[English] 日本語
Yorodumi
- EMDB-20283: Active State of Manduca sexta soluble Guanylate Cyclase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20283
TitleActive State of Manduca sexta soluble Guanylate Cyclase
Map dataMap of the Active Ms sGC dimer
Sample
  • Complex: Active state of heterodimeric Ms sGC
    • Protein or peptide: Soluble guanylyl cyclase alpha-1 subunit
    • Protein or peptide: Soluble guanylyl cyclase beta-1 subunit
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsNitric oxide / cyclase / H-NOX / stimulator / SIGNALING PROTEIN
Function / homology
Function and homology information


guanylate cyclase / guanylate cyclase complex, soluble / guanylate cyclase activity / response to oxygen levels / cGMP-mediated signaling / heme binding / GTP binding
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 / 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 domain superfamily / Haem NO binding associated / 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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
guanylate cyclase / Guanylate cyclase soluble subunit beta-1
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsYokom AL / Horst BG
CitationJournal: Elife / Year: 2019
Title: Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy.
Authors: Benjamin G Horst / Adam L Yokom / Daniel J Rosenberg / Kyle L Morris / Michal Hammel / James H Hurley / Michael A Marletta /
Abstract: Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length sGC in both inactive and active states ...Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.
History
DepositionJun 11, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseOct 23, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6pat
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20283.png

Downloads & links

-
Map

FileDownload / File: emd_20283.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the Active Ms sGC dimer
Voxel sizeX=Y=Z: 1.137 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-2.0826836 - 3.3797805
Average (Standard dev.)0.003689861 (±0.061063442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 291.072 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1371.1371.137
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z291.072291.072291.072
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.0833.3800.004

-
Supplemental data

-
Half map: Half Map 2 of the Active Ms sGC

Fileemd_20283_half_map_1.map
AnnotationHalf Map 2 of the Active Ms sGC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 1 of the Active Ms sGC dimer

Fileemd_20283_half_map_2.map
AnnotationHalf Map 1 of the Active Ms sGC dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Active state of heterodimeric Ms sGC

EntireName: Active state of heterodimeric Ms sGC
Components
  • Complex: Active state of heterodimeric Ms sGC
    • Protein or peptide: Soluble guanylyl cyclase alpha-1 subunit
    • Protein or peptide: Soluble guanylyl cyclase beta-1 subunit
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

-
Supramolecule #1: Active state of heterodimeric Ms sGC

SupramoleculeName: Active state of heterodimeric Ms sGC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Manduca sexta (tobacco hornworm)

-
Macromolecule #1: Soluble guanylyl cyclase alpha-1 subunit

MacromoleculeName: Soluble guanylyl cyclase alpha-1 subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Manduca sexta (tobacco hornworm)
Molecular weightTheoretical: 78.598727 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
SequenceString: MTCPFRRASS QHQFANGGSS APKKPEFRSR TSSVHLTGPE EEDGERNTLT LKHMSEALQL LTAPSNECLH AAVTSLTKNQ SDHYHKYNC LRRLPDDVKT CRNYAYLQEI YDAVRATDSV NTKDFMAKLG EYLILTAFSH NCRLERAFKC LGTNLTEFLT T LDSVHDVL ...String:
MTCPFRRASS QHQFANGGSS APKKPEFRSR TSSVHLTGPE EEDGERNTLT LKHMSEALQL LTAPSNECLH AAVTSLTKNQ SDHYHKYNC LRRLPDDVKT CRNYAYLQEI YDAVRATDSV NTKDFMAKLG EYLILTAFSH NCRLERAFKC LGTNLTEFLT T LDSVHDVL HDQDTPLKDE TMEYEANFVC TTSQEGKIQL HLTTESEPVA YLLVGSLKAI AKRLYDTQTD IRLRSYTNDP RR FRYEINA VPLHQKSKED SCELVNEAAS VATSTKVTDL KIGVASFCKA FPWHFITDKR LELVQLGAGF MRLFGTHLAT HGS SLGTYF RLLRPRGVPL DFREILKRVN TPFMFCLKMP GSTALAEGLE IKGQMVFCAE SDSLLFVGSP FLDGLEGLTG RGLF ISDIP LHDATRDVIL VGEQARAQDG LRRRMDKLKN SIEEASKAVD KEREKNVSLL HLIFPPHIAK RLWLGEKIEA KSHDD VTML FSDIVGFTSI CATATPMMVI AMLEDLYSVF DIFCEELDVY KVETIGDAYC VASGLHRKVE THAPQIAWMA LRMVET CAQ HLTHEGNPIK MRIGLHTGTV LAGVVGKTML KYCLFGHNVT LANKFESGSE PLKINVSPTT YEWLIKFPGF DMEPRDR SC LPNSFPKDIH GTCYFLHKYT HPGTDPGEPQ VKHIREALKD YGIGQANSTD VDTEEPT

UniProtKB: guanylate cyclase

-
Macromolecule #2: Soluble guanylyl cyclase beta-1 subunit

MacromoleculeName: Soluble guanylyl cyclase beta-1 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Manduca sexta (tobacco hornworm)
Molecular weightTheoretical: 68.182 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
SequenceString: MYGFVNYALE LLVMKTFDEE TWETIKKKAD VAMEGSFLVR QIYEDEITYN LITAAVEVLQ IPADAILELF GKTFFEFCQD SGYDKILQV LGATPRDFLQ NLDGLHDHLG TLYPGMRSPS FRCTERPEDG ALVLHYYSDR PGLEHIVIGI VKTVASKLHN T EVKVEILK ...String:
MYGFVNYALE LLVMKTFDEE TWETIKKKAD VAMEGSFLVR QIYEDEITYN LITAAVEVLQ IPADAILELF GKTFFEFCQD SGYDKILQV LGATPRDFLQ NLDGLHDHLG TLYPGMRSPS FRCTERPEDG ALVLHYYSDR PGLEHIVIGI VKTVASKLHN T EVKVEILK TKEECDHVQF LITETSTTGR VSAPEIAEIE TLSLEPKVSP ATFCRVFPFH LMFDRDLNIV QAGRTVSRLL PR VTRPGCK ITDVLDTVRP HLEMTFANVL AHINTVYVLK TKPEEMSVTD PHEEIASLRL KGQMLYIPET DVVVFQCYPS VTN LDDLTR RGLCIADIPL HDATRDLVLM SEQFEADYKL TQNLEVLTDK LQQTFRELEL EKQKTDRLLY SVLPISVATE LRHR RPVPA RRYDTVTLLF SGIVGFANYC ARNSDHKGAM KIVRMLNDLY TAFDVLTDPK RNPNVYKVET VGDKYMAVSG LPEYE VAHA KHISLLALDM MDLSQTVTVD GEPVGITIGI HSGEVVTGVI GHRMPRYCLF GNTVNLTSRC ETTGVPGTIN VSEDTY NYL MREDNHDEQF ELTYRGHVTM KGKAEPMQTW FLTRKIH

UniProtKB: Guanylate cyclase soluble subunit beta-1

-
Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40469
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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://pdbjlvh1.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