7QHA: PDB entry 7QHA

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in amphipol. Determined by electron microscopy at 2.97 Å resolution. Released 21 Dec 2022.

Method
Electron microscopy
Resolution
2.97 Å
Organisms
Photobacterium profundum SS9, Helicobacter pylori, synthetic construct
Chains
3
Atoms
5,282
Mol. weight
120.24 kDa
Released
21 Dec 2022

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

Secondary structure: helices and β-sheets

7QHA contains 38 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-helix3-64
α-helix9-3022
α-helix31-355
α-helix42-6322
α-helix74-763
α-helix79-11032
β-strand115-11621
β-strand121-12221
α-helix124-1274
α-helix129-15123
Chain B: 28 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-1413
α-helix18-3215
α-helix38-469
α-helix47-493
α-helix53-553
α-helix56-6914
α-helix72-8413
α-helix91-10212
α-helix109-12517
α-helix131-14010
α-helix141-1444
α-helix152-16110
α-helix165-1717
α-helix173-19422
α-helix199-2035
α-helix204-21310
α-helix219-22911
α-helix235-24915
α-helix259-29335
α-helix296-30611
α-helix310-32415
α-helix330-3367
α-helix338-3469
α-helix352-36615
α-helix374-38310
α-helix390-3945
α-helix395-3973
α-helix399-41012
Chain C: 2 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand18-2252
β-strand34-3961
β-strand46-5161
β-strand57-5931
α-helix61-633
β-strand68-7252
β-strand77-8262
β-strand91-9661
α-helix104-1063
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 constructB5Z8H1 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7QHA_1 Putative TRAP-type C4-dicarboxylate transport system, small permease component (chains A)
MFRKIIDNIEEIITVPLMIALLCILTWQISSRWLFDSPSLWSEELARVLFLHMAIIGGAI
AIKKDDHVKITFFSDKLPRNFRYSLLFALELLVLITIVAMIYYGYAHVQRTAFFELITLG
ISSSWMTYALPVGGCFMLVRQCQKLYFVLIDWRINENKNTSHLTACDINE
Sequence of entity 2 (B), FASTA
>7QHA_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
>7QHA_3 Megabody c7HopQ (chains C)
QVQLQESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNDTYEQLS
RLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMG
YAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSL
SIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYAGGSLRLSCAASGNIFD
RGYMGWYRQAPGKERELVAGISYGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDT
AVYYCAAYPLYDDPYYYWGQGTQVTVSSLE

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:

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