[English] 日本語
Yorodumi
- PDB-4usv: Crystal structure of human soluble Adenylyl Cyclase with pyrophos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4usv
TitleCrystal structure of human soluble Adenylyl Cyclase with pyrophosphate resulting from soaking with ATP and Calcium
ComponentsADENYLATE CYCLASE TYPE 10
KeywordsLYASE / REACTION PRODUCT
Function / homology
Function and homology information


negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / regulation of mitophagy / 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 / astrocyte end-foot / mitochondrial ATP transmembrane transport / epithelial cilium movement involved in extracellular fluid movement / bicarbonate binding / regulation of mitophagy / 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 / 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 / positive regulation of reactive oxygen species biosynthetic process / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of mitochondrial depolarization / 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 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 / dendrite / neuronal cell body / 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
ACETATE ION / PYROPHOSPHATE 2- / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENYLATE CYCLASE TYPE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7968
Polymers54,2701
Non-polymers5277
Water3,333185
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)164,38924
Polymers162,8093
Non-polymers1,58021
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 area11420 Å2
ΔGint-93.6 kcal/mol
Surface area55190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.870, 100.870, 97.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
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

-
Non-polymers , 7 types, 192 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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→87.36 Å / Num. obs: 37919 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.11
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
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→87.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.852 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20893 1929 5.1 %RANDOM
Rwork0.15994 ---
obs0.16235 35990 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.485 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2→87.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 29 185 3821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193743
X-RAY DIFFRACTIONr_bond_other_d0.0010.023551
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.965076
X-RAY DIFFRACTIONr_angle_other_deg0.94138172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44124.578166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9161513
X-RAY DIFFRACTIONr_chiral_restr0.1270.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02858
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_it3.2133.1171841
X-RAY DIFFRACTIONr_mcbond_other3.0473.1131839
X-RAY DIFFRACTIONr_mcangle_it4.4334.6532299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4953.6691902
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 149 -
Rwork0.254 2617 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 22.3829 Å / Origin y: 25.7083 Å / Origin z: 0.823 Å
111213212223313233
T0.0209 Å20.0118 Å20.0073 Å2-0.0821 Å20.0362 Å2--0.0428 Å2
L0.8241 °2-0.0092 °20.2555 °2-0.6389 °2-0.1565 °2--0.8271 °2
S-0.0253 Å °-0.0234 Å °0.0088 Å °0.0129 Å °0.0746 Å °0.153 Å °-0.0005 Å °-0.1726 Å °-0.0493 Å °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more