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- PDB-9j05: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue -

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Basic information

Entry
Database: PDB / ID: 9j05
TitleApo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
Components
  • Antibody 1b3 Fab Heavy chain
  • Antibody 1b3 Fab Light chain
  • P2Y purinoceptor 14,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / Complex / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


G protein-coupled UDP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / hematopoietic stem cell homeostasis / electron transport chain / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding ...G protein-coupled UDP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / hematopoietic stem cell homeostasis / electron transport chain / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
P2Y14 purinoceptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / P2Y purinoceptor 14
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, T.X. / Tang, W.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
Authors: Wang, T.X. / Tang, W.Q.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 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: P2Y purinoceptor 14,Soluble cytochrome b562
B: Antibody 1b3 Fab Heavy chain
C: Antibody 1b3 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)116,5573
Polymers116,5573
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 P2Y purinoceptor 14,Soluble cytochrome b562 / P2Y14 purinergic receptor， / P2Y14 / G-protein coupled receptor 105 / UDP-glucose receptor / ...P2Y14 purinergic receptor， / P2Y14 / G-protein coupled receptor 105 / UDP-glucose receptor / Cytochrome b-562


Mass: 58084.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: P2RY14, GPR105, KIAA0001, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15391, UniProt: P0ABE7
#2: Antibody Antibody 1b3 Fab Heavy chain


Mass: 30704.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody Antibody 1b3 Fab Light chain


Mass: 27768.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
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: Apo state purinergic receptor P2Y14-BRIL/PPTN/1B3 Fab-4/9Glue
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88888 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046049
ELECTRON MICROSCOPYf_angle_d0.6288242
ELECTRON MICROSCOPYf_dihedral_angle_d4.872850
ELECTRON MICROSCOPYf_chiral_restr0.041954
ELECTRON MICROSCOPYf_plane_restr0.0051043

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