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 1.2 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

  • DOI: 10.1016/j.chom.2018.09.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and opening Env to enable gp41-mediated fusion. We present 3. ...

    HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and opening Env to enable gp41-mediated fusion. We present 3.54 Å and 4.06 Å cryoelectron microscopy structures of partially open soluble native-like Env trimers (SOSIPs) bound to CD4. One structure, a complex with a coreceptor-mimicking antibody that binds both CD4 and gp120, stabilizes the displaced V1V2 and reveals its structure. Comparing partially and fully open Envs with closed Envs shows that gp41 rearrangements are independent of the CD4-induced rearrangements that result in V1V2 displacement and formation of a 4-stranded bridging sheet. These findings suggest ordered conformational changes before coreceptor binding: (1) gp120 opening inducing side-chain rearrangements and a compact gp41 central helix conformation, and (2) 4-stranded bridging-sheet formation and V1V2 displacement. These analyses illuminate potential receptor-induced Env changes and inform design of therapeutics disrupting viral entry.


    Organizational Affiliation

    Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA. Electronic address: bjorkman@caltech.edu.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.




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 Sciences (NIH/NIGMS)United StatesP50 GM082545-06
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI100148

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence, Other