6IEQ

Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report



Literature

Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence.

Sliepen, K.Han, B.W.Bontjer, I.Mooij, P.Garces, F.Behrens, A.J.Rantalainen, K.Kumar, S.Sarkar, A.Brouwer, P.J.M.Hua, Y.Tolazzi, M.Schermer, E.Torres, J.L.Ozorowski, G.van der Woude, P.de la Pena, A.T.van Breemen, M.J.Camacho-Sanchez, J.M.Burger, J.A.Medina-Ramirez, M.Gonzalez, N.Alcami, J.LaBranche, C.Scarlatti, G.van Gils, M.J.Crispin, M.Montefiori, D.C.Ward, A.B.Koopman, G.Moore, J.P.Shattock, R.J.Bogers, W.M.Wilson, I.A.Sanders, R.W.

(2019) Nat Commun 10: 2355-2355

  • DOI: 10.1038/s41467-019-10262-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinant ...

    Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 Å resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.


    Organizational Affiliation

    Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10021, USA. r.w.sanders@amc.uva.nl.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160G497Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160B153Human immunodeficiency virus 1Mutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PGT124 Fab Light ChainL214Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PGT124 Fab Heavy ChainH236Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
35O22 Fab Heavy ChainD240Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
35O22 Fab Light ChainE216Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
A
6 N-Glycosylation
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
C
4 N-Glycosylation
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, M, O
2 N-Glycosylation
Entity ID: 10
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-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-glucopyranose
I, K, N
5 N/A
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose
J
2 N/A
Entity ID: 12
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-glucopyranose
P
8 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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B, G
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

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H, L
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.59α = 90
b = 127.59β = 90
c = 315.507γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary