6UUH

Crystal structure of broad and potent HIV-1 neutralizing antibody 438-B11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Literature

A V H 1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite.

Kumar, S.Ju, B.Shapero, B.Lin, X.Ren, L.Zhang, L.Li, D.Zhou, Z.Feng, Y.Sou, C.Mann, C.J.Hao, Y.Sarkar, A.Hou, J.Nunnally, C.Hong, K.Wang, S.Ge, X.Su, B.Landais, E.Sok, D.Zwick, M.B.He, L.Zhu, J.Wilson, I.A.Shao, Y.

(2020) Sci Adv 6

  • DOI: 10.1126/sciadv.abb1328
  • Primary Citation of Related Structures:  
    6UUH, 6UUL, 6UUM

  • PubMed Abstract: 
  • An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1-infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires ...

    An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1-infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires. Monoclonal antibodies 438-B11 and 438-D5 were isolated that potently neutralize HIV-1 with moderate breadth, are encoded by the V H 1-69 germline gene, and have a disulfide-linked long HCDR3 loop. Crystal structures of Env-bound and unbound antibodies revealed heavy chain-mediated recognition of the glycan supersite with a unique angle of approach and a critical role of the intra-HCDR3 disulfide. The mechanism of viral escape was examined via single-genome amplification/sequencing and glycan mutations around the N332 supersite. Our findings further emphasize the V3 glycan supersite as a prominent target for Env-based vaccine design.


    Organizational Affiliation

    The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B11 Fab Heavy ChainD [auth A], A [auth C]235Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
B11 Fab Light ChainE [auth B], B [auth D]215Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein GC [auth E], F66Streptococcus sp. 'group GMutation(s): 0 
Gene Names: spg
UniProt
Find proteins for P19909 (Streptococcus sp. group G)
Explore P19909 
Go to UniProtKB:  P19909
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G35261RT
GlyCosmos:  G35261RT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
H [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.157α = 90
b = 72.751β = 101.17
c = 108.716γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references