9W4M: RatTRPV1

ratTRPV1 bound with antagonist AMG517. Determined by electron microscopy at 2.7 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Escherichia coli K-12, Rattus norvegicus
Chains: 4
Atoms: 17,546
Mol. weight: 563.63 kDa
Ligands: A1D6R
Released: 26 Nov 2025

Explore 9W4M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W4M contains 104 α-helices and 24 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 D: 26 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	198-201	4
α-helix	204-210	7
α-helix	214-223	10
α-helix	251-257	7
α-helix	261-269	9
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-339	4
α-helix	340-344	5
α-helix	346-353	8
α-helix	360-362	3
β-strand	369-373	5	1
β-strand	377-381	5	1
α-helix	395-398	4
α-helix	412-414	3
α-helix	417-429	13
α-helix	432-453	22
α-helix	469-498	30
α-helix	512-530	19
α-helix	537-550	14
α-helix	551-558	8
α-helix	560-574	15
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	724-730	7	2
β-strand	736-741	6	2
β-strand	743	1	1
β-strand	746-747	2	1

Chain B: 26 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	204-210	7
α-helix	214-223	10
α-helix	251-257	7
α-helix	261-269	9
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-339	4
α-helix	340-344	5
α-helix	346-353	8
α-helix	360-362	3
β-strand	369-374	6	3
β-strand	377-381	5	3
α-helix	395-398	4
α-helix	412-414	3
α-helix	417-429	13
α-helix	432-453	22
α-helix	470-498	29
α-helix	505-507	3
α-helix	512-530	19
α-helix	537-550	14
α-helix	551-558	8
α-helix	560-574	15
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	724-730	7	4
β-strand	736-741	6	4
β-strand	743	1	3
β-strand	746-747	2	3

Chain C: 26 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	204-210	7
α-helix	214-223	10
α-helix	251-257	7
α-helix	261-269	9
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-339	4
α-helix	340-344	5
α-helix	346-353	8
α-helix	360-362	3
β-strand	369-374	6	5
β-strand	377-381	5	5
α-helix	395-398	4
α-helix	412-414	3
α-helix	417-426	10
α-helix	432-453	22
α-helix	470-498	29
α-helix	505-507	3
α-helix	512-530	19
α-helix	537-550	14
α-helix	551-558	8
α-helix	560-574	15
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	724-730	7	6
β-strand	736-741	6	6
β-strand	743	1	5
β-strand	746-747	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel…	A, B, C, D	protein	1252	Escherichia coli K-12, Rattus norvegicus	O35433 (AlphaFold model)

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

>9W4M_1 Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDE
ALKDAQTNSGTGGGSGDDDDKSPMGSHHHHHHHHGSDYDIPTTENLYFQGAMDPMEQRAS
LDSEESESPPQENSCLDPPDRDPNCKPPPVKPHIFTTRSRTRLFGKGDSEEASPLDCPYE
EGGLASCPIITVSSVLTIQRPGDGPASVRPSSQDSVSAGEKPPRLYDRRSIFDAVAQSNC
QELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLHNGQNDTIALLLDVARKTDSL
KQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGADVQAAANGDFFKKTKGRPGFY
FGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVDNTKFVT
SMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKIGVLAYILQREIHEPECRHLS
RKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKW
DRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGV
YFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLA
MGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKNNS
LPMESTPHKCRGSACKPGNSYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAY
VILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLL
QVGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFSLRSGRVSGRN
WKNFALVPLLRDASTRDRHATQQEEVQLKHYTGSLKPEDAEVFKDSMVPGEK

Ligands and cofactors

ID	Name	Formula	Copies
A1D6R	~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]…	C20 H13 F3 N4 O2 S	4

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

Primary citation

Structures of TRPV1 bound by hyperthermia-inducing analgesics. Gao, Y.H., Huang, Y.Z., Li, Z.X. et al. Cell Rep (2026) 45:116765-116765. DOI 10.1016/j.celrep.2025.116765 · 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
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

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