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



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