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- PDB-4usw: Crystal structure of human soluble Adenylyl Cyclase with ATP -

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Basic information

Entry
Database: PDB / ID: 4usw
TitleCrystal structure of human soluble Adenylyl Cyclase with ATP
ComponentsADENYLATE CYCLASE TYPE 10
KeywordsLYASE / ATP SUBSTRATE
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 / positive regulation of protein targeting to mitochondrion / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of ATP biosynthetic process / positive regulation of reactive oxygen species biosynthetic process / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / spermatid development / negative regulation of mitochondrial membrane potential / positive regulation of axon extension / Hedgehog 'off' state / positive regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / 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 / 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
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)55,0106
Polymers54,2701
Non-polymers7405
Water3,639202
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)165,03018
Polymers162,8093
Non-polymers2,22115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
Buried area12590 Å2
ΔGint-88.7 kcal/mol
Surface area54500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.090, 101.090, 96.750
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


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, 207 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsADENOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) (ATP): SYN CONFORMATION

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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: 0.91705
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: COLLIMATOR
RadiationMonochromator: SI111-DCM WITH SAGITTAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91705 Å / Relative weight: 1
ReflectionResolution: 2.05→87.55 Å / Num. obs: 35253 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.31
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.9 / 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: 2.05→87.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.649 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED ATP BUILD IN SYN CONFORMATION ATP IN ANTI CONFORMATION IS ALSO PRESENT BUT WITH MINOR OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.21215 1775 5 %RANDOM
Rwork0.16418 ---
obs0.16659 33478 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.05→87.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 46 202 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193780
X-RAY DIFFRACTIONr_bond_other_d0.0010.023577
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9685131
X-RAY DIFFRACTIONr_angle_other_deg0.92238234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87124.551167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24615636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.711513
X-RAY DIFFRACTIONr_chiral_restr0.120.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02869
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_it2.8933.0031843
X-RAY DIFFRACTIONr_mcbond_other2.8863.0021840
X-RAY DIFFRACTIONr_mcangle_it4.1334.4792299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3033.5751937
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 114 -
Rwork0.262 2508 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: -11.0178 Å / Origin y: -32.1442 Å / Origin z: -1.0016 Å
111213212223313233
T0.0387 Å20.0229 Å20.0186 Å2-0.0344 Å20.0169 Å2--0.0108 Å2
L0.1726 °2-0.0076 °2-0.1686 °2-0.2296 °20.0728 °2--0.3594 °2
S0.0509 Å °0.0567 Å °0.0345 Å °0.0423 Å °-0.0237 Å °0.0093 Å °-0.0549 Å °-0.0411 Å °-0.0271 Å °

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