8B01: PDB entry 8B01

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc. Determined by electron microscopy at 3.03 Å resolution. Released 15 Mar 2023.

Method
Electron microscopy
Resolution
3.03 Å
Organisms
Photobacterium profundum SS9, Helicobacter pylori, synthetic construct
Chains
3
Atoms
5,478
Mol. weight
123.25 kDa
Ligands
OCT, PTY, TWT, D10
Released
15 Mar 2023

Explore 8B01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B01 contains 39 α-helices and 11 β-strands across 3 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: 8 helices, 2 β-strands

ElementResiduesLengthSheet
α-helix3-75
α-helix9-3426
α-helix38-392
α-helix42-6322
α-helix74-763
α-helix79-11032
β-strand115-11621
β-strand121-12221
α-helix124-1274
α-helix129-15123
Chain B: 31 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-1413
α-helix18-3215
α-helix36-405
α-helix41-499
α-helix53-553
α-helix56-6914
α-helix72-8413
α-helix93-10311
α-helix109-12618
α-helix131-14111
α-helix144-1474
α-helix152-16110
α-helix165-1717
α-helix173-19422
α-helix199-2035
α-helix204-2129
α-helix216-2183
α-helix219-22911
α-helix235-24814
α-helix249-2535
α-helix259-29133
α-helix295-30612
α-helix310-32415
α-helix330-3367
α-helix338-34811
α-helix352-36615
α-helix374-38310
α-helix387-3948
α-helix395-3973
α-helix399-41012
α-helix413-42210
Chain C: 0 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand17-2262
β-strand34-3961
β-strand45-5171
β-strand57-5931
β-strand67-7262
β-strand77-8372
β-strand91-9661
β-strand10711
β-strand112-11431

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Putative TRAP-type C4-dicarboxylate transport system, small permease componentAprotein170Photobacterium profundum SS9Q6LPW0 (AlphaFold model)
Putative TRAP-type C4-dicarboxylate transport system, large permease componentBprotein427Photobacterium profundum SS9Q6LPW1 (AlphaFold model)
Megabody c7HopQCprotein510Helicobacter pylori, synthetic constructQ8GDI9 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8B01_1 Putative TRAP-type C4-dicarboxylate transport system, small permease component (chains A)
MFRKIIDNIEEIITVPLMIALLCILTWQISSRWLFDSPSLWSEELARVLFLHMAIIGGAI
AIKKDDHVKITFFSDKLPRNFRYSLLFALELLVLITIVAMIYYGYAHVQRTAFFELITLG
ISSSWMTYALPVGGCFMLVRQCQKLYFVLIDWRINENKNTSHLTACDINE
Sequence of entity 2 (B), FASTA
>8B01_2 Putative TRAP-type C4-dicarboxylate transport system, large permease component (chains B)
MFTSIVGWLGLLFAGMPVGFSLIFVGLAFLVLTESTGINFAAQQMIGGLDNFTLLAVPFF
VLTGHLMNSAGITERIFNFAKAMVGHITGSLGHVNILASLLFSGMSGSALADAGGLGQLE
IKSMRDAKYDDDFAGGLTAASCIIGPLVPPSIPLVIYGVVSNTSIGALFLAGAIPGLLCC
IALCIMTYFIAKKRGYMTLPRASRKERLIAFRDAFLSLLTPFIIIGGIFSGKFTPTEAAI
ISSLYALFLGTVVYKSLTMDKFIKLVQETVTTTSVVALMVMGVTVFGWIVAREQLPQQLA
ELFLSISDNPLILLLLINLLLLFLGTFIESLALLLLLVPFLVPVATSVGIDPVHFGVMAI
LNLMIGILTPPMGMALYVVSKVGNIPFHVLTRGVLPLLVPLFIVLGLIIVFPQITLFLPQ
LVLGYGL
Sequence of entity 3 (C), FASTA
>8B01_3 Megabody c7HopQ (chains C)
QVQLQESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNDTYEQLS
RLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMG
YAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSL
SIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYAGGSLRLSCAASGNIFD
RGYMGWYRQAPGKERELVAGISYGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDT
AVYYCAAYPLYDDPYYYWGQGTQVTVSSLE

Ligands and cofactors

IDNameFormulaCopies
OCTN-octaneC8 H186
PTYPhosphatidylethanolamineC40 H80 N O8 P2
TWTDocosaneC22 H461
D10DecaneC10 H222
HEXHexaneC6 H141
TRDTridecaneC13 H281

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

Primary citation

Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter. Davies, J.S., Currie, M.J., North, R.A. et al. Nat Commun (2023) 14:1120-1120. DOI 10.1038/s41467-023-36590-1 · PubMed

Other PDB entries of the same protein (UniProt Q6LPW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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