PDB entry 6mpg

View 6mpg on RCSB PDB site
Description: cryo-em structure at 3.2 a resolution of hiv-1 fusion peptide-directed antibody, a12v163-b.01, elicited by vaccination of rhesus macaques, in complex with stabilized hiv-1 env bg505 ds-sosip, which was also bound to antibodies vrc03 and pgt122
Deposited on 2018-10-06, released 2019-07-24
Made obsolete on 2020-10-22

The last revision was dated 2020-07-01, with a file datestamp of 2020-06-26.
Experiment type: EM
Resolution: 3.2 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '2':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6 (0-472)
      • conflict (170)
      • conflict (300)
      • conflict (400)
      • conflict (468)
  • Chain '3':
    Compound: A12V163-b.01 Heavy Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-116)
  • Chain '4':
    Compound: A12V163-b.01 Light Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-112)
  • Chain '5':
    Compound: PGT122 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-131)
  • Chain '6':
    Compound: PGT122 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (Start-106)
  • Chain '7':
    Compound: VRC03 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-101)
  • Chain '8':
    Compound: VRC03 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-End)
  • Chain 'A':
    Compound: envelope glycoprotein gp41
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S7 (0-152)
      • conflict (93)
  • Chain 'B':
    Compound: A12V163-b.01 Light Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-112)
  • Chain 'C':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6 (0-472)
      • conflict (170)
      • conflict (300)
      • conflict (400)
      • conflict (468)
  • Chain 'D':
    Compound: envelope glycoprotein gp41
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S7 (0-152)
      • conflict (93)
  • Chain 'M':
    Compound: PGT122 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-131)
  • Chain 'N':
    Compound: PGT122 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (Start-106)
  • Chain 'Q':
    Compound: VRC03 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-End)
  • Chain 'R':
    Compound: VRC03 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-101)
  • Chain 'U':
    Compound: envelope glycoprotein gp41
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S7 (0-152)
      • conflict (93)
  • Chain 'V':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6 (0-472)
      • conflict (170)
      • conflict (300)
      • conflict (400)
      • conflict (468)
  • Chain 'W':
    Compound: A12V163-b.01 Heavy Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-116)
  • Chain 'X':
    Compound: A12V163-b.01 Heavy Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-116)
  • Chain 'Y':
    Compound: A12V163-b.01 Light Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-112)
  • Chain 'm':
    Compound: PGT122 heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-131)
  • Chain 'n':
    Compound: PGT122 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (Start-106)
  • Chain 'q':
    Compound: VRC03 Heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-End)
  • Chain 'r':
    Compound: VRC03 Light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MPG (0-101)
  • Heterogens: NAG, BMA, MAN

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 '2':
    Sequence, based on SEQRES records:
    >6mpg2 (2:)
aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsactqacpkvsf
epipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeev
mirsenitnnaknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahc
nvskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglf
nstwisntsvqgsnstgsndsitlpcrikqiinmwqrigqcmyappiqgvircvsnitgl
iltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrv

    Sequence, based on observed residues (ATOM records):
    >6mpg2 (2:)
aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinsnkeyrlincntsactqacpkvsfepipihyca
pagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitn
naknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahcnvskatwne
tlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglfnstwisnnd
sitlpcrikqiinmwqrigqcmyappiqgvircvsnitgliltrdggstnsttetfrpgg
gdmrdnwrselykykvvkieplgvaptrckrrv

  • Chain '3':
    Sequence; same for both SEQRES and ATOM records:
    >6mpg3 (3:)
evqlvesggglakpggslrlscaasgftfsdyymdwvrqapgkglewvsrisnsgitwyt
dsvrgrftifrdnakntlylqmnslraedtavyyctkesaaaighywgqgvlvtvss

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records:
    >6mpg4 (4:)
divmtqspdslavslgervtlnckssqsllassnnknylawyyqkpgqapklliywastr
esgvpnrfsgsgsgsdftltisglqaedvavyycqqyyttpltfgggtkveik

  • Chain '5':
    Sequence; same for both SEQRES and ATOM records:
    >6mpg5 (5:)
qvhlqesgpglvkpsetlsltcnvsgtlvrdnywswirqplgkqpewigyvhdsgdtnyn
pslksrvhlsldksknlvslrltgvtaadsaiyycattkhgrriygvvafkewftyfymd
vwgkgtsvtvss

  • Chain '6':
    Sequence, based on SEQRES records:
    >6mpg6 (6:)
aptfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgsp
gstfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivl

    Sequence, based on observed residues (ATOM records):
    >6mpg6 (6:)
tfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgspgs
tfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivl

  • Chain '7':
    Sequence; same for both SEQRES and ATOM records:
    >6mpg7 (7:)
eivltqspgilslspgetatlfckasqggnamtwyqkrrgqvprlliydtsrrasgvpdr
fvgsgsgtdffltinkldredfavyycqqfeffglgselevh

  • Chain '8':
    Sequence, based on SEQRES records:
    >6mpg8 (8:)
qvqlvqsgaviktpgssvkiscrasgynfrdysihwvrlipdkgfewigwikplwgavsy
arqlqgrvsmtrqlsqdpddpdwgvaymefsgltpadtaeyfcvrrgscdycgdfpwqyw
gqgtvvvvssastkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgvhtfp
avlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

    Sequence, based on observed residues (ATOM records):
    >6mpg8 (8:)
qvqlvqsgaviktpgssvkiscrasgynfrdysihwvrlipdkgfewigwikplwgavsy
arqlqgrvsmtrqlsqdpddpdwgvaymefsgltpadtaeyfcvrrgscdycgdfpwqyw
gqgtvvvv

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6mpgA (A:)
avgigavflgflgaagstmgaasmtltvqarnllsgivqqqsnllraieaqqhllkltvw
gikqlqarvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqw
dkeisnytqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6mpgA (A:)
avgigavflgflgaagstmgaasmtltvqarnllsgtvwgikqlqarvlaverylrdqql
lgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnq
qekneqdllald

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgB (B:)
divmtqspdslavslgervtlnckssqsllassnnknylawyyqkpgqapklliywastr
esgvpnrfsgsgsgsdftltisglqaedvavyycqqyyttpltfgggtkveik

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6mpgC (C:)
aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsactqacpkvsf
epipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeev
mirsenitnnaknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahc
nvskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglf
nstwisntsvqgsnstgsndsitlpcrikqiinmwqrigqcmyappiqgvircvsnitgl
iltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrv

    Sequence, based on observed residues (ATOM records):
    >6mpgC (C:)
aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinsnkeyrlincntsactqacpkvsfepipihyca
pagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitn
naknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahcnvskatwne
tlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglfnstwisnnd
sitlpcrikqiinmwqrigqcmyappiqgvircvsnitgliltrdggstnsttetfrpgg
gdmrdnwrselykykvvkieplgvaptrckrrv

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6mpgD (D:)
avgigavflgflgaagstmgaasmtltvqarnllsgivqqqsnllraieaqqhllkltvw
gikqlqarvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqw
dkeisnytqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6mpgD (D:)
avgigavflgflgaagstmgaasmtltvqarnllsgtvwgikqlqarvlaverylrdqql
lgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnq
qekneqdllald

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgM (M:)
qvhlqesgpglvkpsetlsltcnvsgtlvrdnywswirqplgkqpewigyvhdsgdtnyn
pslksrvhlsldksknlvslrltgvtaadsaiyycattkhgrriygvvafkewftyfymd
vwgkgtsvtvss

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6mpgN (N:)
aptfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgsp
gstfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivl

    Sequence, based on observed residues (ATOM records):
    >6mpgN (N:)
tfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgspgs
tfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivl

  • Chain 'Q':
    Sequence, based on SEQRES records:
    >6mpgQ (Q:)
qvqlvqsgaviktpgssvkiscrasgynfrdysihwvrlipdkgfewigwikplwgavsy
arqlqgrvsmtrqlsqdpddpdwgvaymefsgltpadtaeyfcvrrgscdycgdfpwqyw
gqgtvvvvssastkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgvhtfp
avlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

    Sequence, based on observed residues (ATOM records):
    >6mpgQ (Q:)
qvqlvqsgaviktpgssvkiscrasgynfrdysihwvrlipdkgfewigwikplwgavsy
arqlqgrvsmtrqlsqdpddpdwgvaymefsgltpadtaeyfcvrrgscdycgdfpwqyw
gqgtvvvv

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgR (R:)
eivltqspgilslspgetatlfckasqggnamtwyqkrrgqvprlliydtsrrasgvpdr
fvgsgsgtdffltinkldredfavyycqqfeffglgselevh

  • Chain 'U':
    Sequence, based on SEQRES records:
    >6mpgU (U:)
avgigavflgflgaagstmgaasmtltvqarnllsgivqqqsnllraieaqqhllkltvw
gikqlqarvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqw
dkeisnytqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6mpgU (U:)
avgigavflgflgaagstmgaasmtltvqarnllsgtvwgikqlqarvlaverylrdqql
lgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnq
qekneqdllald

  • Chain 'V':
    Sequence, based on SEQRES records:
    >6mpgV (V:)
aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsactqacpkvsf
epipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeev
mirsenitnnaknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahc
nvskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglf
nstwisntsvqgsnstgsndsitlpcrikqiinmwqrigqcmyappiqgvircvsnitgl
iltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrv

    Sequence, based on observed residues (ATOM records):
    >6mpgV (V:)
aenlwvtvyygvpvwkdaettlfcasdakayetekhnvwathacvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinsnkeyrlincntsactqacpkvsfepipihyca
pagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitn
naknilvqfntpvqinctrpnnntrksirigpgqafyatgdiigdirqahcnvskatwne
tlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglfnstwisnnd
sitlpcrikqiinmwqrigqcmyappiqgvircvsnitgliltrdggstnsttetfrpgg
gdmrdnwrselykykvvkieplgvaptrckrrv

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgW (W:)
evqlvesggglakpggslrlscaasgftfsdyymdwvrqapgkglewvsrisnsgitwyt
dsvrgrftifrdnakntlylqmnslraedtavyyctkesaaaighywgqgvlvtvss

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgX (X:)
evqlvesggglakpggslrlscaasgftfsdyymdwvrqapgkglewvsrisnsgitwyt
dsvrgrftifrdnakntlylqmnslraedtavyyctkesaaaighywgqgvlvtvss

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgY (Y:)
divmtqspdslavslgervtlnckssqsllassnnknylawyyqkpgqapklliywastr
esgvpnrfsgsgsgsdftltisglqaedvavyycqqyyttpltfgggtkveik

  • Chain 'm':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgm (m:)
qvhlqesgpglvkpsetlsltcnvsgtlvrdnywswirqplgkqpewigyvhdsgdtnyn
pslksrvhlsldksknlvslrltgvtaadsaiyycattkhgrriygvvafkewftyfymd
vwgkgtsvtvss

  • Chain 'n':
    Sequence, based on SEQRES records:
    >6mpgn (n:)
aptfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgsp
gstfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivl

    Sequence, based on observed residues (ATOM records):
    >6mpgn (n:)
tfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgspgs
tfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivl

  • Chain 'q':
    Sequence, based on SEQRES records:
    >6mpgq (q:)
qvqlvqsgaviktpgssvkiscrasgynfrdysihwvrlipdkgfewigwikplwgavsy
arqlqgrvsmtrqlsqdpddpdwgvaymefsgltpadtaeyfcvrrgscdycgdfpwqyw
gqgtvvvvssastkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgvhtfp
avlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

    Sequence, based on observed residues (ATOM records):
    >6mpgq (q:)
qvqlvqsgaviktpgssvkiscrasgynfrdysihwvrlipdkgfewigwikplwgavsy
arqlqgrvsmtrqlsqdpddpdwgvaymefsgltpadtaeyfcvrrgscdycgdfpwqyw
gqgtvvvv

  • Chain 'r':
    Sequence; same for both SEQRES and ATOM records:
    >6mpgr (r:)
eivltqspgilslspgetatlfckasqggnamtwyqkrrgqvprlliydtsrrasgvpdr
fvgsgsgtdffltinkldredfavyycqqfeffglgselevh