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TitleOpen-state cryo-EM structure of full-length human TRPV4 in complex with agonist 4a-PDD
AuthorsTalyzina IA, Nadezhdin KD, Neuberger A, Sobolevsky AI
MethodSingle Particle(Reported Resolution 3.35 Å)PDB:8t1d
EMDB image
Primary CitationStructure of human TRPV4 in complex with GTPase RhoA. Nadezhdin KD, Talyzina IA, Parthasarathy A, Neuberger A, Zhang DX, Sobolevsky AI Nat Commun (2023) PubMed DOI show all entries for this citation
Funding SourceGerman Research Foundation (DFG), NIH National Heart, Lung, and Blood Institute (NIH/NHLBI), NIH National Cancer Institute (NIH/NCI), NIH National Institute of Neurological Disorders and Stroke (NIH/NINDS), NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)
StatusDepositedReleasedLast Update
REL2023-06-022023-07-052024-11-06

Name: full-length human TRPV4 in complex with agonist 4a-PDDSpecimenType: particle MW: 0.51 MDa pH: 8

Component Typescomplex
Component Names

full-length human TRPV4 in complex with agonist 4a-PDD

Molecular Typesligand, protein
Molecule Names
  • (1aR,1bS,4aS,7aS,7bS,8R,9R,9aS)-9a-(decanoyloxy)-4a,7b-dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1a,1b,4,4a,5,7a,7b,8,9,9a-decahydro-1H-cyclopropa[3,4]benzo[1,2-e]azulen-9-yl decanoate
  • Transient receptor potential cation channel subfamily V member 4/Enhanced green fluorescent protein chimera
Sources

Human betaherpesvirus 5 ncbi:10359

Homo sapiens ncbi:9606

Ligand IDs: XS9

Specimen Preparation Details: human TRPV4

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK IV
MicroscopeTFS KRIOS (300 kV)
DetectorGATAN K3 (6k x 4k)
Images Collected15624
Electron Dose60 (e/sq. Å)
Number of Particles80823
Map File Size131 Mbytes
Voxel Dimensions (Å)0.7888 x 0.7888 x 0.7888
Map Dimensions (voxels) 320 x 320 x 320
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -0.219Max 0.323Avg 0.001Std 0.01
Recommended Contour Level0.045 (4.4 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-40960.xml emd-40960.cif.gz
Primary Mapemd_40960.map.gz (131 Mbytes)
Imagesemd_40960.png
FSC Curvesemd_40960_fsc.xml
Half Maps
emd_40960_half_map_2.map.gz
emd_40960_half_map_1.map.gz
Fitted PDB8t1d


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_40960_full_validation.pdf.gz
wwPDB Model Validation Report8t1d_full_validation.pdf.gz
View EMDB map entry EMD-40960: EMDB PDBj 3Dbionotes
View associated model PDB 8t1d: RCSB-PDB PDBe PDBj