9BNP | pdb_00009bnp

Cryo-EM structure of rhesus antibody V033-a.01 in complex with HIV-1 Env BG505 DS-SOSIP

PDB DOI: https://doi.org/10.2210/pdb9BNP/pdb
EM Map EMD-44733: EMDB EMDataResource

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

Deposited: 2024-05-02 Released: 2025-05-07
Deposition Author(s): Roark, R.S., Shapiro, L., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.17 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

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 Med 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: 254.57 kDa
Atom Count: 16,537
Modeled Residue Count: 1,920
Deposited Residue Count: 2,078
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp120	A, C [auth E], F [auth I]	468	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain C [auth E] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp41	B, D [auth F], G [auth J]	145	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth F] Focus chain G [auth J]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V033-a.01 heavy chain	E [auth H]	132	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V033-a.01 light chain	H [auth L]	107	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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	BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], I [auth C], IA [auth i], J [auth D], K [auth G], KA [auth k], M, N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, T, U, V, X, Y	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth C] Focus chain IA [auth i] Focus chain J [auth D] Focus chain K [auth G] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth C] Focus chain IA [auth i] Focus chain J [auth D] Focus chain K [auth G] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	L [auth K], W	4		N-Glycosylation	Interactions Focus chain L [auth K] Focus chain W Interactions & Density Focus chain L [auth K] Focus chain W
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
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	Z	6		N-Glycosylation	Interactions Focus chain Z Interactions & Density Focus chain Z
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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)-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	AA [auth a]	7		N-Glycosylation	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G23799GS GlyCosmos: G23799GS GlyGen: G23799GS

Entity ID: 9
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	JA [auth j], MA [auth m]	3		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain MA [auth m] Interactions & Density Focus chain JA [auth j] Focus chain MA [auth m]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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]	4		N-Glycosylation	Interactions Focus chain LA [auth l] Interactions & Density Focus chain LA [auth l]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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 ZA [auth E] SDF format, chain YA [auth E] SDF format, chain XA [auth A] SDF format, chain WA [auth A] SDF format, chain VA [auth A] SDF format, chain UA [auth A] SDF format, chain TA [auth A] SDF format, chain SA [auth A] SDF format, chain JB [auth J] SDF format, chain IB [auth J] SDF format, chain HB [auth I] SDF format, chain GB [auth I] SDF format, chain FB [auth I] SDF format, chain EB [auth I] SDF format, chain DB [auth I] SDF format, chain CB [auth F] SDF format, chain BB [auth E] SDF format, chain AB [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain XA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain JB [auth J] MOL2 format, chain IB [auth J] MOL2 format, chain HB [auth I] MOL2 format, chain GB [auth I] MOL2 format, chain FB [auth I] MOL2 format, chain EB [auth I] MOL2 format, chain DB [auth I] MOL2 format, chain CB [auth F] MOL2 format, chain BB [auth E] MOL2 format, chain AB [auth E] mmCIF format, chain ZA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain XA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain JB [auth J] mmCIF format, chain IB [auth J] mmCIF format, chain HB [auth I] mmCIF format, chain GB [auth I] mmCIF format, chain FB [auth I] mmCIF format, chain EB [auth I] mmCIF format, chain DB [auth I] mmCIF format, chain CB [auth F] mmCIF format, chain BB [auth E] mmCIF format, chain AB [auth E]	AB [auth E] BB [auth E] CB [auth F] DB [auth I] EB [auth I] AB [auth E], BB [auth E], CB [auth F], DB [auth I], EB [auth I], FB [auth I], GB [auth I], HB [auth I], IB [auth J], JB [auth J], SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth E], ZA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth F] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain FB [auth I] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IB [auth J] Focus chain JB [auth J] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth F] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain FB [auth I] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IB [auth J] Focus chain JB [auth J] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth E] Focus chain ZA [auth E]