9BTI | pdb_00009bti

Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env

PDB DOI: https://doi.org/10.2210/pdb9BTI/pdb
EM Map EMD-44891: EMDB EMDataResource

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

Deposited: 2024-05-15 Released: 2025-06-11
Deposition Author(s): Gorman, J., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.14 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies.

Roark, R.S., Habib, R., Gorman, J., Li, H., Connell, A.J., Bonsignori, M., Guo, Y., Hogarty, M.P., Olia, A.S., Sowers, K.J., Zhang, B., Bibollet-Ruche, F., Bylund, T., Callaghan, S., Carey, J.W., Cerutti, G., Harris, D.R., He, W., Lewis, E., Liu, T., Mason, R.D., Qiao, Y., Park, Y., Rando, J.M., Singh, A., Wolff, J.J., Lei, Q.P., Louder, M.K., Andrabi, R., Doria-Rose, N.A., Saunders, K.O., Seaman, M.S., Haynes, B.F., Kulp, D.W., Mascola, J.R., Roederer, M., Pierson, T.C., Sheng, Z., Hahn, B.H., Shaw, G.M., Kwong, P.D., Shapiro, L.

(2025) J Exp Medicine 222

PubMed: 40824240 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1084/jem.20250638
Primary Citation Related Structures:
9BNK, 9BNL, 9BNM, 9BNP, 9BTH, 9BTI, 9BTJ, 9BTL, 9BTV

PubMed Abstract:
Broadly neutralizing antibodies targeting the V2 apex of HIV-1 envelope are desired as vaccine design templates, but few have been described. Here, we report 11 lineages of V2 apex-neutralizing antibodies from simian-human immunodeficiency virus (SHIV)-infected rhesus macaques and determine cryo-EM structures for 9. A single V2 apex-neutralizing lineage accounted for cross-clade breadth in most macaques, and somatic hypermutation relative to breadth was generally low, exemplified by antibody V033-a.01 with <5% nucleotide mutation and 37% breadth (208-strain panel). Envelope complex structures revealed eight different antibody classes (one multi-donor) and the complete repertoire of all five possible recognition topologies, recapitulating canonical human modes of apex insertion and C-strand hydrogen bonding. Despite this diversity in recognition, all rhesus-V2 apex antibodies were derived from reading frame two of the DH3-15*01 gene. Collectively, these results define-in rhesus-the structural and genetic basis of HIV-1 V2 apex recognition and demonstrate unprecedented structural plasticity of a highly selected immunogenetic element.

Organizational Affiliation

Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons , New York, NY, USA.

Macromolecule Content

Total Structure Weight: 282.34 kDa
Atom Count: 16,447
Modeled Residue Count: 1,919
Deposited Residue Count: 2,355
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	A [auth B], E [auth A], G [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for B0F016 (Human immunodeficiency virus type 1) Explore B0F016 Go to UniProtKB: B0F016
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0F016
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	B [auth G], F [auth C], H	479	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for A0A8A0W558 (Human immunodeficiency virus type 1) Explore A0A8A0W558 Go to UniProtKB: A0A8A0W558
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8A0W558
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain B [auth G] Focus chain F [auth C] Focus chain H
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 40591-a.01 heavy chain	C [auth D]	245	Macaca mulatta	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 40591-a.01 light chain	D [auth E]	214	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	I, R	4		N-Glycosylation	Interactions Focus chain I Focus chain R Interactions & Density Focus chain I Focus chain R
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	AA [auth a], BA [auth b], CA [auth c], DA [auth d], GA [auth g], AA [auth a], BA [auth b], CA [auth c], DA [auth d], GA [auth g], HA [auth h], J, K, L, M, P, Q, S, T, U, V, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain V Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain V Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
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	EA [auth e], N, W	3		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain N Focus chain W Interactions & Density Focus chain EA [auth e] Focus chain N Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
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	FA [auth f], O, X	5		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain O Focus chain X Interactions & Density Focus chain FA [auth f] Focus chain O Focus chain X
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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	IA [auth i]	6		N-Glycosylation	Interactions Focus chain IA [auth i] Interactions & Density Focus chain IA [auth i]
Glycosylation Resources
GlyTouCan: G02763QD GlyCosmos: G02763QD GlyGen: G02763QD

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 AB [auth H] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain OA [auth G] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth H] SDF format, chain WA [auth H] SDF format, chain XA [auth H] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] SDF format, chain RA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain WA [auth H] MOL2 format, chain XA [auth H] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] MOL2 format, chain RA [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain WA [auth H] mmCIF format, chain XA [auth H] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H] mmCIF format, chain RA [auth C]	AB [auth H] JA [auth G] KA [auth G] LA [auth G] MA [auth G] AB [auth H], JA [auth G], KA [auth G], LA [auth G], MA [auth G], NA [auth G], OA [auth G], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth H], WA [auth H], XA [auth H], YA [auth H], ZA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth H] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth H] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain ZA [auth H]