7N28

Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 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 1.2 of the entry. See complete history


Literature

Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2.

Gao, N.Gai, Y.Meng, L.Wang, C.Wang, W.Li, X.Gu, T.Louder, M.K.Doria-Rose, N.A.Wiehe, K.Nazzari, A.F.Olia, A.S.Gorman, J.Rawi, R.Wu, W.Smith, C.Khant, H.de Val, N.Yu, B.Luo, J.Niu, H.Tsybovsky, Y.Liao, H.Kepler, T.B.Kwong, P.D.Mascola, J.R.Qin, C.Zhou, T.Yu, X.Gao, F.

(2022) Adv Sci (Weinh) 9: e2200063-e2200063

  • DOI: https://doi.org/10.1002/advs.202200063
  • Primary Citation of Related Structures:  
    7MXD, 7N28

  • PubMed Abstract: 

    Understanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 can be highly informative for HIV-1 vaccine development. A lineage of J038 bnAbs is now obtained from a long-term SHIV-infected macaque. J038 neutralizes 54% of global circulating HIV-1 strains. Its binding induces a unique "up" conformation for one of the V2 loops in the trimeric envelope glycoprotein and is heavily dependent on glycan, which provides nearly half of the binding surface. Their unmutated common ancestor neutralizes the autologous virus. Continuous maturation enhances neutralization potency and breadth of J038 lineage antibodies via expanding antibody-Env contact areas surrounding the core region contacted by germline-encoded residues. Developmental details and recognition features of J038 lineage antibodies revealed here provide a new pathway for elicitation and maturation of V2-targeting bnAbs.


  • Organizational Affiliation

    National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A,
D [auth F],
E [auth G]
478Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for I6NF57 (Human immunodeficiency virus 1)
Explore I6NF57 
Go to UniProtKB:  I6NF57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6NF57
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3BNC117 antibody heavy chainB [auth C],
F [auth J],
H [auth S]
226Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
3BNC117 antibody light chainC [auth D],
G [auth K],
I [auth U]
206Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
J033 antibody heavy chainJ [auth X]230Macaca mulattaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
J033 antibody light chainK [auth Y]214Macaca mulattaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41L [auth M],
M [auth B],
N
170Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for I6NF57 (Human immunodeficiency virus 1)
Explore I6NF57 
Go to UniProtKB:  I6NF57
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UniProt GroupI6NF57
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
FA [auth f],
GA [auth g],
AA [auth a],
BA [auth b],
CA [auth c],
FA [auth f],
GA [auth g],
HA [auth h],
IA [auth i],
JA [auth j],
LA [auth l],
O [auth E],
OA [auth o],
P [auth H],
PA [auth p],
Q [auth I],
QA [auth q],
RA [auth r],
SA [auth s],
T [auth P],
TA [auth t],
UA [auth u],
V [auth R],
W [auth T],
X [auth V],
Y [auth W],
Z
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseR [auth L]8N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth e],
S [auth O]
7N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 10
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-glucopyranoseU [auth Q]3N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 11
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-glucopyranoseDA [auth d]4N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseKA [auth k]6N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G34442SS
GlyCosmos:  G34442SS
GlyGen:  G34442SS
Entity ID: 13
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-glucopyranoseMA [auth m]6N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 14
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseNA [auth n]4N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth K]
BB [auth A]
CB [auth A]
CC [auth U]
AB [auth A],
AC [auth K],
BB [auth A],
CB [auth A],
CC [auth U],
EB [auth D],
EC [auth M],
FC [auth M],
GC [auth M],
HB [auth F],
HC [auth B],
IB [auth F],
IC [auth B],
JB [auth F],
JC [auth B],
KB [auth F],
KC [auth B],
LB [auth F],
LC [auth N],
MB [auth F],
MC [auth N],
NB [auth F],
NC [auth N],
OB [auth F],
PB [auth F],
QB [auth F],
RB [auth G],
SB [auth G],
TB [auth G],
UB [auth G],
VA [auth A],
VB [auth G],
WA [auth A],
WB [auth G],
XA [auth A],
XB [auth G],
YA [auth A],
YB [auth G],
ZA [auth A],
ZB [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
BC [auth S],
DC [auth X]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DB [auth A],
FB [auth F],
GB [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.08

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2022-06-22
    Changes: Database references