8TOP | pdb_00008top

Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques.

Wang, H.Cheng, C.Dal Santo, J.L.Shen, C.H.Bylund, T.Henry, A.R.Howe, C.A.Hwang, J.Morano, N.C.Morris, D.J.Pletnev, S.Roark, R.S.Zhou, T.Hansen, B.T.Hoyt, F.H.Johnston, T.S.Wang, S.Zhang, B.Ambrozak, D.R.Becker, J.E.Bender, M.F.Changela, A.Chaudhary, R.Corcoran, M.Corrigan, A.R.Foulds, K.E.Guo, Y.Lee, M.Li, Y.Lin, B.C.Liu, T.Louder, M.K.Mandolesi, M.Mason, R.D.McKee, K.Nair, V.O'Dell, S.Olia, A.S.Ou, L.Pegu, A.Raju, N.Rawi, R.Roberts-Torres, J.Sarfo, E.K.Sastry, M.Schaub, A.J.Schmidt, S.D.Schramm, C.A.Schwartz, C.L.Smith, S.C.Stephens, T.Stuckey, J.Teng, I.T.Todd, J.P.Tsybovsky, Y.Van Wazer, D.J.Wang, S.Doria-Rose, N.A.Fischer, E.R.Georgiev, I.S.Karlsson Hedestam, G.B.Sheng, Z.Woodward, R.A.Douek, D.C.Koup, R.A.Pierson, T.C.Shapiro, L.Shaw, G.M.Mascola, J.R.Kwong, P.D.

(2024) Cell 187: 7214-7231.e23

  • DOI: https://doi.org/10.1016/j.cell.2024.10.003
  • Primary Citation Related Structures: 
    8TDX, 8TE7, 8TJR, 8TJS, 8TKC, 8TL2, 8TL3, 8TL4, 8TL5, 8TNU, 8TO7, 8TO9, 8TOP

  • PubMed Abstract: 

    An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the fusion-peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45%-77% breadth (geometric mean 50% inhibitory dilution [ID 50 ] ∼100) on a 208-strain panel. Molecular dissection of these responses by antibody isolation and cryo-electron microscopy (cryo-EM) structure determination revealed 15 of 16 antibody lineages with cross-clade neutralization to be directed toward the fusion-peptide site of vulnerability. In each macaque, isolated antibodies from memory B cells recapitulated the plasma-neutralizing response, with fusion-peptide-binding antibodies reaching breadths of 40%-60% (50% inhibitory concentration [IC 50 ] < 50 μg/mL) and total lineage-concentrations estimates of 50-200 μg/mL. Longitudinal mapping indicated that these responses arose prior to SHIV infection. Collectively, these results provide in vivo molecular examples for one to a few B cell lineages affording potent, broadly neutralizing plasma responses.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 744.59 kDa 
  • Atom Count: 38,845 
  • Modeled Residue Count: 4,755 
  • Deposited Residue Count: 6,510 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 BG505 DS-SOSIP gp120481Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 BG505 DS-SOSIP glycoprotein gp41153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of antibody GPZ6-b.01237Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of antibody GPZ6-b.01214Macaca mulattaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
CA [auth c],
EA [auth e],
GA [auth g],
HA [auth h],
AA [auth a],
CA [auth c],
EA [auth e],
GA [auth g],
HA [auth h],
JA [auth j],
KA [auth k],
MA [auth m],
Y [auth G]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranose
BA [auth b],
DA [auth d],
FA [auth f],
IA [auth i],
LA [auth l],
BA [auth b],
DA [auth d],
FA [auth f],
IA [auth i],
LA [auth l],
Z [auth I]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth Q]
AC [auth S]
AD [auth C]
BB [auth Q]
BC [auth T]
AB [auth Q],
AC [auth S],
AD [auth C],
BB [auth Q],
BC [auth T],
BD [auth C],
CB [auth Q],
CC [auth A],
CD [auth D],
DB [auth Q],
DC [auth A],
DD [auth D],
EB [auth Q],
EC [auth A],
ED [auth E],
FB [auth Q],
FC [auth A],
FD [auth E],
GB [auth Q],
GC [auth A],
GD [auth E],
HB [auth Q],
HC [auth A],
HD [auth E],
IB [auth Q],
IC [auth A],
ID [auth E],
JB [auth Q],
JC [auth A],
JD [auth E],
KB [auth Q],
KC [auth A],
KD [auth E],
LB [auth Q],
LC [auth A],
LD [auth E],
MB [auth Q],
MC [auth A],
MD [auth E],
NA [auth O],
NB [auth R],
NC [auth A],
ND [auth E],
OA [auth O],
OB [auth R],
OC [auth A],
OD [auth E],
PA [auth O],
PB [auth S],
PC [auth A],
PD [auth E],
QA [auth O],
QB [auth S],
QC [auth C],
QD [auth F],
RA [auth O],
RB [auth S],
RC [auth C],
SA [auth O],
SB [auth S],
SC [auth C],
TA [auth O],
TB [auth S],
TC [auth C],
UA [auth O],
UB [auth S],
UC [auth C],
VA [auth O],
VB [auth S],
VC [auth C],
WA [auth O],
WB [auth S],
WC [auth C],
XA [auth O],
XB [auth S],
XC [auth C],
YA [auth O],
YB [auth S],
YC [auth C],
ZA [auth Q],
ZB [auth S],
ZC [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



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: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-01-15
    Changes: Data collection, Database references