6UM7

Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex with CH848 10.17DT Env


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Targeted selection of HIV-specific antibody mutations by engineering B cell maturation.

Saunders, K.O.Wiehe, K.Tian, M.Acharya, P.Bradley, T.Alam, S.M.Go, E.P.Scearce, R.Sutherland, L.Henderson, R.Hsu, A.L.Borgnia, M.J.Chen, H.Lu, X.Wu, N.R.Watts, B.Jiang, C.Easterhoff, D.Cheng, H.L.McGovern, K.Waddicor, P.Chapdelaine-Williams, A.Eaton, A.Zhang, J.Rountree, W.Verkoczy, L.Tomai, M.Lewis, M.G.Desaire, H.R.Edwards, R.J.Cain, D.W.Bonsignori, M.Montefiori, D.Alt, F.W.Haynes, B.F.

(2019) Science 366

  • DOI: https://doi.org/10.1126/science.aay7199
  • Primary Citation of Related Structures:  
    6UM5, 6UM6, 6UM7

  • PubMed Abstract: 

    A major goal of HIV-1 vaccine development is the design of immunogens that induce broadly neutralizing antibodies (bnAbs). However, vaccination of humans has not resulted in the induction of affinity-matured and potent HIV-1 bnAbs. To devise effective vaccine strategies, we previously determined the maturation pathway of select HIV-1 bnAbs from acute infection through neutralizing antibody development. During their evolution, bnAbs acquire an abundance of improbable amino acid substitutions as a result of nucleotide mutations at variable region sequences rarely targeted by activation-induced cytidine deaminase, the enzyme responsible for antibody mutation. A subset of improbable mutations is essential for broad neutralization activity, and their acquisition represents a key roadblock to bnAb development.


  • Organizational Affiliation

    Human Vaccine Institute and Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA. kevin.saunders@duke.edu barton.haynes@duke.edu alt@enders.tch.harvard.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A,
F [auth E],
L [auth I]
463Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
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 gp41B [auth H],
E [auth D],
I [auth 1]
161Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
Explore Q2N0S7 
Go to UniProtKB:  Q2N0S7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DH270.mu1 Fab Heavy ChainC [auth J],
G [auth F],
J [auth B]
251Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DH270.mu1 Fab Light chainD [auth K],
H [auth G],
K [auth C]
235Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
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 Z],
M [auth L],
N [auth M],
P [auth O],
Q [auth P],
AA [auth Z],
M [auth L],
N [auth M],
P [auth O],
Q [auth P],
R [auth Q],
S [auth R],
U [auth T],
V [auth U],
W [auth V],
X [auth W],
Z [auth Y]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseO [auth N],
T [auth S],
Y [auth X]
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
FA [auth A]
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth E],
KA [auth E],
LA [auth E],
MA [auth E],
NA [auth E],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth I],
SA [auth I],
TA [auth I],
UA [auth I],
VA [auth I],
WA [auth I],
XA [auth I],
YA [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 StatesUM1-AI100645
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: 2019-12-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary