7L2U: DkTx-bound minimal TRPV1 in open state

cryo-EM structure of DkTx-bound minimal TRPV1 in open state. Determined by electron microscopy at 3.47 Å resolution. Released 22 Sept 2021.

Method: Electron microscopy
Resolution: 3.47 Å
Organisms: Rattus norvegicus, Cyriopagopus schmidti
Chains: 6
Atoms: 18,817
Mol. weight: 313.86 kDa
Ligands: XKP, XJ7
Released: 22 Sept 2021

Explore 7L2U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L2U contains 121 α-helices and 48 β-strands across 6 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.

Chain A: 29 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	193	1	1
β-strand	203	1	1
α-helix	204-210	7
α-helix	214-222	9
α-helix	234-236	3
α-helix	251-257	7
α-helix	261-268	8
α-helix	287-293	7
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-352	7
α-helix	363-365	3
β-strand	368-373	6	2
β-strand	377-383	7	2
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	463-464	2
α-helix	469-499	31
α-helix	505-507	3
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	560-572	13
α-helix	573-577	5
α-helix	578-598	21
α-helix	630-641	12
α-helix	659-681	23
α-helix	688-711	24
α-helix	717-719	3
β-strand	726	1	3
β-strand	738	1	3
β-strand	741-747	7	2

Chain B: 29 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	204-210	7
α-helix	214-222	9
α-helix	234-236	3
α-helix	251-257	7
α-helix	261-269	9
α-helix	287-293	7
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-352	7
α-helix	363-365	3
β-strand	368-373	6	16
β-strand	377-383	7	16
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	464-466	3
α-helix	469-497	29
α-helix	505-507	3
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	560-572	13
α-helix	573-577	5
α-helix	578-598	21
α-helix	630-642	13
α-helix	659-680	22
α-helix	681-684	4
α-helix	689-710	22
β-strand	726	1	17
β-strand	738	1	17
β-strand	741-747	7	16

Chain C: 26 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	193	1	18
β-strand	203	1	18
α-helix	204-210	7
α-helix	214-222	9
α-helix	251-257	7
α-helix	261-269	9
α-helix	287-293	7
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-353	8
α-helix	363-365	3
β-strand	368-373	6	19
β-strand	377-383	7	19
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	469-499	31
α-helix	503-508	6
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	560-575	16
α-helix	577-598	22
α-helix	630-641	12
α-helix	659-682	24
α-helix	689-692	4
α-helix	696-711	16
β-strand	726	1	20
β-strand	738	1	20
β-strand	741-747	7	19

Chain D: 29 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	204-210	7
α-helix	215-222	8
α-helix	234-236	3
α-helix	251-257	7
α-helix	261-269	9
α-helix	287-293	7
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-352	7
α-helix	363-365	3
β-strand	368-373	6	21
β-strand	377-383	7	21
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	463-464	2
α-helix	469-499	31
α-helix	503-506	4
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	560-575	16
α-helix	577-598	22
α-helix	630-641	12
α-helix	659-681	23
α-helix	682-684	3
α-helix	689-692	4
α-helix	695-710	16
β-strand	726	1	22
β-strand	738	1	22
β-strand	741-747	7	21

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	10
β-strand	8	1	11
β-strand	15	1	10
β-strand	21-22	2	12
β-strand	30	1	11
β-strand	32-33	2	12
α-helix	38-40	3
β-strand	45	1	13
β-strand	50	1	14
α-helix	51	1
β-strand	57	1	13
β-strand	61-62	2	15
β-strand	70	1	14
β-strand	72-73	2	15

Chain F: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
β-strand	8	1	5
β-strand	15	1	4
β-strand	21-22	2	6
β-strand	30	1	5
β-strand	32-33	2	6
α-helix	34-36	3
α-helix	38-40	3
β-strand	45	1	7
α-helix	46	1
β-strand	50	1	8
α-helix	51	1
α-helix	56	1
β-strand	57	1	7
α-helix	58	1
β-strand	62	1	9
β-strand	70	1	8
β-strand	72	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	protein	637	Rattus norvegicus	O35433 (AlphaFold model)
Tau-theraphotoxin-Hs1a	E, F	protein	76	Cyriopagopus schmidti	P0CH43 (AlphaFold model)

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

>7L2U_1 Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
GAMGSRLYDRRSIFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLN
LHNGQNDTIALLLDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENG
ADVQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVG
NTVLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSG
KIGVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSS
ETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYK
LKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFML
VSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVY
LVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYV
ILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQ
VGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPG

Sequence of entity 2 (E, F), FASTA

>7L2U_2 Tau-theraphotoxin-Hs1a (chains E, F)
MDCAKEGEVCSWGKKCCDLDNFYCPMEFIPHCKKYKPYVPVTTNCAKEGEVCGWGSKCCH
GLDCPLAFIPYCEKYR

Ligands and cofactors

ID	Name	Formula	Copies
XKP	(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphahept…	C23 H46 N O8 P	4
XJ7	(2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydrox…	C26 H49 O13 P	4

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

Primary citation

Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Zhang, K., Julius, D., Cheng, Y. Cell (2021) 184:5138-5150.e12. DOI 10.1016/j.cell.2021.08.012 · 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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