8TR3

Cryo-EM structure of HmAb64 scFv in complex with CNE40 SOSIP trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Human CD4-binding site antibody elicited by polyvalent DNA prime-protein boost vaccine neutralizes cross-clade tier-2-HIV strains.

Wang, S.Chan, K.W.Wei, D.Ma, X.Liu, S.Hu, G.Park, S.Pan, R.Gu, Y.Nazzari, A.F.Olia, A.S.Xu, K.Lin, B.C.Louder, M.K.McKee, K.Doria-Rose, N.A.Montefiori, D.Seaman, M.S.Zhou, T.Kwong, P.D.Arthos, J.Kong, X.P.Lu, S.

(2024) Nat Commun 15: 4301-4301

  • DOI: https://doi.org/10.1038/s41467-024-48514-8
  • Primary Citation of Related Structures:  
    8TR3

  • PubMed Abstract: 

    The vaccine elicitation of HIV tier-2-neutralization antibodies has been a challenge. Here, we report the isolation and characterization of a CD4-binding site (CD4bs) specific monoclonal antibody, HmAb64, from a human volunteer immunized with a polyvalent DNA prime-protein boost HIV vaccine. HmAb64 is derived from heavy chain variable germline gene IGHV1-18 and light chain germline gene IGKV1-39. It has a third heavy chain complementarity-determining region (CDR H3) of 15 amino acids. On a cross-clade panel of 208 HIV-1 pseudo-virus strains, HmAb64 neutralized 20 (10%), including tier-2 strains from clades B, BC, C, and G. The cryo-EM structure of the antigen-binding fragment of HmAb64 in complex with a CNE40 SOSIP trimer revealed details of its recognition; HmAb64 uses both heavy and light CDR3s to recognize the CD4-binding loop, a critical component of the CD4bs. This study demonstrates that a gp120-based vaccine can elicit antibodies capable of tier 2-HIV neutralization.


  • Organizational Affiliation

    Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CNE40 SOSIP Envelope glycoprotein gp120A,
E [auth C],
I [auth E]
489Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: env
UniProt
Find proteins for D7S2E5 (Human immunodeficiency virus 1)
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Go to UniProtKB:  D7S2E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7S2E5
Glycosylation
Glycosylation Sites: 11
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CNE40 SOSIP Transmembrane protein gp41B,
F [auth D],
J [auth F]
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for D7S2E5 (Human immunodeficiency virus 1)
Explore D7S2E5 
Go to UniProtKB:  D7S2E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7S2E5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HmAb64 Fv heavy chainC [auth H],
G [auth I],
K [auth J]
124Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HmAb64 Fv light chainD [auth L],
H [auth M],
L [auth N]
109Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M [auth P],
N [auth R],
O [auth c],
P [auth e],
Q [auth p],
M [auth P],
N [auth R],
O [auth c],
P [auth e],
Q [auth p],
R [auth r]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth A],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth E],
LA [auth E],
MA [auth E],
NA [auth E],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth E],
S [auth A],
SA [auth E],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [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: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.20.1-4487

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: 2024-06-19
    Type: Initial release