6WIX

Crystal Structure of HIV-1 MI369 RnS-DS.SOSIP Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Automated Design by Structure-Based Stabilization and Consensus Repair to Achieve Prefusion-Closed Envelope Trimers in a Wide Variety of HIV Strains.

Rawi, R.Rutten, L.Lai, Y.T.Olia, A.S.Blokland, S.Juraszek, J.Shen, C.H.Tsybovsky, Y.Verardi, R.Yang, Y.Zhang, B.Zhou, T.Chuang, G.Y.Kwong, P.D.Langedijk, J.P.M.

(2020) Cell Rep 33: 108432-108432

  • DOI: https://doi.org/10.1016/j.celrep.2020.108432
  • Primary Citation of Related Structures:  
    6WIX

  • PubMed Abstract: 

    Soluble envelope (Env) trimers, stabilized in a prefusion-closed conformation, can elicit neutralizing responses against HIV-1 strains closely related to the immunizing trimer. However, to date such stabilization has succeeded with only a limited number of HIV-1 strains. To address this issue, here we develop ADROITrimer, an automated procedure involving structure-based stabilization and consensus repair, and generate "RnS-DS-SOSIP"-stabilized Envs from 180 diverse Env sequences. The vast majority of these RnS-DS-SOSIP Envs fold into prefusion-closed conformations as judged by antigenic analysis and size exclusion chromatography. Additionally, representative strains from clades AE, B, and C are stabilized in prefusion-closed conformations as shown by negative-stain electron microscopy, and the crystal structure of a clade A strain MI369.A5 Env trimer provides 3.5 Å resolution detail into stabilization and repair mutations. The automated procedure reported herein that yields well-behaved, soluble, prefusion-closed Env trimers from a majority of HIV-1 strains could have substantial impact on the development of an HIV-1 vaccine.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41A [auth B]153Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for O55774 (Human immunodeficiency virus 1)
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Go to UniProtKB:  O55774
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UniProt GroupO55774
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
35O22 scFv heavy chainB [auth D]134Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
35O22 scFv light chainC [auth E]114Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120D [auth G]498Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q0H5Z3 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q0H5Z3
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UniProt GroupQ0H5Z3
Glycosylation
Glycosylation Sites: 14
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
3H109L Fab heavy chainE [auth H]244Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
3H109L Fab light chainF [auth L]217Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth A]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth C],
I [auth F],
K [auth J],
M,
P
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I],
O
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K]10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.86α = 90
b = 131.86β = 90
c = 316.39γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description