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TitleClass 1 IP3-bound human type 3 1 4 5-inositol trisphosphate receptor
AuthorsHite RK, Paknejad N
MethodSingle Particle(Reported Resolution 3.33 Å)PDB:6dqn
EMDB image
Primary CitationStructural basis for the regulation of inositol trisphosphate receptors by Ca2+and IP3. Paknejad N, Hite RK Nat Struct Mol Biol (2018) PubMed DOI show all entries for this citation
StatusDepositedReleasedLast Update
REL2018-06-112018-08-012024-10-23

Name: human type 3 inositol 1,4,5-trisphosphate receptorSpecimenType: particle MW: 1.22 MDa pH: 8

Component Typesorganelle/cell component
Component Names

human type 3 inositol 1,4,5-trisphosphate receptor

Molecular Typesligand, protein
Molecule Names
  • D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Inositol 1,4,5-trisphosphate receptor type 3
  • ZINC ION
Sources

Homo sapiens ncbi:9606

Ligand IDs: ZN I3P

Specimen Preparation Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA 50 micromolar IP3

Vitrification Details: Blot for 2 seconds prior to freezing.

Selection Details: Movie frames were aligned with MotionCor2

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK IV
MicroscopeFEI TITAN KRIOS (300 kV)
Specimen HolderFEI TITAN KRIOS AUTOGRID HOLDER
DetectorGATAN K2 SUMMIT (4k x 4k)
Images Collected1801
Electron Dose61 (e/sq. Å)
Number of Particles38777
Imposed SymmetryC4
Reconstruction SoftwareFREALIGN
Fitting ProtocolAB INITIO MODEL

Details: Class 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor

Map File Size226 Mbytes
Voxel Dimensions (Å)1.088 x 1.088 x 1.088
Map Dimensions (voxels) 384 x 384 x 384
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -27.584Max 40.044Avg -0.009Std 1.073
Recommended Contour Level5.13 (4.8 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-7981.xml emd-7981.cif.gz
Primary Mapemd_7981.map.gz (226 Mbytes)
Imagesemd_7981.png
Fitted PDB6dqn


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_7981_full_validation.pdf.gz
wwPDB Model Validation Report6dqn_full_validation.pdf.gz
View EMDB map entry EMD-7981: EMDB PDBj 3Dbionotes
View associated model PDB 6dqn: RCSB-PDB PDBe PDBj