7MZ5: RTX-bound full-length TRPV1 in C2 state

Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state. Determined by electron microscopy at 2.76 Å resolution. Released 22 Sept 2021.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 14,291
Mol. weight: 383.9 kDa
Ligands: 6EU
Released: 22 Sept 2021

Explore 7MZ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MZ5 contains 85 α-helices and 28 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.

Chain A: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-342	7
α-helix	346-353	8
α-helix	363-365	3
β-strand	369-373	5	1
β-strand	378-383	6	1
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	462-466	5
α-helix	469-499	31
α-helix	511-531	21
α-helix	537-556	20
β-strand	557	1	2
β-strand	559	1	2
α-helix	563-571	9
α-helix	572-576	5
α-helix	577-598	22
β-strand	599	1	3
α-helix	630-641	12
β-strand	653	1	3
α-helix	656-682	27
α-helix	689-711	23
β-strand	723	1	1
β-strand	741-744	4	1

Chain B: 21 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-342	7
α-helix	346-353	8
α-helix	363-365	3
β-strand	369-373	5	9
β-strand	378-383	6	9
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	511-531	21
α-helix	537-556	20
α-helix	563-571	9
α-helix	572-576	5
α-helix	577-598	22
β-strand	599	1	10
α-helix	630-641	12
β-strand	653	1	10
α-helix	656-682	27
α-helix	689-711	23
β-strand	723	1	9
β-strand	741-744	4	9

Chain C: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-342	7
α-helix	346-353	8
α-helix	363-365	3
β-strand	369-373	5	4
β-strand	378-383	6	4
α-helix	395-400	6
α-helix	410-414	5
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	462-466	5
α-helix	469-499	31
α-helix	511-531	21
α-helix	537-556	20
β-strand	557	1	5
β-strand	559	1	5
α-helix	563-571	9
α-helix	572-576	5
α-helix	577-598	22
β-strand	599	1	6
α-helix	630-641	12
β-strand	653	1	6
α-helix	656-682	27
α-helix	689-711	23
β-strand	723	1	4
β-strand	741-744	4	4

Chain D: 22 helices, 6 β-strands

Element	Residues	Length	Sheet
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
α-helix	363-365	3
β-strand	369-373	5	7
β-strand	378-383	6	7
α-helix	395-400	6
α-helix	409-414	6
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	511-531	21
α-helix	537-551	15
α-helix	553-556	4
α-helix	563-571	9
α-helix	572-576	5
α-helix	577-598	22
β-strand	599	1	8
α-helix	630-641	12
β-strand	653	1	8
α-helix	656-682	27
α-helix	688-711	24
β-strand	723	1	7
β-strand	741-744	4	7

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)

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

>7MZ5_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

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
9W4T 2.87 Å, ratTRPV1 bound with antagonist AMG9810

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