5UM8

Crystal structure of HIV-1 envelope trimer 16055 NFL TD CC (T569G) in complex with Fabs 35022 and PGT124

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.935 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Glycine Substitution at Helix-to-Coil Transitions Facilitates the Structural Determination of a Stabilized Subtype C HIV Envelope Glycoprotein.

Guenaga, J., Garces, F., de Val, N., Stanfield, R.L., Dubrovskaya, V., Higgins, B., Carrette, B., Ward, A.B., Wilson, I.A., Wyatt, R.T.

(2017) Immunity 46: 792-803.e3

  • DOI: 10.1016/j.immuni.2017.04.014

  • PubMed Abstract: 

    • Advances in HIV-1 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and G structures and elicit neutralizing antibodies. However, a high-resolution clade C structure is critical, as this subtype accounts ...

    Advances in HIV-1 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and G structures and elicit neutralizing antibodies. However, a high-resolution clade C structure is critical, as this subtype accounts for the majority of HIV infections worldwide, but well-ordered clade C Env trimers are more challenging to produce due to their instability. Based on targeted glycine substitutions in the Env fusion machinery, we defined a general approach that disfavors helical transitions leading to post-fusion conformations, thereby favoring the pre-fusion state. We generated a stabilized, soluble clade C Env (16055 NFL) and determined its crystal structure at 3.9 Å. Its overall conformation is similar to SOSIP.664 and native Env trimers but includes a covalent linker between gp120 and gp41, an engineered 201-433 disulfide bond, and density corresponding to 22 N-glycans. Env-structure-guided design strategies resulted in multiple homogeneous cross-clade immunogens with the potential to advance HIV vaccine development.

    Organizational Affiliation: 

    IAVI Neutralizing Antibody Center at The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycoprotein gp120
G
485Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for A1EAI1 (Human immunodeficiency virus 1)
Go to UniProtKB:  A1EAI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
glycoprotein gp41
B
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for A1EAI1 (Human immunodeficiency virus 1)
Go to UniProtKB:  A1EAI1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab PGT124 light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab PGT124 heavy chain
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Fab 35022 heavy chain
D
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Fab 35022 light chain
E
216N/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 
G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.935 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.260 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 126.456α = 90.00
b = 126.456β = 90.00
c = 314.093γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
International AIDS Vaccine InitativeUnited StatesOPP1084519
International AIDS Vaccine InitativeUnited StatesOPP1115782

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Source and taxonomy, Structure summary