6BF4

Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.

Zhou, T.Zheng, A.Baxa, U.Chuang, G.Y.Georgiev, I.S.Kong, R.O'Dell, S.Shahzad-Ul-Hussan, S.Shen, C.H.Tsybovsky, Y.Bailer, R.T.Gift, S.K.Louder, M.K.McKee, K.Rawi, R.Stevenson, C.H.Stewart-Jones, G.B.E.Taft, J.D.Waltari, E.Yang, Y.Zhang, B.Shivatare, S.S.Shivatare, V.S.Lee, C.D.Wu, C.Y.Mullikin, J.C.Bewley, C.A.Burton, D.R.Polonis, V.R.Shapiro, L.Wong, C.H.Mascola, J.R.Kwong, P.D.Wu, X.

(2018) Immunity 48: 500-513.e6

  • DOI: 10.1016/j.immuni.2018.02.013
  • Primary Citation of Related Structures:  
    6BF4

  • PubMed Abstract: 
  • Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified antibody VRC-PG05, which neutralized 27% of HIV-1 strains ...

    Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified antibody VRC-PG05, which neutralized 27% of HIV-1 strains. The crystal structure of the antigen-binding fragment of VRC-PG05 in complex with gp120 revealed an epitope comprised primarily of N-linked glycans from N262, N295, and N448 at the silent face center. Somatic hypermutation occurred preferentially at antibody residues that interacted with these glycans, suggesting somatic development of glycan recognition. Resistance to VRC-PG05 in donor #74 involved shifting of glycan-N448 to N446 or mutation of glycan-proximal residue E293. HIV-1 neutralization can thus be achieved at the silent face center by glycan-recognizing antibody; along with other known epitopes, the VRC-PG05 epitope completes coverage by neutralizing antibody of all major exposed regions of the prefusion closed trimer.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY 10016, USA. Electronic address: xwu@adarc.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 clade AE gp120 coreA, D [auth G]344Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for D7S2G1 (Human immunodeficiency virus 1)
Explore D7S2G1 
Go to UniProtKB:  D7S2G1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VRC-PG05 Fab heavy chainB, E [auth H]229Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VRC-PG05 Fab light chainC, F [auth L]219Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D]10N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G12406PI
GlyCosmos:  G12406PI
GlyGen:  G12406PI
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]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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:  G36544AC
GlyCosmos:  G36544AC
GlyGen:  G36544AC
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I], N9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G95416NX
GlyCosmos:  G95416NX
GlyGen:  G95416NX
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J]11N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G13847GJ
GlyCosmos:  G13847GJ
GlyGen:  G13847GJ
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21381MC
GlyCosmos:  G21381MC
GlyGen:  G21381MC
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G75436UI
GlyCosmos:  G75436UI
GlyGen:  G75436UI
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth G] , BA [auth G] , CA [auth G] , DA [auth G] , EA [auth G] , HA [auth L] , O [auth A] , P [auth A] , 
AA [auth G],  BA [auth G],  CA [auth G],  DA [auth G],  EA [auth G],  HA [auth L],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  Y [auth C],  Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth G], GA [auth H], IA [auth L], JA [auth L], U [auth A], V [auth B], W [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
X [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.438α = 90
b = 89.255β = 119.15
c = 123.407γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2017-10-25 
  • Released Date: 2018-03-07 
  • Deposition Author(s): Zhou, T., Kwong, P.D.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary