PDB entry 6itc

View 6itc on RCSB PDB site
Description: structure of a substrate engaged seca-secy protein translocation machine
Deposited on 2018-11-21, released 2019-06-12
The last revision was dated 2019-11-06, with a file datestamp of 2019-11-01.
Experiment type: EM
Resolution: 3.45 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Protein translocase subunit secA
    Species: Bacillus subtilis (strain 168) [TaxId:224308]
    Gene: SECA, DIV+, BSU35300
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Translocating peptide
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6ITC (Start-58)
  • Chain 'C':
    Compound: Nanobody
    Species: Lama glama [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6ITC (0-111)
  • Chain 'E':
    Compound: protein translocase subunit sece
    Species: Geobacillus thermodenitrificans (strain NG80-2) [TaxId:420246]
    Gene: secE, GTNG_0091
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Green fluorescent protein
    Species: Aequorea victoria [TaxId:6100]
    Gene: GFP
    Database cross-references and differences (RAF-indexed):
    • Uniprot P42212
      • chromophore (65)
      • engineered mutation (79)
      • engineered mutation (98)
      • engineered mutation (152)
      • engineered mutation (162)
  • Chain 'V':
    Compound: Nanobody
    Species: Lama glama [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6ITC (0-115)
  • Chain 'Y':
    Compound: Protein translocase subunit SecY
    Species: Geobacillus thermodenitrificans (strain NG80-2) [TaxId:420246]
    Gene: secY, GTNG_0125
    Database cross-references and differences (RAF-indexed):
    • Uniprot A4IJK8 (Start-423)
      • engineered mutation (59)
      • engineered mutation (201)
      • engineered mutation (206)
  • Heterogens: MG, BEF, ADP, PGV

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6itcA (A:)
mlgilnkmfdptkrtlnryekiandidairgdyenlsddalkhktiefkerlekgattdd
llveafavvreasrrvtgmfpfkvqlmggvalhdgniaemktgegktltstlpvylnalt
gkgvhvvtvneylasrdaeqmgkifeflgltvglnlnsmskdekreayaaditystnnel
gfdylrdnmvlykeqmvqrplhfavidevdsilideartpliisgqaakstklyvqanaf
vrtlkaekdytydiktkavqlteegmtkaekafgidnlfdvkhvalnhhinqalkahvam
qkdvdyvvedgqvvivdsftgrlmkgrryseglhqaieakegleiqnesmtlatitfqny
frmyeklagmtgtakteeeefrniynmqvvtiptnrpvvrddrpdliyrtmegkfkavae
dvaqrymtgqpvlvgtvavetseliskllknkgiphqvlnaknhereaqiieeagqkgav
tiatnmagrgtdiklgegvkelgglavvgterhesrridnqlrgrsgrqgdpgitqfyls
medelmrrfgaertmamldrfgmddstpiqskmvsravessqkrvegnnfdsrkqllqyd
dvlrqqreviykqrfevidsenlreivenmikssleraiaaytpreelpeewkldglvdl
inttyldegaleksdifgkepdemlelimdriitkynekeeqfgkeqmrefekvivlrav
dskwmdhidamdqlrqgihlrayaqtnplreyqmegfamfehmiesiedevakfvmkaei

    Sequence, based on observed residues (ATOM records):
    >6itcA (A:)
rtlnryekiandidairgdyenlsddalkhktiefkerlekgattddllveafavvreas
rrvtgmfpfkvqlmggvalhdgniaemktgegktltstlpvylnaltgkgvhvvtvneyl
asrdaeqmgkifeflgltvglnlnsmskdekreayaaditystnnelgfdylrdnmvlyk
eqmvqrplhfavidevdsilideartpliisgqaakstklyvqanafvrtlkaekdytyd
iktkavqlteegmtkaekafgidnlfdvkhvalnhhinqalkahvamqkdvdyvvedgqv
vivdsftgrlmkgrryseglhqaieakegleiqnesmtlatitfqnyfrmyeklagmtgt
akteeeefrniynmqvvtiptnrpvvrddrpdliyrtmegkfkavaedvaqrymtgqpvl
vgtvavetseliskllknkgiphqvlnaknhereaqiieeagqkgavtiatnmagrgtdi
klgegvkelgglavvgterhesrridnqlrgrsgrqgdpgitqfylsmedelmrrfgaer
tmamldrfgmddstpiqskmvsravessqkrvegnnfdsrkqllqyddvlrqqreviykq
rfevidsenlreivenmikssleraiaaytpreelpeewkldglvdlinttyldegalek
sdifgkepdemlelimdriitkynekeeqfgkeqmrefekvivlravdskwmdhidamdq
lrqgihlrayaqtnplreyqmegfamfehmiesiedevakfvmka

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6itcB (B:)
makktaiaiavalagfatvasyaqyedgcsgelerqhtfaggarsisgdgdsphsyhsg

    Sequence, based on observed residues (ATOM records):
    >6itcB (B:)
akktaiaiavalagfatvasyaqyedgcsgelerdsphsyhsg

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >6itcC (C:)
valvesggalvqpggslrlscaasgfpvnrysmrwyrqapgkerewvagmsagdrssyed
svkgrftisrddarntvylqmnslkpedtavyycnvnvgfeywgqgtqvtvs

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6itcE (E:)
mqrvtnffkevvrelkkvswpnrkelvnytavvlatvafftvffavidlgisqlirlvfe
gghhhhhhhh

    Sequence, based on observed residues (ATOM records):
    >6itcE (E:)
qrvtnffkevvrelkkvswpnrkelvnytavvlatvafftvffavidlgisqlirlvf

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6itcG (G:)
mskgeelftgvvpilveldgdvnghkfsvsgegegdatygkltlkficttgklpvpwptl
vttfsygvqcfsrypdhmkrhdffksampegyvqertisfkddgnyktraevkfegdtlv
nrielkgidfkedgnilghkleynynshnvyitadkqkngikanfkirhniedgsvqlad
hyqqntpigdgpvllpdnhylstqsalskdpnekrdhmvllefvtaagithgmdelyk

    Sequence, based on observed residues (ATOM records):
    >6itcG (G:)
kgeelftgvvpilveldgdvnghkfsvsgegegdatygkltlkficttgklpvpwptlvt
tfsygvqcfsrypdhmkrhdffksampegyvqertisfkddgnyktraevkfegdtlvnr
ielkgidfkedgnilghkleynynshnvyitadkqkngikanfkirhniedgsvqladhy
qqntpigdgpvllpdnhylstqsalskdpnekrdhmvllefvtaagi

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records:
    >6itcV (V:)
qvqlvetggglvqpggslrlscgasgsifnmyamgwyrqapgkrrevvariatddstmyp
dsvkgrftisrdnakntvylqmnslkpedtavyycyyqrtvmsqpywgqgtqvtvs

  • Chain 'Y':
    Sequence, based on SEQRES records:
    >6itcY (Y:)
mfrtisnfmrvsdirnkiiftllmlivfrigtfipvpsvntdvlklqdqlnafgvlnifc
ggalqnfsifamgvmpyitasiivqllqmdvvpkfaewskqgemgrrklaqftryftivl
gfiqalgmsygfnnlaggmliqnpgigtylliavvltagtaflmwlgeqitakgvgngis
iiifagivsgiptilnqiyaqtfgglnivrlllvalavvavivgviyiqqafrkipiqya
krlegrnpvgghsthlplkvnpagvipvifavsfliapptiasffgtndvtlwirrtfdy
thpvgmtiyvvliiaftyfyafvqvnpeqmadnlkkqggyipgirpgkntqeyvtrilyr
ltlvgslflafiavlpvffvnfanlppsaqiggtsllivvgvaletmkqlesqlvkrhyr
gfik

    Sequence, based on observed residues (ATOM records):
    >6itcY (Y:)
frtisnfmrvsdirnkiiftllmlivfrigtfipvpsvntdvlklqdqlnafgvlnifcg
galqnfsifamgvmpyitasiivqllqmdvvpkfaewskqgemgrrklaqftryftivlg
fiqalgmsygfnnlaggmliqnpgigtylliavvltagtaflmwlgeqitakgvgngisi
iifagivsgiptilnqiyaqtlnivrlllvalavvavivgviyiqqafrkipiqyakrle
grnpvgghsthlplkvnpagvipvifavsfliapptiasffgtndvtlwirrtfdythpv
gmtiyvvliiaftyfyafvqvnpeqmadnlkkqggyipgirpgkntqeyvtrilyrltlv
gslflafiavlpvffvnfanlppsaqiggtsllivvgvaletmkqlesqlvkrhyrgfik