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- EMDB-34627: Structure of human soluble guanylate cyclase in the NO+Rio state ... -

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Basic information

Entry
Database: EMDB / ID: EMD-34627
TitleStructure of human soluble guanylate cyclase in the NO+Rio state at 3.1 angstrom
Map data
Sample
  • Complex: human soluble guanylate cyclase
    • Protein or peptide: Guanylate cyclase soluble subunit alpha-1
    • Protein or peptide: Guanylate cyclase soluble subunit beta-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate
  • Ligand: NITRIC OXIDE
Keywordssoluble guanylate cyclase / SIGNALING PROTEIN
Function / homology
Function and homology information


retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / guanylate cyclase complex, soluble / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / presynaptic active zone cytoplasmic component / response to oxygen levels / Nitric oxide stimulates guanylate cyclase / nitric oxide binding ...retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / guanylate cyclase complex, soluble / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / presynaptic active zone cytoplasmic component / response to oxygen levels / Nitric oxide stimulates guanylate cyclase / nitric oxide binding / relaxation of vascular associated smooth muscle / adenylate cyclase activity / blood circulation / cGMP-mediated signaling / positive regulation of nitric oxide mediated signal transduction / nitric oxide mediated signal transduction / Smooth Muscle Contraction / nitric oxide-cGMP-mediated signaling / cellular response to nitric oxide / GABA-ergic synapse / Hsp90 protein binding / regulation of blood pressure / signaling receptor activity / heme binding / protein-containing complex binding / GTP binding / glutamatergic synapse / metal ion binding / cytosol
Similarity search - Function
Haem NO binding associated / Haem NO binding associated domain superfamily / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain ...Haem NO binding associated / Haem NO binding associated domain superfamily / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / 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: 3.1 Å
AuthorsChen L / Liu R
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31821091 China
National Natural Science Foundation of China (NSFC)31870833 China
CitationJournal: Nitric Oxide / Year: 2023
Title: NO binds to the distal site of haem in the fully activated soluble guanylate cyclase.
Authors: Rui Liu / Yunlu Kang / Lei Chen /
Abstract: Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO). The binding of NO to the haem of sGC induces a large conformational change in the enzyme and activates its cyclase ...Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO). The binding of NO to the haem of sGC induces a large conformational change in the enzyme and activates its cyclase activity. However, whether NO binds to the proximal site or the distal site of haem in the fully activated state remains under debate. Here, we present cryo-EM maps of sGC in the NO-activated state at high resolutions, allowing the observation of the density of NO. These cryo-EM maps show the binding of NO to the distal site of haem in the NO-activated state.
History
DepositionOct 28, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34627.png

Downloads & links

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Map

FileDownload / File: emd_34627.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 267.52 Å		1.05 Å/pix.
x 256 pix.
= 267.52 Å		1.05 Å/pix.
x 256 pix.
= 267.52 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-6.1099424 - 14.983826000000001
Average (Standard dev.)-0.0019091164 (±0.14464855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.52 Å
α=β=γ: 90.0 °

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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 cyclase
Components
  • Complex: human soluble guanylate cyclase
    • Protein or peptide: Guanylate cyclase soluble subunit alpha-1
    • Protein or peptide: Guanylate cyclase soluble subunit beta-1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate
  • Ligand: NITRIC OXIDE

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Supramolecule #1: human soluble guanylate cyclase

SupramoleculeName: human soluble guanylate cyclase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanylate cyclase soluble subunit alpha-1

MacromoleculeName: Guanylate cyclase soluble subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: guanylate cyclase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.566484 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFCTKLKDLK ITGECPFSLL APGQVPNESS EEAAGSSESC KATMPICQDI PEKNIQESLP QRKTSRSRVY LHTLAESICK LIFPEFERL NVALQRTLAK HKIKESRKSL EREDFEKTIA EQAVAAGVPV EVIKESLGEE VFKICYEEDE NILGVVGGTL K DFLNSFST ...String:
MFCTKLKDLK ITGECPFSLL APGQVPNESS EEAAGSSESC KATMPICQDI PEKNIQESLP QRKTSRSRVY LHTLAESICK LIFPEFERL NVALQRTLAK HKIKESRKSL EREDFEKTIA EQAVAAGVPV EVIKESLGEE VFKICYEEDE NILGVVGGTL K DFLNSFST LLKQSSHCQE AGKRGRLEDA SILCLDKEDD FLHVYYFFPK RTTSLILPGI IKAAAHVLYE TEVEVSLMPP CF HNDCSEF VNQPYLLYSV HMKSTKPSLS PSKPQSSLVI PTSLFCKTFP FHFMFDKDMT ILQFGNGIRR LMNRRDFQGK PNF EEYFEI LTPKINQTFS GIMTMLNMQF VVRVRRWDNS VKKSSRVMDL KGQMIYIVES SAILFLGSPC VDRLEDFTGR GLYL SDIPI HNALRDVVLI GEQARAQDGL KKRLGKLKAT LEQAHQALEE EKKKTVDLLC SIFPCEVAQQ LWQGQVVQAK KFSNV TMLF SDIVGFTAIC SQCSPLQVIT MLNALYTRFD QQCGELDVYK VETIGDAYCV AGGLHKESDT HAVQIALMAV KMMELS DEV MSPHGEPIKM RIGLHSGSVF AGVVGVKMPR YCLFGNNVTL ANKFESCSVP RKINVSPTTY RLLKDCPGFV FTPRSRE EL PPNFPSEIPG ICHFLDAYQQ GTNSKPCFQK KDVEDGNANF LGKASGID

UniProtKB: Guanylate cyclase soluble subunit alpha-1

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Macromolecule #2: Guanylate cyclase soluble subunit beta-1

MacromoleculeName: Guanylate cyclase soluble subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: guanylate cyclase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.59932 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYGFVNHALE LLVIRNYGPE VWEDIKKEAQ LDEEGQFLVR IIYDDSKTYD LVAAASKVLN LNAGEILQMF GKMFFVFCQE SGYDTILRV LGSNVREFLQ NLDALHDHLA TIYPGMRAPS FRCTDAEKGK GLILHYYSER EGLQDIVIGI IKTVAQQIHG T EIDMKVIQ ...String:
MYGFVNHALE LLVIRNYGPE VWEDIKKEAQ LDEEGQFLVR IIYDDSKTYD LVAAASKVLN LNAGEILQMF GKMFFVFCQE SGYDTILRV LGSNVREFLQ NLDALHDHLA TIYPGMRAPS FRCTDAEKGK GLILHYYSER EGLQDIVIGI IKTVAQQIHG T EIDMKVIQ QRNEECDHTQ FLIEEKESKE EDFYEDLDRF EENGTQESRI SPYTFCKAFP FHIIFDRDLV VTQCGNAIYR VL PQLQPGN CSLLSVFSLV RPHIDISFHG ILSHINTVFV LRSKEGLLDV EKLECEDELT GTEISCLRLK GQMIYLPEAD SIL FLCSPS VMNLDDLTRR GLYLSDIPLH DATRDLVLLG EQFREEYKLT QELEILTDRL QLTLRALEDE KKKTDTLLYS VLPP SVANE LRHKRPVPAK RYDNVTILFS GIVGFNAFCS KHASGEGAMK IVNLLNDLYT RFDTLTDSRK NPFVYKVETV GDKYM TVSG LPEPCIHHAR SICHLALDMM EIAGQVQVDG ESVQITIGIH TGEVVTGVIG QRMPRYCLFG NTVNLTSRTE TTGEKG KIN VSEYTYRCLM SPENSDPQFH LEHRGPVSMK GKKEPMQVWF LSRKNTGTEE TKQDDD

UniProtKB: Guanylate cyclase soluble subunit beta-1

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Macromolecule #3: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #6: methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazol...

MacromoleculeName: methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate
type: ligand / ID: 6 / Number of copies: 1 / Formula: GZO
Molecular weightTheoretical: 422.416 Da
Chemical component information

ChemComp-GZO:
methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate / medication*YM

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Macromolecule #7: NITRIC OXIDE

MacromoleculeName: NITRIC OXIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: NO
Molecular weightTheoretical: 30.006 Da
Chemical component information

ChemComp-NO:
NITRIC OXIDE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 330636
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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