7MZC: Minimal TRPV1 with RTX bound in C1 state

Cryo-EM structure of minimal TRPV1 with RTX bound in C1 state. Determined by electron microscopy at 3.03 Å resolution. Released 22 Sept 2021.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 17,334
Mol. weight: 294.63 kDa
Ligands: 6EU
Released: 22 Sept 2021

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

Secondary structure: helices and β-sheets

7MZC contains 113 α-helices and 26 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 and B: 28 helices, 7 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	261-268	8
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	368-373	6	1
β-strand	377-382	6	1
β-strand	385	1	2
β-strand	389	1	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	463-466	4
α-helix	469-499	31
α-helix	505-508	4
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	562-574	13
α-helix	576-598	23
α-helix	630-641	12
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-711	37
β-strand	726	1	3
β-strand	738	1	3
β-strand	742-747	6	1

Chain C: 28 helices, 7 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	261-268	8
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	368-373	6	9
β-strand	377-382	6	9
β-strand	385	1	10
β-strand	389	1	10
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	463-466	4
α-helix	469-499	31
α-helix	505-508	4
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	560-574	15
α-helix	576-598	23
α-helix	630-641	12
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-711	37
β-strand	726	1	11
β-strand	738	1	11
β-strand	742-747	6	9

Chain D: 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	261-268	8
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	368-373	6	4
β-strand	377-382	6	4
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	463-466	4
α-helix	469-499	31
α-helix	505-508	4
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	563-571	9
α-helix	572-576	5
α-helix	577-598	22
α-helix	630-641	12
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-711	37
β-strand	726	1	5
β-strand	738	1	5
β-strand	742-747	6	4

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)

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

>7MZC_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

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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