6V9V: PDB entry 6V9V

Structure of TRPA1 modified by Bodipy-iodoacetamide with bound calcium, LMNG. Determined by electron microscopy at 2.6 Å resolution. Released 6 May 2020.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 18,976
Mol. weight: 511.91 kDa
Ligands: CA, QT4
Released: 6 May 2020

Explore 6V9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V9V contains 136 α-helices and 20 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, B, C and D: 34 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	448-455	8
α-helix	459-466	8
α-helix	485-491	7
α-helix	495-504	10
α-helix	517-522	6
α-helix	527-533	7
α-helix	551-557	7
α-helix	561-569	9
α-helix	583-589	7
α-helix	593-601	9
α-helix	605-609	5
α-helix	622-628	7
α-helix	631-641	11
β-strand	642-643	2	1
β-strand	656-659	4	1
α-helix	684-691	8
α-helix	695-698	4
α-helix	701-710	10
α-helix	711-715	5
α-helix	716-739	24
β-strand	746-747	2	2
β-strand	750-751	2	2
α-helix	767-794	28
α-helix	804-818	15
α-helix	820-822	3
α-helix	828-849	22
α-helix	857-871	15
α-helix	874-891	18
α-helix	901-910	10
α-helix	911-913	3
α-helix	919-923	5
α-helix	924-927	4
α-helix	934-945	12
α-helix	946-952	7
α-helix	953-969	17
α-helix	971-989	19
α-helix	992-998	7
β-strand	1002-1005	4	1
α-helix	1041-1070	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily A member 1	A, B, C, D	protein	1119	Homo sapiens	O75762 (AlphaFold model)

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

>6V9V_1 Transient receptor potential cation channel subfamily A member 1 (chains A, B, C, D)
MKRSLRKMWRPGEKKEPQGVVYEDVPDDTEDFKESLKVVFEGSAYGLQNFNKQKKLKRCD
DMDTFFLHYAAAEGQIELMEKITRDSSLEVLHEMDDYGNTPLHCAVEKNQIESVKFLLSR
GANPNLRNFNMMAPLHIAVQGMNNEVMKVLLEHRTIDVNLEGENGNTAVIIACTTNNSEA
LQILLKKGAKPCKSNKWGCFPIHQAAFSGSKECMEIILRFGEEHGYSRQLHINFMNNGKA
TPLHLAVQNGDLEMIKMCLDNGAQIDPVEKGRCTAIHFAATQGATEIVKLMISSYSGSVD
IVNTTDGCHETMLHRASLFDHHELADYLISVGADINKIDSEGRSPLILATASASWNIVNL
LLSKGAQVDIKDNFGRNFLHLTVQQPYGLKNLRPEFMQMQQIKELVMDEDNDGCTPLHYA
CRQGGPGSVNNLLGFNVSIHSKSKDKKSPLHFAASYGRINTCQRLLQDISDTRLLNEGDL
HGMTPLHLAAKNGHDKVVQLLLKKGALFLSDHNGWTALHHASMGGYTQTMKVILDTNLKC
TDRLDEDGNTALHFAAREGHAKAVALLLSHNADIVLNKQQASFLHLALHNKRKEVVLTII
RSKRWDECLKIFSHNSPGNKCPITEMIEYLPECMKVLLDFCMLHSTEDKSCRDYYIEYNF
KYLQCPLEFTKKTPTQDVIYEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHM
MNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLS
SIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVY
FYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSS
PLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLA
VGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQKSTIVYPNKPRSGGMLFHIF
CFLFCTGEIRQEIPNADKSLEMEILKQKYRLKDLTFLLEKQHELIKLIIQKMEIISETED
DDSHCSFQDRFKKEQMEQRNSRWNTVLRAVKAKTHHLEP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
QT4	~{N}-[[2,2-bis(fluoranyl)-10,12-dimethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0…	C14 H17 B F2 N3 O	4

Primary citation

Irritant-evoked activation and calcium modulation of the TRPA1 receptor. Zhao, J., Lin King, J.V., Paulsen, C.E. et al. Nature (2020) 585:141-145. DOI 10.1038/s41586-020-2480-9 · PubMed

Other PDB entries of the same protein (UniProt O75762 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HC8 1.9 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPA1 (313-339)
9VU1 2.59 Å, Structure of hTRPA1 complexed with LIQA
7OR0 2.64 Å, Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60,…
7OR1 2.64 Å, Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60,…
9MOE 2.7 Å, Preclinical and clinical evaluation of a novel TRPA1 antagonist LY3526318
6PQQ 2.81 Å, Cryo-EM structure of human TRPA1 C621S mutant in the apo state
6PQO 2.88 Å, Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist…
6X2J 3.0 Å, Structure of human TRPA1 in complex with agonist GNE551
7JUP 3.05 Å, Structure of human TRPA1 in complex with antagonist compound 21
6PQP 3.06 Å, Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist BITC
6V9W 3.1 Å, Structure of TRPA1 (ligand-free) with bound calcium, LMNG
9M8S 3.1 Å, Cryo-EM structure of the human TRPA1 ion channel in ligand-free state.

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