7LG6

BG505 SOSIP.v5.2 in complex with VRC40.01 and RM19R Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies.

Cottrell, C.A.Manne, K.Kong, R.Wang, S.Zhou, T.Chuang, G.Y.Edwards, R.J.Henderson, R.Janowska, K.Kopp, M.Lin, B.C.Louder, M.K.Olia, A.S.Rawi, R.Shen, C.H.Taft, J.D.Torres, J.L.Wu, N.R.Zhang, B.Doria-Rose, N.A.Cohen, M.S.Haynes, B.F.Shapiro, L.Ward, A.B.Acharya, P.Mascola, J.R.Kwong, P.D.

(2021) Cell Rep 37: 109922-109922

  • DOI: https://doi.org/10.1016/j.celrep.2021.109922
  • Primary Citation of Related Structures:  
    7LG6, 7LL1, 7LL2, 7LLK

  • PubMed Abstract: 

    Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.


  • Organizational Affiliation

    IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A,
G [auth E],
M [auth F]
475Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VRC40.01 Fab Heavy ChainB [auth H],
H [auth O],
N [auth P]
231Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VRC40.01 Fab Kappa Light ChainC [auth L],
I [auth Q],
O [auth R]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41D [auth B],
J [auth G],
P [auth I]
153Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RM19R Fab Kappa Light ChainE [auth D],
K [auth M],
Q [auth N]
214Macaca mulattaMutation(s): 0 
Entity Groups  
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RM19R Fab Heavy ChainF [auth C],
L [auth J],
R [auth K]
225Macaca mulattaMutation(s): 0 
Entity Groups  
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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],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
CB [auth 2],
DA [auth d],
DB [auth 3],
EA [auth e],
EB [auth 4],
FB [auth 5],
GA [auth g],
GB [auth 6],
IA [auth i],
JA [auth j],
MA [auth m],
NA [auth n],
OA [auth o],
PA [auth p],
QA [auth q],
RA [auth r],
S,
SA [auth s],
U,
UA [auth u],
V,
WA [auth w],
XA [auth x],
Y,
Z
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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-glucopyranoseHA [auth h],
T,
VA [auth v]
3N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
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-glucopyranoseKA [auth k],
W,
YA [auth y]
6N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseLA [auth l],
X,
ZA [auth z]
8N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f],
HB [auth 7],
TA [auth t]
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
IB [auth A]
JB [auth A]
KB [auth A]
LB [auth A]
MB [auth B]
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth B],
NB [auth B],
OB [auth E],
PB [auth E],
QB [auth E],
RB [auth E],
SB [auth G],
TB [auth G],
UB [auth F],
VB [auth F],
WB [auth F],
XB [auth F],
YB [auth I],
ZB [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: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTRosetta

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 AI144462
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF31 AI131873

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references