7LP9: Full-length TRPV1 at 4 degrees Celsius

Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius. Determined by electron microscopy at 2.63 Å resolution. Released 28 Jul 2021.

Method: Electron microscopy
Resolution: 2.63 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 20,977
Mol. weight: 427.65 kDa
Ligands: YFP, 6OU, LBN, T7X
Released: 28 Jul 2021

Explore 7LP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LP9 contains 140 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 and C: 35 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	114-122	9
α-helix	129-139	11
α-helix	146-148	3
α-helix	157-163	7
β-strand	166	1	1
β-strand	169	1	1
α-helix	172-182	11
α-helix	186-190	5
β-strand	193	1	2
β-strand	203	1	2
α-helix	204-210	7
α-helix	214-222	9
α-helix	251-257	7
α-helix	261-268	8
α-helix	274-276	3
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-353	8
β-strand	368-373	6	3
β-strand	377-382	6	3
α-helix	395-400	6
α-helix	412-414	3
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	463-465	3
α-helix	469-499	31
α-helix	503-508	6
α-helix	511-531	21
α-helix	537-551	15
α-helix	552-558	7
α-helix	560-572	13
α-helix	573-577	5
α-helix	578-598	21
α-helix	630-641	12
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-688	14
α-helix	690-711	22
β-strand	724-730	7	4
β-strand	736-741	6	4
β-strand	742-747	6	3

Chain D: 35 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	114-122	9
α-helix	129-139	11
α-helix	146-148	3
α-helix	157-163	7
β-strand	166	1	13
β-strand	169	1	13
α-helix	172-182	11
α-helix	186-190	5
β-strand	193	1	14
β-strand	203	1	14
α-helix	204-210	7
α-helix	214-222	9
α-helix	251-257	7
α-helix	261-269	9
α-helix	274-276	3
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-353	8
β-strand	368-373	6	15
β-strand	377-382	6	15
α-helix	395-400	6
α-helix	412-414	3
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	463-465	3
α-helix	469-499	31
α-helix	503-508	6
α-helix	511-531	21
α-helix	537-551	15
α-helix	552-558	7
α-helix	560-572	13
α-helix	573-577	5
α-helix	578-598	21
α-helix	630-641	12
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-688	14
α-helix	690-711	22
β-strand	724-730	7	16
β-strand	736-741	6	16
β-strand	742-747	6	15

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

>7LP9_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
YFP	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol	C40 H77 O10 P	4
6OU	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…	C39 H76 N O8 P	28
LBN	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine	C42 H82 N O8 P	8
T7X	Phosphatidylinositol	C47 H83 O13 P	4

Water and common crystallization additives (NA) are not listed.

Primary citation

Heat-dependent opening of TRPV1 in the presence of capsaicin. Kwon, D.H., Zhang, F., Suo, Y. et al. Nat Struct Mol Biol (2021) 28:554-563. DOI 10.1038/s41594-021-00616-3 · 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
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
9W4T 2.87 Å, ratTRPV1 bound with antagonist AMG9810

Browse structure collections

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