4YDK

Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex with HIV-1 clade AE strain 93TH057 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.

Zhou, T.Lynch, R.M.Chen, L.Acharya, P.Wu, X.Doria-Rose, N.A.Joyce, M.G.Lingwood, D.Soto, C.Bailer, R.T.Ernandes, M.J.Kong, R.Longo, N.S.Louder, M.K.McKee, K.O'Dell, S.Schmidt, S.D.Tran, L.Yang, Z.Druz, A.Luongo, T.S.Moquin, S.Srivatsan, S.Yang, Y.Zhang, B.Zheng, A.Pancera, M.Kirys, T.Georgiev, I.S.Gindin, T.Peng, H.P.Yang, A.S.Mullikin, J.C.Gray, M.D.Stamatatos, L.Burton, D.R.Koff, W.C.Cohen, M.S.Haynes, B.F.Casazza, J.P.Connors, M.Corti, D.Lanzavecchia, A.Sattentau, Q.J.Weiss, R.A.West, A.P.Bjorkman, P.J.Scheid, J.F.Nussenzweig, M.C.Shapiro, L.Mascola, J.R.Kwong, P.D.

(2015) Cell 161: 1280-1292

  • DOI: 10.1016/j.cell.2015.05.007
  • Primary Citation of Related Structures:  
    4RX4, 4RWY, 4YE4, 4YDI, 4YDJ, 4YDK, 4YDL, 4YFL

  • PubMed Abstract: 
  • The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors ...

    The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: pdkwong@nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160,Envelope glycoprotein gp160A [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN OF ANTIBODY C38-VRC16.01B [auth H]234Homo 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
LIGHT CHAIN OF ANTIBODY C38-VRC16.01C [auth L]214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth G] , E [auth G] , F [auth G] , G , H [auth G] , I [auth G] , J [auth G] , K [auth G] , 
D [auth G],  E [auth G],  F [auth G],  G,  H [auth G],  I [auth G],  J [auth G],  K [auth G],  L [auth G],  M [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NHE
Query on NHE

Download Ideal Coordinates CCD File 
S [auth G]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth L], CA [auth L], N [auth G], O [auth G], P [auth G], Q [auth G], X [auth H]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth H] , DA [auth L] , EA [auth L] , FA [auth L] , GA [auth L] , HA [auth L] , R [auth G] , T [auth G] , 
AA [auth H],  DA [auth L],  EA [auth L],  FA [auth L],  GA [auth L],  HA [auth L],  R [auth G],  T [auth G],  U [auth G],  V [auth G],  W [auth G],  Y [auth H],  Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.836α = 90
b = 109.686β = 126.26
c = 100.063γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2015-06-17
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary