7T2P | pdb_00007t2p

The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11

PDB DOI: https://doi.org/10.2210/pdb7T2P/pdb
EM Map EMD-25621: EMDB EMDataResource

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

Deposited: 2021-12-06 Released: 2022-10-19
Deposition Author(s): Berndsen, Z.T., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.47 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

Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus.

Zhao, F., Berndsen, Z.T., Pedreno-Lopez, N., Burns, A., Allen, J.D., Barman, S., Lee, W.H., Chakraborty, S., Gnanakaran, S., Sewall, L.M., Ozorowski, G., Limbo, O., Song, G., Yong, P., Callaghan, S., Coppola, J., Weisgrau, K.L., Lifson, J.D., Nedellec, R., Voigt, T.B., Laurino, F., Louw, J., Rosen, B.C., Ricciardi, M., Crispin, M., Desrosiers, R.C., Rakasz, E.G., Watkins, D.I., Andrabi, R., Ward, A.B., Burton, D.R., Sok, D.

(2022) Nat Commun 13: 5236-5236

PubMed: 36068229 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-32783-2
Primary Citation Related Structures:
7T2P, 7T4G

PubMed Abstract:
SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model.

Organizational Affiliation

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.

Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

Department of Pathology, George Washington University, Washington, DC, 20037, USA.

School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.

IAVI, New York, NY, 10004, USA.

Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.

AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA.

Department of Pathology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. andrabi@scripps.edu.

IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. andrabi@scripps.edu.

Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA. andrabi@scripps.edu.

IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. andrew@scripps.edu.

Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA. andrew@scripps.edu.

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. andrew@scripps.edu.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. burton@scripps.edu.

IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. burton@scripps.edu.

Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA. burton@scripps.edu.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, 02139, USA. burton@scripps.edu.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. dsok@iavi.org.

IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA. dsok@iavi.org.

Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA. dsok@iavi.org.

IAVI, New York, NY, 10004, USA. dsok@iavi.org.

Macromolecule Content

Total Structure Weight: 167.73 kDa
Atom Count: 7,632
Modeled Residue Count: 873
Deposited Residue Count: 1,403
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A	527	Simian immunodeficiency virus	Mutation(s): 1 Gene Names: env
UniProt
Find proteins for Q5QG95 (Simian immunodeficiency virus) Explore Q5QG95 Go to UniProtKB: Q5QG95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5QG95
Glycosylation
Glycosylation Sites: 22	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B	159	Simian immunodeficiency virus	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q5QG95 (Simian immunodeficiency virus) Explore Q5QG95 Go to UniProtKB: Q5QG95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5QG95
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
K11 Fab heavy chain	C [auth H]	485	Macaca mulatta	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
K11 Fab light chain	D [auth L]	232	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranose	E [auth C]	8		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G34499SX GlyCosmos: G34499SX GlyGen: G34499SX

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], L [auth K], M, O, P	2		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain L [auth K] Focus chain M Focus chain O Focus chain P Interactions & Density Focus chain F [auth D] Focus chain L [auth K] Focus chain M Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E], H [auth F], I [auth G]	3		N-Glycosylation	Interactions Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Interactions & Density Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 8
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	J [auth I]	6		N-Glycosylation	Interactions Focus chain J [auth I] Interactions & Density Focus chain J [auth I]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 9
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	K [auth J]	5		N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 10
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	N	3		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] Q [auth A] R [auth A] AA [auth B], BA [auth B], CA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.47 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

Berndsen, Z.T.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462
Bill & Melinda Gates Foundation	United States	OPP1196345/INV-008813