8SWW

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody IF3

• PDB DOI: https://doi.org/10.2210/pdb8SWW/pdb
• EM Map EMD-40823: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Macaca mulatta
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-05-19 Released: 2024-05-22 
• Deposition Author(s): Pratap, P.P., Antansijevic, A., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Focusing antibody responses to the fusion peptide in rhesus macaques

Cottrell, C.A., Pratap, P.P., Ward, A.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 254.16 kDa 
• Atom Count: 14,799 
• Modelled Residue Count: 1,881 
• Deposited Residue Count: 2,231 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein gp120	A, D [auth E], F	516	Human immunodeficiency virus 1	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	B, C, E [auth D]	153	Human immunodeficiency virus 1	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NHP polyclonal antibody IF3 Heavy Chain	G [auth H]	111	Macaca mulatta	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NHP polyclonal antibody IF3 Light Chain	H [auth L]	113	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], J [auth I], K [auth J], M, O	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	N	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth E], GA [auth F], HA [auth F], IA [auth F], JA [auth F], KA [auth F], LA [auth F], MA [auth F], NA [auth F], OA [auth F], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth B], X [auth B], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Pratap, P.P., Antansijevic, A., Ward, A.B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI136621
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1AI10066
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release