASE TYPE 10
KeywordsLYASE
Function / homology
Function and homology information


negative regulation of cardiac muscle cell contraction / regulation of mitophagy / astrocyte end-foot / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / neuron projection retraction / positive regulation of glycogen catabolic process / central region of growth cone / cellular response to inorganic substance ...negative regulation of cardiac muscle cell contraction / regulation of mitophagy / astrocyte end-foot / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / neuron projection retraction / positive regulation of glycogen catabolic process / central region of growth cone / cellular response to inorganic substance / glucose catabolic process / regulation of membrane repolarization / adenylate cyclase / basal part of cell / cAMP biosynthetic process / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of ossification / adenylate cyclase activity / positive regulation of reactive oxygen species biosynthetic process / positive regulation of protein targeting to mitochondrion / positive regulation of vascular associated smooth muscle cell apoptotic process / neuron projection extension / positive regulation of ATP biosynthetic process / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / spermatid development / negative regulation of mitochondrial membrane potential / positive regulation of mitochondrial depolarization / positive regulation of axon extension / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / positive regulation of peptidyl-threonine phosphorylation / cilium / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / apical plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenylate cyclase, type 10 / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / PYROPHOSPHATE 2- / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKleinboelting, S. / Weyand, M. / Steegborn, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal Structures of Human Soluble Adenylyl Cyclase Reveal Mechanisms of Catalysis and of its Activation Through Bicarbonate.
Authors: Kleinboelting, S. / Diaz, A. / Moniot, S. / Van Den Heuvel, J. / Weyand, M. / Levin, L.R. / Buck, J. / Steegborn, C.
History
DepositionJan 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENYLATE CYCLASE TYPE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2267
Polymers54,2701
Non-polymers9566
Water1,910106
1
A: ADENYLATE CYCLASE TYPE 10
hetero molecules

A: ADENYLATE CYCLASE TYPE 10
hetero molecules

A: ADENYLATE CYCLASE TYPE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,67821
Polymers162,8093
Non-polymers2,86918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area11990 Å2
ΔGint-104.2 kcal/mol
Surface area55770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.970, 100.970, 97.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ADENYLATE CYCLASE TYPE 10 / AH-RELATED PROTEIN / ADENYLATE CYCLASE HOMOLOG / GERM CELL SOLUBLE ADENYLYL CYCLASE / HSAC / SAC / ...AH-RELATED PROTEIN / ADENYLATE CYCLASE HOMOLOG / GERM CELL SOLUBLE ADENYLYL CYCLASE / HSAC / SAC / TESTICULAR SOLUBLE ADENYLYL CYCLASE / SOLUBLE ADENYLYL CYCLASE


Mass: 54269.664 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1392 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q96PN6, adenylate cyclase

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Non-polymers , 6 types, 112 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.75 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6
Details: 0.1 M SODIUM ACETATE PH 4.8, 0.2 M TRI-SODIUM-CITRATE, 15% (W/V) PEG 4000, 10% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013 / Details: COLLIMATOR
RadiationMonochromator: SI111-DCM WITH SAGITTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.95→87.44 Å / Num. obs: 40997 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CLF
Resolution: 1.95→87.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.28 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22015 2065 5 %RANDOM
Rwork0.17341 ---
obs0.17571 38932 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.795 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→87.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 59 106 3823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193825
X-RAY DIFFRACTIONr_bond_other_d0.0010.023624
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.9765191
X-RAY DIFFRACTIONr_angle_other_deg0.94338351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21724.583168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5291513
X-RAY DIFFRACTIONr_chiral_restr0.1290.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6182.2751852
X-RAY DIFFRACTIONr_mcbond_other2.6062.2741851
X-RAY DIFFRACTIONr_mcangle_it4.0143.392313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.052.8441973
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 133 -
Rwork0.258 2898 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 22.2796 Å / Origin y: 25.7032 Å / Origin z: 0.7765 Å
111213212223313233
T0.0064 Å20.0074 Å20.0084 Å2-0.033 Å20.0057 Å2--0.0262 Å2
L0.5421 °20.0512 °20.1657 °2-0.4622 °2-0.0458 °2--0.7254 °2
S-0.0077 Å °-0.0039 Å °0.0174 Å °0.0079 Å °0.002 Å °0.0908 Å °-0.0064 Å °-0.1319 Å °0.0057 Å °

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