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- PDB-4ni2: Crystal structure of the heterodimeric catalytic domain of wild-t... -

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Basic information

Entry
Database: PDB / ID: 4ni2
TitleCrystal structure of the heterodimeric catalytic domain of wild-type human soluble guanylate cyclase
Components
  • Guanylate cyclase soluble subunit alpha-3
  • Guanylate cyclase soluble subunit beta-1
KeywordsLYASE / heterodimeric / cGMP biosynthesis / nitric oxide / cyclase / GTP-binding / metal-binding / nucleotide binding / CYTOSOL
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 / molecular replacement / Resolution: 1.9 Å
AuthorsSeeger, F. / Williams, G.J. / Tainer, J.A. / Garcin, E.D.
CitationJournal: Biochemistry / Year: 2014
Title: Interfacial residues promote an optimal alignment of the catalytic center in human soluble guanylate cyclase: heterodimerization is required but not sufficient for activity.
Authors: Seeger, F. / Quintyn, R. / Tanimoto, A. / Williams, G.J. / Tainer, J.A. / Wysocki, V.H. / Garcin, E.D.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7268
Polymers45,3532
Non-polymers3726
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-19 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.545, 55.834, 139.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 21786.258 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 468-661
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) pGRO7 chaperone / 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: 23567.053 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 408-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUC1B3, GUCSB3, GUCY1B1, GUCY1B3 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pGRO7 chaperone / References: UniProt: Q02153, guanylate cyclase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% tryptone, 50mM HEPES pH 7.0, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.9→69.7 Å / Num. all: 31908 / Num. obs: 31270 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UVJ

3uvj


Resolution: 1.9→69.684 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.21 / σ(F): 1.37 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 1573 5.04 %
Rwork0.16 --
obs0.162 31205 99.73 %
all-31289 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 24 310 3330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043093
X-RAY DIFFRACTIONf_angle_d0.8174180
X-RAY DIFFRACTIONf_dihedral_angle_d12.2421135
X-RAY DIFFRACTIONf_chiral_restr0.03472
X-RAY DIFFRACTIONf_plane_restr0.003539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96140.25311220.23922608X-RAY DIFFRACTION97
1.9614-2.03150.23621370.20542645X-RAY DIFFRACTION100
2.0315-2.11280.23371530.17482643X-RAY DIFFRACTION100
2.1128-2.2090.20961390.16682657X-RAY DIFFRACTION100
2.209-2.32540.23041380.16832686X-RAY DIFFRACTION100
2.3254-2.47110.20141630.16072653X-RAY DIFFRACTION100
2.4711-2.66190.20781220.16312703X-RAY DIFFRACTION100
2.6619-2.92980.20081450.16642700X-RAY DIFFRACTION100
2.9298-3.35380.17691560.14972699X-RAY DIFFRACTION100
3.3538-4.22530.18381560.14312744X-RAY DIFFRACTION100
4.2253-69.73090.1981420.15322894X-RAY DIFFRACTION100
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)
10.28420.2287-0.33410.34840.01140.746-0.01540.0716-0.0439-0.0710.09340.207-0.0494-0.0607-00.23180.0099-0.01480.20440.03330.243511.751236.12410.607
20.0902-0.08230.07020.0714-0.0630.0510.0936-0.1-0.483-0.01930.0149-0.19640.0919-0.2378-0.00020.23250.0206-0.00470.30030.04760.323834.653923.194418.7189
31.30210.53430.43750.6711-0.09730.27880.1670.4301-0.7184-0.3037-0.0237-0.27110.41060.0150.01840.2843-0.01560.07350.2899-0.04150.243226.665622.57275.3212
40.02620.0732-0.07190.2151-0.2050.192-0.12240.1031-0.0677-0.2120.1452-0.1111-0.2126-0.0860.00010.2603-0.0132-0.02660.257-0.00610.209718.544631.01867.7119
50.12930.0885-0.16320.0938-0.08070.2144-0.18540.0219-0.36680.06130.30940.0566-0.254-0.09790.00010.25290.0038-0.07940.28030.02710.25397.024531.28995.1817
60.1530.16230.14010.24470.24190.23960.14350.3795-0.1682-0.1992-0.0405-0.0460.1451-0.1520.00220.23280.00260.01070.2236-0.040.228813.98618.9168.9828
70.86670.6387-0.36420.4964-0.14530.3808-0.12260.0258-0.2562-0.03720.0255-0.0503-0.0329-0.0196-0.05850.23350.01050.02940.1840.01880.240319.919725.3914.155
80.26580.05690.150.3967-0.06490.1561-0.06870.21570.2718-0.2383-0.01250.2143-0.53490.2412-0.25310.3755-0.0187-0.05730.26840.02980.19515.703439.64484.4598
90.090.1105-0.13170.1279-0.15740.17950.1004-0.2094-0.05770.0079-0.1063-0.1806-0.14250.0497-0.00020.25140.0159-0.01890.25530.0040.228513.410832.230821.6041
100.2215-0.0875-0.40560.3661-0.00910.8369-0.0693-0.0569-0.245-0.0116-0.00720.20280.0294-0.114800.1870.0074-0.00880.21290.00250.26166.05319.507918.5856
110.159-0.08070.04120.05250.01390.1112-0.0608-0.63690.0990.28270.1509-0.2883-0.2681-0.39460.00650.32150.05880.02450.3178-0.01370.27588.432326.482829.9482
120.54240.2666-0.07750.14830.09270.8243-0.0282-0.1408-0.19870.1214-0.0230.06940.1789-0.40430.0710.19750.02870.00960.27490.01170.27514.674520.925920.9838
130.2960.409-0.20120.5884-0.27140.47120.05330.05120.1313-0.1491-0.0312-0.2870.0870.0631-0.01350.24720.03280.04770.18680.00130.178636.710937.532915.5021
140.1227-0.06330.13610.5705-0.12320.14710.11140.14470.27740.08820.16590.60210.20440.32550.00310.26550.03040.02940.3140.04040.37348.923550.724515.9741
150.20340.2305-0.17020.3155-0.33150.3824-0.25470.34340.6348-0.38440.0508-0.0127-0.0004-0.1388-0.00360.28370.02120.01480.25980.02690.266422.082654.847610.8776
160.8596-0.46470.04271.2125-0.82170.99680.09310.09060.1943-0.217-0.1173-0.16750.00070.1236-0.00060.21760.0110.04510.19650.02360.217835.685949.041315.9582
170.61360.64560.17720.73040.30490.26880.0163-0.07630.2399-0.01360.0013-0.06620.03590.05310.00640.20130.0140.02040.17760.0280.186826.500347.692918.9428
180.2368-0.1156-0.06770.05120.03070.0196-0.11270.2934-0.0879-0.499-0.1223-0.01220.37420.203-0.0850.43310.01990.02190.24980.00750.147630.823833.07934.8945
190.0383-0.0164-0.06930.1496-0.22530.4807-0.02940.0196-0.1215-0.01010.02210.20570.0519-0.0229-0.00020.19090.00680.01410.2002-0.00920.188226.322440.93125.456
200.9998-0.2284-0.01150.37880.56231.90860.0523-0.28330.04530.1231-0.021-0.15580.04030.06240.00220.2162-0.0029-0.00120.22650.00380.187735.655944.767932.053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 471 through 487 )
2X-RAY DIFFRACTION2chain 'A' and (resid 488 through 498 )
3X-RAY DIFFRACTION3chain 'A' and (resid 499 through 519 )
4X-RAY DIFFRACTION4chain 'A' and (resid 520 through 532 )
5X-RAY DIFFRACTION5chain 'A' and (resid 533 through 544 )
6X-RAY DIFFRACTION6chain 'A' and (resid 545 through 562 )
7X-RAY DIFFRACTION7chain 'A' and (resid 563 through 587 )
8X-RAY DIFFRACTION8chain 'A' and (resid 588 through 598 )
9X-RAY DIFFRACTION9chain 'A' and (resid 599 through 609 )
10X-RAY DIFFRACTION10chain 'A' and (resid 610 through 636 )
11X-RAY DIFFRACTION11chain 'A' and (resid 637 through 646 )
12X-RAY DIFFRACTION12chain 'A' and (resid 647 through 662 )
13X-RAY DIFFRACTION13chain 'B' and (resid 411 through 427 )
14X-RAY DIFFRACTION14chain 'B' and (resid 428 through 442 )
15X-RAY DIFFRACTION15chain 'B' and (resid 443 through 461 )
16X-RAY DIFFRACTION16chain 'B' and (resid 462 through 509 )
17X-RAY DIFFRACTION17chain 'B' and (resid 510 through 533 )
18X-RAY DIFFRACTION18chain 'B' and (resid 534 through 544 )
19X-RAY DIFFRACTION19chain 'B' and (resid 545 through 561 )
20X-RAY DIFFRACTION20chain 'B' and (resid 562 through 608 )

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