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- PDB-9u3u: Cryo-EM structure of human AC9_delC -

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Basic information

Entry
Database: PDB / ID: 9u3u
TitleCryo-EM structure of human AC9_delC
ComponentsAdenylate cyclase type 9,Protein M2-1
KeywordsMEMBRANE PROTEIN / enzyme
Function / homology
Function and homology information


Adenylate cyclase activating pathway / regulation of viral transcription / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / PKA activation / viral transcription / PKA activation in glucagon signalling / Hedgehog 'off' state / Adenylate cyclase inhibitory pathway ...Adenylate cyclase activating pathway / regulation of viral transcription / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / PKA activation / viral transcription / PKA activation in glucagon signalling / Hedgehog 'off' state / Adenylate cyclase inhibitory pathway / adenylate cyclase-activating adrenergic receptor signaling pathway / FCGR3A-mediated IL10 synthesis / bioluminescence / transcription antitermination / generation of precursor metabolites and energy / virion component / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / in utero embryonic development / host cell cytoplasm / intracellular signal transduction / ciliary basal body / cilium / axon / dendrite / host cell nucleus / structural molecule activity / signal transduction / zinc ion binding / ATP binding / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Nucleotide cyclase / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Protein M2-1 / Adenylate cyclase type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSuzuki, S. / Nomura, R. / Suzuki, H. / Nishikawa, K. / Fujiyoshi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00451 Japan
Japan Society for the Promotion of Science (JSPS)20K17245 Japan
CitationJournal: To Be Published
Title: Activation mechanism of human adenylyl cyclase 9 observed by cryo-electron microscopy
Authors: Nomura, S. / Suzuki, S. / Nishikawa, K. / Suzuki, H. / Fujiyoshi, Y.
History
DepositionMar 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate cyclase type 9,Protein M2-1


Theoretical massNumber of molelcules
Total (without water)181,5601
Polymers181,5601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Adenylate cyclase type 9,Protein M2-1 / ATP pyrophosphate-lyase 9 / Adenylate cyclase type IX / ACIX / Adenylyl cyclase 9 / AC9 / Envelope- ...ATP pyrophosphate-lyase 9 / Adenylate cyclase type IX / ACIX / Adenylyl cyclase 9 / AC9 / Envelope-associated 22 kDa protein / Transcription antitermination factor M2-1


Mass: 181560.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Human respiratory syncytial virus
Gene: ADCY9, KIAA0520, M2-1mGFP / Production host: Homo sapiens (human)
References: UniProt: O60503, UniProt: A0A1S5SHT2, adenylate cyclase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hADCY9 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132622 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026852
ELECTRON MICROSCOPYf_angle_d0.4899283
ELECTRON MICROSCOPYf_dihedral_angle_d3.665911
ELECTRON MICROSCOPYf_chiral_restr0.0361064
ELECTRON MICROSCOPYf_plane_restr0.0031159

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