6MPG

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Vaccine-Induced Developmental Pathways in Rhesus Macaques for Neutralizing Antibodies Targeting the HIV-1 Fusion Peptide

Kong, R.Duan, H.Sheng, Z.Xu, K.Acharya, P.Kwong, P.D.Mascola, J.M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A12V163-b.01 Light Chain
B, 4, Y
113N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp41
U, A, D
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp120
V, 2, C
473Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
A12V163-b.01 Heavy Chain
W, 3, X
117N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PGT122 Heavy chain
m, 5, M
132N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PGT122 Light chain
n, 6, N
107N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
VRC03 heavy chain
q, 8, Q
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
VRC03 Light chain
r, 7, R
102N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
2, C, V
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
2, 3, C, V, W, X
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
2, 3, A, C, D, U, V, W, X
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release