8TO9 | pdb_00008to9

Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120
A, B, C
463Homo sapiensMutation(s): 0 
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Glycosylation
Glycosylation Sites: 18
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRNM-f*01 heavy chain
D, E, H
126Macaca mulattaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TRNM-f*01 light chainF,
G,
K [auth L]
107Macaca mulattaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41I,
J,
L [auth Z]
153Homo sapiensMutation(s): 0 
Entity Groups  
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Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c],
N [auth M],
T [auth S],
Z [auth Y]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
CB [auth B]
DB [auth B]
EA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-12-25
    Changes: Data collection, Database references
  • Version 1.4: 2025-01-15
    Changes: Data collection, Database references