6UM5

Cryo-EM structure of HIV-1 neutralizing antibody DH270 UCA3 in complex with CH848 10.17DT Env


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CH848 10.17 DT gp120
A, E, I
462Human 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 gp160
B, F, J
153Human 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 UCA3 Fab Heavy Chain
C, G, K
238Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DH270 UCA3 Fab Light Chain
D, H, L
216Homo sapiensMutation(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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
EA [auth e],
GA [auth g],
M,
Q,
AA [auth a],
EA [auth e],
GA [auth g],
M,
Q,
S,
T,
X,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
N,
U
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G27327VV
GlyCosmos:  G27327VV
GlyGen:  G27327VV
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c],
O,
V
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G95663PY
GlyCosmos:  G95663PY
Entity ID: 8
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
DA [auth d],
FA [auth f],
P,
R,
W,
DA [auth d],
FA [auth f],
P,
R,
W,
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 I]
BB [auth I]
CB [auth I]
DB [auth I]
EB [auth I]
AB [auth I],
BB [auth I],
CB [auth I],
DB [auth I],
EB [auth I],
FB [auth I],
GB [auth I],
HA [auth A],
HB [auth I],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth E],
RA [auth E],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
XA [auth E],
YA [auth E],
ZA [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: 4.20 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 Human Genome Research Institute (NIH/NHGRI)United StatesUM1-AI100645
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesUM1-AI144371

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary