8DTO

Vaccine elicited Antibody MU89 bound to CH848.D949.10.17_N133D_N138T.DS.SOSIP.664 HIV-1 Env trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mutation-guided vaccine design: A process for developing boosting immunogens for HIV broadly neutralizing antibody induction.

Wiehe, K.Saunders, K.O.Stalls, V.Cain, D.W.Venkatayogi, S.Martin Beem, J.S.Berry, M.Evangelous, T.Henderson, R.Hora, B.Xia, S.M.Jiang, C.Newman, A.Bowman, C.Lu, X.Bryan, M.E.Bal, J.Sanzone, A.Chen, H.Eaton, A.Tomai, M.A.Fox, C.B.Tam, Y.K.Barbosa, C.Bonsignori, M.Muramatsu, H.Alam, S.M.Montefiori, D.C.Williams, W.B.Pardi, N.Tian, M.Weissman, D.Alt, F.W.Acharya, P.Haynes, B.F.

(2024) Cell Host Microbe 32: 693-709.e7

  • DOI: https://doi.org/10.1016/j.chom.2024.04.006
  • Primary Citation of Related Structures:  
    8DTO, 8DY6

  • PubMed Abstract: 

    A major goal of HIV-1 vaccine development is the induction of broadly neutralizing antibodies (bnAbs). Although success has been achieved in initiating bnAb B cell lineages, design of boosting immunogens that select for bnAb B cell receptors with improbable mutations required for bnAb affinity maturation remains difficult. Here, we demonstrate a process for designing boosting immunogens for a V3-glycan bnAb B cell lineage. The immunogens induced affinity-matured antibodies by selecting for functional improbable mutations in bnAb precursor knockin mice. Moreover, we show similar success in prime and boosting with nucleoside-modified mRNA-encoded HIV-1 envelope trimer immunogens, with improved selection by mRNA immunogens of improbable mutations required for bnAb binding to key envelope glycans. These results demonstrate the ability of both protein and mRNA prime-boost immunogens for selection of rare B cell lineage intermediates with neutralizing breadth after bnAb precursor expansion, a key proof of concept and milestone toward development of an HIV-1 vaccine.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: kevin.wiehe@duke.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CH848.3.D0949.10.17chim.6R.DS.SOSIP.664_N133D_N138T gp120A [auth E],
E [auth A],
I
487Human immunodeficiency virusMutation(s): 0 
UniProt
Find proteins for A0A1W6IPB2 (Human immunodeficiency virus 1)
Explore A0A1W6IPB2 
Go to UniProtKB:  A0A1W6IPB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6IPB2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope Glycoprotein gp141B [auth F],
F [auth B],
J
153Human immunodeficiency virusMutation(s): 0 
UniProt
Find proteins for A0A6H1V945 (Simian-Human immunodeficiency virus)
Explore A0A6H1V945 
Go to UniProtKB:  A0A6H1V945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6H1V945
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MU89 Heavy ChainC [auth G],
G [auth C],
K
126Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MU89 Light ChainD [auth H],
H [auth D],
L
106Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM,
NA [auth n],
Z
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
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-glucopyranose
AA [auth a],
CA [auth c],
GA [auth g],
JA [auth j],
LA [auth l],
AA [auth a],
CA [auth c],
GA [auth g],
JA [auth j],
LA [auth l],
MA [auth m],
N,
OA [auth o],
P,
T,
UA [auth u],
W,
X,
XA [auth x]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
HA [auth h],
O,
PA [auth p],
U,
BA [auth b],
HA [auth h],
O,
PA [auth p],
U,
VA [auth v]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
EA [auth e],
KA [auth k],
Q,
QA [auth q],
DA [auth d],
EA [auth e],
KA [auth k],
Q,
QA [auth q],
R,
RA [auth r],
SA [auth s],
Y,
YA [auth y]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f],
S,
TA [auth t]
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseIA [auth i],
V,
WA [auth w]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth E]
BB [auth E]
CB [auth E]
DB [auth A]
EB [auth A]
AB [auth E],
BB [auth E],
CB [auth E],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth I],
HB [auth I],
IB [auth I],
JB [auth I],
KB [auth I],
ZA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE

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 StatesUM1-AI144371

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-05-08
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Database references