7LG6 | pdb_00007lg6

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

• PDB DOI: https://doi.org/10.2210/pdb7LG6/pdb
• EM Map EMD-23312: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens, Macaca mulatta
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-01-19 Released: 2021-09-15 
• Deposition Author(s): Cottrell, C.A., Torres, J.L., Wu, N.R., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

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

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

• PubMed: 34731616 
• DOI: https://doi.org/10.1016/j.celrep.2021.109922
• Primary Citation 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.

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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.
Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Departments of Medicine, Epidemiology, and Microbiology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 18-mer - A3B3C3D3E3F3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 18-mer - A12B3C3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 526.22 kDa 
• Atom Count: 26,550 
• Modeled Residue Count: 3,153 
• Deposited Residue Count: 4,536 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A, G [auth E], M [auth F]	475	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6
Glycosylation
Glycosylation Sites: 17

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC40.01 Fab Heavy Chain	B [auth H], H [auth O], N [auth P]	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC40.01 Fab Kappa Light Chain	C [auth L], I [auth Q], O [auth R]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	D [auth B], J [auth G], P [auth I]	153	Human immunodeficiency virus 1	Mutation(s): 3  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6
Glycosylation
Glycosylation Sites: 3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RM19R Fab Kappa Light Chain	E [auth D], K [auth M], Q [auth N]	214	Macaca mulatta	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RM19R Fab Heavy Chain	F [auth C], L [auth J], R [auth K]	225	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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], 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	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], T, VA [auth v]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	KA [auth k], W, YA [auth y]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	LA [auth l], X, ZA [auth z]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], HB [auth 7], TA [auth t]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Rosetta

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Cottrell, C.A., Torres, J.L., Wu, N.R., Ward, A.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	F31 AI131873

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2021-11-17
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary