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- EMDB-9885: Structure of human soluble guanylate cyclase in the NO activated state -

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Basic information

Entry
Database: EMDB / ID: EMD-9885
TitleStructure of human soluble guanylate cyclase in the NO activated state
Map data
Samplehuman soluble guanylate cyclaseSoluble guanylyl cyclase
  • (Guanylate cyclase soluble subunit ...) x 2
  • (ligand) x 3
Function / homology
Function and homology information


retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase complex, soluble / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cGMP biosynthetic process / guanylate cyclase / guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / blood circulation / relaxation of vascular associated smooth muscle / cGMP-mediated signaling ...retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase complex, soluble / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cGMP biosynthetic process / guanylate cyclase / guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / blood circulation / relaxation of vascular associated smooth muscle / cGMP-mediated signaling / presynaptic active zone / nitric oxide-cGMP-mediated signaling pathway / Smooth Muscle Contraction / GABA-ergic synapse / cellular response to nitric oxide / positive regulation of nitric oxide mediated signal transduction / nitric oxide mediated signal transduction / regulation of blood pressure / signaling receptor activity / glutamatergic synapse / GTP binding / heme binding / metal ion binding
Similarity search - Function
Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Heme NO-binding / Haem-NO-binding / H-NOX domain superfamily / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain ...Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Heme NO-binding / Haem-NO-binding / H-NOX domain superfamily / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Adenylyl cyclase class-3/4/guanylyl cyclase / Nucleotide cyclase
Similarity search - Domain/homology
Guanylate cyclase soluble subunit alpha-1 / Guanylate cyclase soluble subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen L / Kang Y / Liu R / Wu J-X
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
National Natural Science Foundation of China31821091 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31870833 China
CitationJournal: Nature / Year: 2019
Title: Structural insights into the mechanism of human soluble guanylate cyclase.
Authors: Yunlu Kang / Rui Liu / Jing-Xiang Wu / Lei Chen /
Abstract: Soluble guanylate cyclase (sGC) is the primary sensor of nitric oxide. It has a central role in nitric oxide signalling and has been implicated in many essential physiological processes and disease ...Soluble guanylate cyclase (sGC) is the primary sensor of nitric oxide. It has a central role in nitric oxide signalling and has been implicated in many essential physiological processes and disease conditions. The binding of nitric oxide boosts the enzymatic activity of sGC. However, the mechanism by which nitric oxide activates the enzyme is unclear. Here we report the cryo-electron microscopy structures of the human sGCα1β1 heterodimer in different functional states. These structures revealed that the transducer module bridges the nitric oxide sensor module and the catalytic module. Binding of nitric oxide to the β1 haem-nitric oxide and oxygen binding (H-NOX) domain triggers the structural rearrangement of the sensor module and a conformational switch of the transducer module from bending to straightening. The resulting movement of the N termini of the catalytic domains drives structural changes within the catalytic module, which in turn boost the enzymatic activity of sGC.
History
DepositionApr 8, 2019-
Header (metadata) releaseSep 4, 2019-
Map releaseSep 4, 2019-
UpdateOct 23, 2019-
Current statusOct 23, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jt2
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9885.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 250.8 Å
1.05 Å/pix.
x 240 pix.
= 250.8 Å
1.05 Å/pix.
x 240 pix.
= 250.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.105027266 - 0.21015477
Average (Standard dev.)0.0003341003 (±0.0037423703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 250.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z250.800250.800250.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-2600
NX/NY/NZ264044
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1050.2100.000

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Supplemental data

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Sample components

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Entire human soluble guanylate cyclase

EntireName: human soluble guanylate cyclaseSoluble guanylyl cyclase
Number of Components: 6

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Component #1: protein, human soluble guanylate cyclase

ProteinName: human soluble guanylate cyclaseSoluble guanylyl cyclase
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Guanylate cyclase soluble subunit alpha-1

ProteinName: Guanylate cyclase soluble subunit alpha-1 / Details: GenBank: AAH28384.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 77.566484 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Guanylate cyclase soluble subunit beta-1

ProteinName: Guanylate cyclase soluble subunit beta-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.59932 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #4: ligand, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

LigandName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.521208 kDa

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #6: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 50 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 497303
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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