6XRT | pdb_00006xrt

Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664

• PDB DOI: https://doi.org/10.2210/pdb6XRT/pdb
• EM Map EMD-22295: EMDB EMDataResource

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


• Deposited: 2020-07-13 Released: 2020-10-07 
• Deposition Author(s): Gorman, J., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth.

Roark, R.S., Li, H., Williams, W.B., Chug, H., Mason, R.D., Gorman, J., Wang, S., Lee, F.H., Rando, J., Bonsignori, M., Hwang, K.K., Saunders, K.O., Wiehe, K., Moody, M.A., Hraber, P.T., Wagh, K., Giorgi, E.E., Russell, R.M., Bibollet-Ruche, F., Liu, W., Connell, J., Smith, A.G., DeVoto, J., Murphy, A.I., Smith, J., Ding, W., Zhao, C., Chohan, N., Okumura, M., Rosario, C., Ding, Y., Lindemuth, E., Bauer, A.M., Bar, K.J., Ambrozak, D., Chao, C.W., Chuang, G.Y., Geng, H., Lin, B.C., Louder, M.K., Nguyen, R., Zhang, B., Lewis, M.G., Raymond, D.D., Doria-Rose, N.A., Schramm, C.A., Douek, D.C., Roederer, M., Kepler, T.B., Kelsoe, G., Mascola, J.R., Kwong, P.D., Korber, B.T., Harrison, S.C., Haynes, B.F., Hahn, B.H., Shaw, G.M.

(2021) Science 371

• PubMed: 33214287 
• DOI: https://doi.org/10.1126/science.abd2638
• Primary Citation Related Structures: 
  6XCJ, 6XRT


• PubMed Abstract: 
  

  Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.

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Organizational Affiliation: 
• Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Departments of Immunology and Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
Departments of Pediatrics and Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Bioqual, Inc., Rockville, MD 20850, USA.
Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA.
Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA.
Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo 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.

Macromolecule Content 

• Total Structure Weight: 257.74 kDa 
• Atom Count: 16,647 
• Modeled Residue Count: 1,947 
• Deposited Residue Count: 2,125 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth G], C [auth E], D [auth F]	476	Human immunodeficiency virus 1	Mutation(s): 0  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
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41	B, E [auth C], F [auth A]	153	Human immunodeficiency virus 1	Mutation(s): 2  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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC01.23 Heavy Chain	G [auth H]	133	Macaca mulatta	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC01.23 Light Chain	H [auth L]	105	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth D], L [auth K], M, O, P, Q, R, X, Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	J [auth I], N, T, U	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-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-glucopyranose	K [auth J]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

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	S, W	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-(1-3)-[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	V	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	AA [auth G], AB [auth F], BA [auth G], BB [auth F], CA [auth G], CB [auth F], DA [auth G], DB [auth F], EA [auth G], EB [auth F], FA [auth G], FB [auth F], GA [auth G], GB [auth F], HA [auth G], HB [auth F], IA [auth B], IB [auth F], JA [auth B], JB [auth C], KA [auth E], KB [auth C], LA [auth E], LB [auth A], MA [auth E], MB [auth A], NA [auth E], NB [auth A], OA [auth E], PA [auth E], 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 F], ZA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	G [auth H]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	2.14

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Gorman, J., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103310
Other private	United States	SF349247

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2021-01-20
  Changes: Database references
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Refinement description, Structure summary