Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - ABCDEF Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer -A2B2CD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 180215.86 
• Atom Count: 12221 
• Residue Count: 1544 
• Unique protein chains: 6

5UM8

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

• DOI: 10.2210/pdb5UM8/pdb

• Classification: Viral Protein/Immune System
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens


• Deposited: 2017-01-26 Released: 2017-05-24 
• Deposition Author(s): Garces, F., Stanfield, R.L., Wilson, I.A.
• Funding Organization(s): International AIDS Vaccine Initative 

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Experimental Data Snapshot

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

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

• PubMed: 28514686 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
glycoprotein gp120	G	485	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for A1EAI1 (Human immunodeficiency virus 1) Go to UniProtKB:  A1EAI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
glycoprotein gp41	B	153	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for A1EAI1 (Human immunodeficiency virus 1) Go to UniProtKB:  A1EAI1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fab PGT124 light chain	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Fab PGT124 heavy chain	H	236	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Fab 35022 heavy chain	D	240	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Fab 35022 light chain	E	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	G	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	G	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	B, G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 126.456	α = 90.00
b = 126.456	β = 90.00
c = 314.093	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-01-26 
• Released Date: 2017-05-24 
• Deposition Author(s): Garces, F., Stanfield, R.L., Wilson, I.A.

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Funding Organization	Country	Grant Number
International AIDS Vaccine Initative	United States	OPP1084519
International AIDS Vaccine Initative	United States	OPP1115782

Revision History 

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