5ESZ

Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.

Gorman, J.Soto, C.Yang, M.M.Davenport, T.M.Guttman, M.Bailer, R.T.Chambers, M.Chuang, G.Y.DeKosky, B.J.Doria-Rose, N.A.Druz, A.Ernandes, M.J.Georgiev, I.S.Jarosinski, M.C.Joyce, M.G.Lemmin, T.M.Leung, S.Louder, M.K.McDaniel, J.R.Narpala, S.Pancera, M.Stuckey, J.Wu, X.Yang, Y.Zhang, B.Zhou, T.Mullikin, J.C.Baxa, U.Georgiou, G.McDermott, A.B.Bonsignori, M.Haynes, B.F.Moore, P.L.Morris, L.Lee, K.K.Shapiro, L.Mascola, J.R.Kwong, P.D.

(2016) Nat Struct Mol Biol 23: 81-90

  • DOI: 10.1038/nsmb.3144
  • Primary Citation of Related Structures:  
    5ESV, 5ESZ

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor ...

    Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CH04 Heavy ChainE [auth A],
A [auth H]
244Homo sapiensMutation(s): 0 
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Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CH04 Light ChainF [auth B],
B [auth L]
215Homo sapiensMutation(s): 0 
Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
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UniProt GroupP01834
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,Envelope glycoprotein gp160C,
D [auth G]
222Haemophilus influenzae Rd KW20Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: ispFHI_0671env
EC: 4.6.1.12
UniProt
Find proteins for Q4QX31 (Human immunodeficiency virus 1)
Explore Q4QX31 
Go to UniProtKB:  Q4QX31
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44815 
Go to UniProtKB:  P44815
Entity Groups  
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UniProt GroupsQ4QX31P44815
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseG [auth D]5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth E],
J [auth I]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-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-glucopyranoseI [auth F]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G34442SS
GlyCosmos:  G34442SS
GlyGen:  G34442SS
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseK [auth J]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseL [auth K]4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.716α = 90
b = 116.716β = 90
c = 249.56γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary