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- PDB-4usu: Crystal structure of human soluble Adenylyl Cyclase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4usu
TitleCrystal structure of human soluble Adenylyl Cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate
ComponentsADENYLATE CYCLASE TYPE 10
KeywordsLYASE / APCPP
Function / homology
Function and homology information


negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / astrocyte end-foot / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process / regulation of mitophagy ...negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / astrocyte end-foot / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process / regulation of mitophagy / regulation of membrane repolarization / adenylate cyclase / basal part of cell / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cAMP biosynthetic process / positive regulation of ossification / adenylate cyclase activity / neuron projection extension / positive regulation of protein targeting to mitochondrion / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of cardiac muscle hypertrophy / positive regulation of mitochondrial depolarization / positive regulation of reactive oxygen species biosynthetic process / positive regulation of ATP biosynthetic process / negative regulation of mitochondrial membrane potential / spermatid development / positive regulation of axon extension / positive regulation of cardiac muscle cell apoptotic process / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / apical part of cell / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / cilium / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adenylate cyclase, type 10 / Nucleotide cyclase, GGDEF domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKleinboelting, S. / Steegborn, C.
CitationJournal: FEBS J. / Year: 2014
Title: Structural Analysis of Human Soluble Adenylyl Cyclase and Crystal Structures of its Nucleotide Complexes -Implications for Cyclase Catalysis and Evolution.
Authors: Kleinbolting, S. / Van Den Heuvel, J. / Steegborn, C.
History
DepositionJul 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 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 1.3Jan 10, 2024Group: 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)55,25811
Polymers54,2701
Non-polymers98910
Water3,657203
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)165,77533
Polymers162,8093
Non-polymers2,96630
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area13350 Å2
ΔGint-125.3 kcal/mol
Surface area55780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.840, 100.840, 96.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2077-

HOH

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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


Mass: 54269.664 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-469
Source method: isolated from a genetically manipulated source
Details: BETA-MERCAPTOETHANOL MODIFICATION AT RESIDUE CYS253
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 , 5 types, 213 molecules

#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 54 % / 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: 1.9→64.83 Å / Num. obs: 40732 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.17
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.82 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CLK

4clk


Resolution: 1.95→64.83 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.772 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21174 1916 4.7 %RANDOM
Rwork0.1593 ---
obs0.16182 38816 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.95→64.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 58 203 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193862
X-RAY DIFFRACTIONr_bond_other_d0.0010.023668
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.9695232
X-RAY DIFFRACTIONr_angle_other_deg0.94938462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.745476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03624.77174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89115661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2121513
X-RAY DIFFRACTIONr_chiral_restr0.1170.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
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_it3.1412.9231868
X-RAY DIFFRACTIONr_mcbond_other3.1252.9221867
X-RAY DIFFRACTIONr_mcangle_it4.4994.362335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3613.4891994
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→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.101 1 -
Rwork0.263 2989 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -22.1677 Å / Origin y: -25.6674 Å / Origin z: 0.9584 Å
111213212223313233
T0.0372 Å20.0128 Å2-0.0054 Å2-0.1162 Å2-0.0677 Å2--0.0632 Å2
L0.8997 °2-0.0967 °2-0.3219 °2-0.6515 °20.1633 °2--0.8396 °2
S-0.0438 Å °-0.0049 Å °-0.03 Å °0.0053 Å °0.1122 Å °-0.1681 Å °0.0049 Å °0.1994 Å °-0.0684 Å °

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