6EDU

B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion.

Wang, H.Barnes, C.O.Yang, Z.Nussenzweig, M.C.Bjorkman, P.J.

(2018) Cell Host Microbe 24: 579-592.e4


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
A, B, C
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for B3UEZ6 (Human immunodeficiency virus 1)
Go to UniProtKB:  B3UEZ6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
D, E, F
516Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for B3UES2 (Human immunodeficiency virus 1)
Go to UniProtKB:  B3UES2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD4
G, H, I
185Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to Gene View: CD4
Go to UniProtKB:  P01730
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
21c Fab VH domain
J, L, N
231N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
21c Fab VL domain
K, M, O
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
8ANC195 G52K5 Fab VH domain
P, R, T
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
8ANC195 G52K5 Fab VL domain
Q, S, U
215N/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 
D, E, F, P, R, T
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
D, E, F, P, R, T
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, P, R, T
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50 GM082545-06
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesP01 AI100148

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references