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- PDB-3uvj: Crystal structure of the catalytic domain of the heterodimeric hu... -

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Basic information

Entry
Database: PDB / ID: 3uvj
TitleCrystal structure of the catalytic domain of the heterodimeric human soluble guanylate cyclase 1.
Components
  • Guanylate cyclase soluble subunit alpha-3
  • Guanylate cyclase soluble subunit beta-1
KeywordsLYASE / Nitric Oxide / Structural Genomics / Structural Genomics Consortium / SGC / CGMP BIOSYNTHESIS / GTP binding METAL-BINDING / NUCLEOTIDE-BINDING / Cystol
Function / homology
Function and homology information


retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / guanylate cyclase complex, soluble / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / response to oxygen levels / presynaptic active zone cytoplasmic component / Nitric oxide stimulates guanylate cyclase ...retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / guanylate cyclase complex, soluble / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / response to oxygen levels / presynaptic active zone cytoplasmic component / Nitric oxide stimulates guanylate cyclase / relaxation of vascular associated smooth muscle / adenylate cyclase activity / blood circulation / cGMP-mediated signaling / nitric oxide-cGMP-mediated signaling / GABA-ergic synapse / Smooth Muscle Contraction / cellular response to nitric oxide / positive regulation of nitric oxide mediated signal transduction / nitric oxide mediated signal transduction / Hsp90 protein binding / regulation of blood pressure / signaling receptor activity / glutamatergic synapse / heme binding / protein-containing complex binding / GTP binding / metal ion binding / cytosol
Similarity search - Function
Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily ...Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Guanylate cyclase soluble subunit alpha-1 / Guanylate cyclase soluble subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsAllerston, C.K. / Berridge, G. / Chalk, R. / Cooper, C.D.O. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. ...Allerston, C.K. / Berridge, G. / Chalk, R. / Cooper, C.D.O. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2013
Title: Crystal structures of the catalytic domain of human soluble guanylate cyclase.
Authors: Allerston, C.K. / von Delft, F. / Gileadi, O.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate cyclase soluble subunit alpha-3
B: Guanylate cyclase soluble subunit beta-1
C: Guanylate cyclase soluble subunit alpha-3
D: Guanylate cyclase soluble subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,55811
Polymers99,0634
Non-polymers4957
Water7,764431
1
A: Guanylate cyclase soluble subunit alpha-3
B: Guanylate cyclase soluble subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8106
Polymers49,5322
Non-polymers2784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area16800 Å2
MethodPISA
2
C: Guanylate cyclase soluble subunit alpha-3
D: Guanylate cyclase soluble subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7485
Polymers49,5322
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-23 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.780, 139.100, 55.460
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Guanylate cyclase soluble subunit alpha-3 / GCS-alpha-3 / GCS-alpha-1 / Soluble guanylate cyclase large subunit


Mass: 24713.471 Da / Num. of mol.: 2
Fragment: soluble guanylate cyclase alpha-1 catalytic domain, UNP residues 468-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUC1A3, GUCSA3, GUCY1A1, GUCY1A3 / Plasmid: pNH-TrxT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Chaperones / References: UniProt: Q02108, guanylate cyclase
#2: Protein Guanylate cyclase soluble subunit beta-1 / GCS-beta-1 / Guanylate cyclase soluble subunit beta-3 / GCS-beta-3 / Soluble guanylate cyclase small subunit


Mass: 24818.244 Da / Num. of mol.: 2
Fragment: soluble guanylate cyclase beta-1 catalytic domain, UNP residues 408-619
Mutation: G476C, C541S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUCY1B3, GUC1B3, GUCSB3, GUCY1B1 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Chaperones / References: UniProt: Q02153, guanylate cyclase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M KH2PO4 20% PEG 8000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.968627 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968627 Å / Relative weight: 1
ReflectionResolution: 2.08→51.5 Å / Num. all: 47912 / Num. obs: 45874 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 36.79 Å2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.08→2.16 Å / Redundancy: 3.3 % / Num. unique all: 6967 / % possible all: 94.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→51.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.9389 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 2319 5.06 %RANDOM
Rwork0.1666 ---
all0.214 47912 --
obs0.1688 45859 99.5 %-
Displacement parametersBiso mean: 39.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.9288 Å20 Å2-0.2428 Å2
2--1.5788 Å20 Å2
3----3.5075 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.08→51.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 32 431 6267
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2762SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes915HARMONIC5
X-RAY DIFFRACTIONt_it6041HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies17HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7225SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6041HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8222HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion2.56
LS refinement shellResolution: 2.08→2.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2243 179 5.25 %
Rwork0.2045 3229 -
all0.2056 3408 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.22810.6339-0.18822.0501-0.09081.1452-0.1410.1333-0.1617-0.20220.0573-0.14310.11170.09180.0837-0.07380.0273-0.0011-0.07320.0095-0.093824.5106-34.1361-29.787
21.76160.42980.2051.91750.43351.66010.078-0.2505-0.13390.2437-0.06840.02970.0519-0.0319-0.0096-0.0670.00630.0113-0.09080.0346-0.07057.7879-28.0666-10.7044
32.6020.28470.13511.5740.28850.9436-0.0730.13150.1859-0.1440.00970.091-0.1425-0.05680.06330.00480.04870.0461-0.11970.0075-0.084.68637.2213-58.2945
42.1407-0.36850.12562.5425-0.68431.5228-0.0879-0.36720.11030.20860.0845-0.1871-0.1662-0.06850.0034-0.06010.0175-0.0162-0.0866-0.0384-0.113620.40521.3418-38.684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A470 - 661
2X-RAY DIFFRACTION2{ B|* }B413 - 608
3X-RAY DIFFRACTION3{ C|* }C470 - 661
4X-RAY DIFFRACTION4{ D|* }D412 - 607

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