7RQY: PDB entry 7RQY

Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an open state, class B. Determined by electron microscopy at 3.04 Å resolution. Released 1 Jun 2022.

Method: Electron microscopy
Resolution: 3.04 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 16,664
Mol. weight: 406.18 kDa
Ligands: 6OU, LBN, 6EU
Released: 1 Jun 2022

Explore 7RQY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RQY contains 116 α-helices and 36 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C and D: 29 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	204-211	8
α-helix	214-223	10
α-helix	251-257	7
α-helix	261-269	9
β-strand	280	1	1
β-strand	286	1	1
α-helix	287-293	7
α-helix	299-319	21
α-helix	336-343	8
α-helix	346-353	8
α-helix	363-365	3
β-strand	372-374	3	2
β-strand	377-379	3	2
β-strand	380-382	3	3
α-helix	395-400	6
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	469-499	31
α-helix	503-505	3
α-helix	506-509	4
α-helix	511-530	20
α-helix	537-550	14
α-helix	551-553	3
α-helix	555-558	4
α-helix	563-571	9
α-helix	572-576	5
α-helix	581-598	18
α-helix	630-641	12
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-690	16
α-helix	693-711	19
α-helix	713-719	7
β-strand	724-730	7	4
β-strand	736-741	6	4
β-strand	742-744	3	3
β-strand	747	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	protein	868	Rattus norvegicus	O35433 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7RQY_1 Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
MEQRASLDSEESESPPQENSCLDPPDRDPNCKPPPVKPHIFTTRSRTRLFGKGDSEEASP
LDCPYEEGGLASCPIITVSSVLTIQRPGDGPASVRPSSQDSVSAGEKPPRLYDRRSIFDA
VAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLHNGQNDTIALLLDVA
RKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGADVQAAANGDFFKKTK
GRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVD
NTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKIGVLAYILQREIHEP
ECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNR
LLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEIL
SVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVAS
MVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIE
DGKNNSLPMESTPHKCRGSACKPGNSYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFI
ILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAF
RSGKLLQVGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFSLRSG
RVSGRNWKNFALVPLLRDASTRDRHATQQEEVQLKHYTGSLKPEDAEVFKDSMVPGEKEN
SLEVLFQGPDYKDDDDKAHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
6OU	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…	C39 H76 N O8 P	8
LBN	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine	C42 H82 N O8 P	4
6EU	resiniferatoxin	C37 H40 O9	4

Primary citation

Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis. Kwon, D.H., Zhang, F., Fedor, J.G. et al. Nat Commun (2022) 13:2874-2874. DOI 10.1038/s41467-022-30602-2 · PubMed

Other PDB entries of the same protein (UniProt O35433 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SUI 1.95 Å, Crystal structure of ca2+-calmodulin in complex with a trpv1 c-terminal peptide
8U4D 2.2 Å, TRPV1 in nanodisc bound with PI-Br4, consensus structure
8U3A 2.3 Å, TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)
8U3C 2.3 Å, TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer)
8U43 2.4 Å, TRPV1 in nanodisc bound with PIP2-Br4
7L2P 2.6 Å, cryo-EM structure of unliganded minimal TRPV1
7L2H 2.63 Å, Cryo-EM structure of unliganded full-length TRPV1 at neutral pH
7LP9 2.63 Å, Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius
2PNN 2.7 Å, Crystal Structure of the Ankyrin Repeat Domain of Trpv1
9W4M 2.7 Å, ratTRPV1 bound with antagonist AMG517
7L2S 2.71 Å, cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-bound state
7MZ5 2.76 Å, Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state

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