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Cryo-EM structure at 3.8 A resolution of HIV-1 fusion peptide-directed antibody, DF1W-a.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

Electron Microscopy
3.8Å resolution
PDB entry 6mph coloured by chain, front view.
PDB entry 6mph coloured by chain, side view.
PDB entry 6mph coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 24-mer (preferred)
Entry contents: 8 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 24-mer
Accessible surface area: 173774.36 Å2
Buried surface area: 98489.31 Å2
Dissociation area: 18,120.95 Å2
Dissociation energy (ΔGdiss): -70.69 kcal/mol
Dissociation entropy (TΔSdiss): 194.04 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-212197

Macromolecules

DF1W-a.01 heavy chain
Chains: 1, 3, H
Length: 118 amino acids
Theoretical weight: 12.96 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
InterPro:
DF1W-a.01 heavy chain in PDB entry 6mph, assembly 1, front view.
DF1W-a.01 heavy chain in PDB entry 6mph, assembly 1, side view.
DF1W-a.01 heavy chain in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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DF1W-a.01 Light chain
Chains: 2, 4, L
Length: 112 amino acids
Theoretical weight: 12.19 KDa
Source organism: Macaca mulatta
Expression system: Homo sapiens
InterPro:
DF1W-a.01 Light chain in PDB entry 6mph, assembly 1, front view.
DF1W-a.01 Light chain in PDB entry 6mph, assembly 1, side view.
DF1W-a.01 Light chain in PDB entry 6mph, assembly 1, top view.
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Transmembrane protein gp41
Chains: 6, D, E
Length: 153 amino acids
Theoretical weight: 17.16 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S7 (Residues: 509-661; Coverage: 18%)
Gene name: env
Pfam: Retroviral envelope protein
InterPro: Retroviral envelope protein GP41-like
Transmembrane protein gp41 in PDB entry 6mph, assembly 1, front view.
Transmembrane protein gp41 in PDB entry 6mph, assembly 1, side view.
Transmembrane protein gp41 in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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Envelope glycoprotein gp160
Chains: A, B, C
Length: 473 amino acids
Theoretical weight: 52.99 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-502; Coverage: 55%)
Gene name: env
Pfam: Envelope glycoprotein GP120
InterPro:
Envelope glycoprotein gp160 in PDB entry 6mph, assembly 1, front view.
Envelope glycoprotein gp160 in PDB entry 6mph, assembly 1, side view.
Envelope glycoprotein gp160 in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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PGT122 heavy chain
Chains: M, X, Y
Length: 132 amino acids
Theoretical weight: 14.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
PGT122 heavy chain in PDB entry 6mph, assembly 1, front view.
PGT122 heavy chain in PDB entry 6mph, assembly 1, side view.
PGT122 heavy chain in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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PGT122 Light Chain
Chains: N, Z, a
Length: 107 amino acids
Theoretical weight: 11.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
PGT122 Light Chain in PDB entry 6mph, assembly 1, front view.
PGT122 Light Chain in PDB entry 6mph, assembly 1, side view.
PGT122 Light Chain in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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VRC03 Heavy chain
Chains: Q, f, g
Length: 227 amino acids
Theoretical weight: 24.65 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
VRC03 Heavy chain in PDB entry 6mph, assembly 1, front view.
VRC03 Heavy chain in PDB entry 6mph, assembly 1, side view.
VRC03 Heavy chain in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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VRC03 Light Chain
Chains: R, h, i
Length: 102 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
InterPro:
VRC03 Light Chain in PDB entry 6mph, assembly 1, front view.
VRC03 Light Chain in PDB entry 6mph, assembly 1, side view.
VRC03 Light Chain in PDB entry 6mph, assembly 1, top view.
Molecule details ›

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