7L2M: DkTx/RTX-bound full-length TRPV1

Cryo-EM structure of DkTx/RTX-bound full-length TRPV1. Determined by electron microscopy at 3.84 Å resolution. Released 22 Sept 2021.

Method: Electron microscopy
Resolution: 3.84 Å
Organisms: Rattus norvegicus, Cyriopagopus schmidti
Chains: 6
Atoms: 15,981
Mol. weight: 401.26 kDa
Ligands: 6EU
Released: 22 Sept 2021

Explore 7L2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L2M contains 93 α-helices and 36 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: 22 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	287-294	8
α-helix	299-319	21
α-helix	336-343	8
α-helix	346-352	7
α-helix	363-365	3
β-strand	368-373	6	1
β-strand	377-382	6	1
α-helix	396-399	4
α-helix	409-412	4
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	464-466	3
α-helix	469-499	31
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	564-574	11
α-helix	577-598	22
α-helix	630-641	12
α-helix	656-667	12
α-helix	668-674	7
α-helix	675-688	14
α-helix	693-711	19
β-strand	742-747	6	1

Chains B, C and D: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	287-294	8
α-helix	299-319	21
α-helix	336-343	8
α-helix	346-352	7
β-strand	368-373	6	4
β-strand	377-382	6	4
α-helix	396-399	4
α-helix	409-412	4
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	464-466	3
α-helix	469-499	31
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	564-575	12
α-helix	577-598	22
α-helix	630-641	12
α-helix	656-667	12
α-helix	668-674	7
α-helix	675-688	14
α-helix	693-711	19
β-strand	742-747	6	4

Chain E: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4	1
β-strand	8	1	6
α-helix	14	1
β-strand	15	1	5
β-strand	21-22	2	7
β-strand	30	1	6
β-strand	32-33	2	7
β-strand	45	1	8
β-strand	50	1	9
α-helix	56	1
β-strand	57	1	8
α-helix	58	1
β-strand	61-62	2	10
β-strand	70	1	9
β-strand	72-73	2	10

Chain F: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	11
α-helix	4	1
β-strand	8	1	12
α-helix	14	1
β-strand	15	1	11
β-strand	21-22	2	13
β-strand	30	1	12
β-strand	32-33	2	13
β-strand	45	1	14
β-strand	50	1	15
α-helix	56	1
β-strand	57	1	14
α-helix	58	1
β-strand	62	1	16
β-strand	70	1	15
β-strand	72	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	protein	842	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

>7L2M_1 Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
GAMGSEQRASLDSEESESPPQENSCLDPPDRDPNCKPPPVKPHIFTTRSRTRLFGKGDSE
EASPLDCPYEEGGLASCPIITVSSVLTIQRPGDGPASVRPSSQDSVSAGEKPPRLYDRRS
IFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLHNGQNDTIALL
LDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGADVQAAANGDFF
KKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVAD
NTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKIGVLAYILQRE
IHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVE
PLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVT
GEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKE
YVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVV
TLIEDGKNNSLPMESTPHKCRGSACKPGNSYNSLYSTCLELFKFTIGMGDLEFTENYDFK
AVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCM
RKAFRSGKLLQVGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFS
LRSGRVSGRNWKNFALVPLLRDASTRDRHATQQEEVQLKHYTGSLKPEDAEVFKDSMVPG
EK

Sequence of entity 2 (E, F), FASTA

>7L2M_2 Tau-theraphotoxin-Hs1a (chains E, F)
MDCAKEGEVCSWGKKCCDLDNFYCPMEFIPHCKKYKPYVPVTTNCAKEGEVCGWGSKCCH
GLDCPLAFIPYCEKYR

Ligands and cofactors

ID	Name	Formula	Copies
6EU	resiniferatoxin	C37 H40 O9	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. 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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