7T6M: TRPV5 in nanodiscs with PI(4,5)P2 at pH6 state 1

Cryo-EM structure of TRPV5 in nanodiscs with PI(4,5)P2 at pH6 state 1. Determined by electron microscopy at 2.8 Å resolution. Released 4 May 2022.

Method
Electron microscopy
Resolution
2.8 Å
Organism
Oryctolagus cuniculus
Chains
4
Atoms
19,600
Mol. weight
338.12 kDa
Ligands
PIO
Released
4 May 2022

Explore 7T6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T6M contains 152 α-helices and 32 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: 38 helices, 8 β-strands

ElementResiduesLengthSheet
α-helix30-4617
α-helix48-558
α-helix82-887
α-helix92-10110
α-helix103-1053
α-helix108-1103
α-helix113-1153
α-helix120-1278
α-helix130-1389
α-helix166-1738
α-helix176-1849
α-helix199-2046
α-helix210-22112
α-helix243-2497
α-helix253-2619
β-strand264-27071
β-strand273-27971
α-helix281-2844
α-helix292-2976
α-helix304-3074
α-helix311-32010
α-helix321-3255
α-helix326-34823
β-strand352-35432
β-strand36613
β-strand368-37032
α-helix371-3722
α-helix380-40324
α-helix405-4084
α-helix412-4176
α-helix423-44422
α-helix451-46313
α-helix464-4718
α-helix476-4838
α-helix484-4907
α-helix491-51020
β-strand51514
α-helix526-53712
α-helix542-5443
α-helix553-56210
α-helix563-5708
α-helix571-58717
α-helix589-60719
α-helix614-6163
β-strand61811
β-strand630-63671
Chain B: 37 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix30-4617
α-helix48-558
α-helix82-887
α-helix92-10110
α-helix103-1053
α-helix113-1153
α-helix120-1278
α-helix130-1389
α-helix166-1738
α-helix176-1849
α-helix199-2046
α-helix210-22112
α-helix243-2497
α-helix253-2619
β-strand264-27075
β-strand273-27975
α-helix281-2844
α-helix292-2976
α-helix304-3074
α-helix311-32010
α-helix321-3255
α-helix326-34823
β-strand352-35436
β-strand36614
β-strand368-37036
α-helix371-3722
α-helix380-40324
α-helix405-4084
α-helix412-4176
α-helix423-44422
α-helix451-46313
α-helix464-4718
α-helix476-4838
α-helix484-4907
α-helix491-51020
β-strand51517
α-helix526-53712
α-helix542-5443
α-helix553-56210
α-helix563-5708
α-helix571-58717
α-helix589-60719
α-helix614-6163
β-strand61815
β-strand630-63675
Chain C: 39 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix30-4617
α-helix48-558
α-helix82-887
α-helix92-10110
α-helix103-1053
α-helix108-1103
α-helix113-1153
α-helix120-1278
α-helix130-1389
α-helix166-1738
α-helix176-1849
α-helix199-2046
α-helix210-22112
α-helix243-2497
α-helix253-2619
β-strand264-27078
β-strand273-27978
α-helix281-2844
α-helix292-2976
α-helix304-3074
α-helix311-32010
α-helix321-3255
α-helix326-34823
β-strand352-35439
β-strand366110
β-strand368-37039
α-helix371-3722
α-helix380-40324
α-helix405-4084
α-helix412-4176
α-helix423-44422
α-helix451-46313
α-helix464-4718
α-helix476-4838
α-helix484-4907
α-helix491-51020
β-strand51513
α-helix526-53712
α-helix542-5443
α-helix553-56210
α-helix563-5708
α-helix571-58717
α-helix589-60719
α-helix614-6163
β-strand61818
α-helix621-6233
β-strand630-63678
Chain D: 38 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix30-4617
α-helix48-558
α-helix82-887
α-helix92-10110
α-helix103-1053
α-helix113-1153
α-helix120-1278
α-helix130-1389
α-helix166-1738
α-helix176-1849
α-helix199-2046
α-helix210-22112
α-helix243-2497
α-helix253-2619
β-strand264-270711
β-strand273-279711
α-helix281-2844
α-helix292-2976
α-helix304-3074
α-helix311-32010
α-helix321-3255
α-helix326-34823
β-strand352-354312
β-strand36617
β-strand368-370312
α-helix371-3722
α-helix380-40324
α-helix405-4084
α-helix412-4176
α-helix423-44422
α-helix451-46313
α-helix464-4718
α-helix476-4838
α-helix484-4907
α-helix491-51020
β-strand515110
α-helix526-53712
α-helix542-5443
α-helix553-56210
α-helix563-5708
α-helix571-58717
α-helix589-60719
α-helix614-6163
β-strand618111
α-helix621-6233
β-strand630-636711

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Transient receptor potential cation channel subfamily V member 5A, B, C, Dprotein739Oryctolagus cuniculusQ9XSM3 (AlphaFold model)
Sequence of entity 1 (A, B, C, D), FASTA
>7T6M_1 Transient receptor potential cation channel subfamily V member 5 (chains A, B, C, D)
MGACPPKAKGPWAQLQKLLISWPVGEQDWEQYRDRVNMLQQERIRDSPLLQAAKENDLRL
LKILLLNQSCDFQQRGAVGETALHVAALYDNLEAATLLMEAAPELAKEPALCEPFVGQTA
LHIAVMNQNLNLVRALLARGASVSARATGAAFRRSPHNLIYYGEHPLSFAACVGSEEIVR
LLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDEHSDHLQSLELVPNHQG
LTPFKLAGVEGNTVMFQHLMQKRKHVQWTCGPLTSTLYDLTEIDSWGEELSFLELVVSSK
KREARQILEQTPVKELVSFKWKKYGRPYFCVLASLYILYMICFTTCCIYRPLKLRDDNRT
DPRDITILQQKLLQEAYVTHQDNIRLVGELVTVTGAVIILLLEIPDIFRVGASRYFGQTI
LGGPFHVIIITYASLVLLTMVMRLTNMNGEVVPLSFALVLGWCSVMYFARGFQMLGPFTI
MIQKMIFGDLMRFCWLMAVVILGFASAFHITFQTEDPNNLGEFSDYPTALFSTFELFLTI
IDGPANYSVDLPFMYCITYAAFAIIATLLMLNLFIAMMGDTHWRVAQERDELWRAQVVAT
TVMLERKMPRFLWPRSGICGYEYGLGDRWFLRVENHHDQNPLRVLRYVEAFKCSDKEDGQ
EQLSEKRPSTVESGMLSRASVAFQTPSLSRTTSQSSNSHRGWEILRRNTLGHLNLGLDLG
EGDGEEVYHFTETSQVAPA

Ligands and cofactors

IDNameFormulaCopies
PIO[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…C25 H49 O19 P34

Primary citation

Structural basis of TRPV5 regulation by physiological and pathophysiological modulators. Fluck, E.C., Yazici, A.T., Rohacs, T. et al. Cell Rep (2022) 39:110737-110737. DOI 10.1016/j.celrep.2022.110737 · PubMed

Other PDB entries of the same protein (UniProt Q9XSM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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