9BNL | pdb_00009bnl

Cryo-EM structure of rhesus antibody 6070-a.01 in complex with HIV-1 Env trimer Q23.17 MD39

PDB DOI: https://doi.org/10.2210/pdb9BNL/pdb
EM Map EMD-44729: 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: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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: 256.92 kDa
Atom Count: 16,749
Modeled Residue Count: 1,911
Deposited Residue Count: 2,056
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, D [auth E]	464	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain C Focus chain D [auth E]
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, E [auth F], F [auth G]	142	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain E [auth F] Focus chain F [auth G]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
6070-a.01 heavy chain	G [auth H]	131	Macaca mulatta	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
6070-a.01 light chain	H [auth L]	107	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 [auth D]	4		N-Glycosylation	Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
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], EA [auth e], GA [auth g], AA [auth a], BA [auth b], CA [auth c], EA [auth e], GA [auth g], IA [auth i], J [auth I], KA [auth k], L [auth K], M, MA [auth m], N, NA [auth n], O, OA [auth o], Q, QA [auth q], R, RA [auth r], T, TA [auth t], U, V, VA [auth v], W, X	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain KA [auth k] Focus chain L [auth K] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain KA [auth k] Focus chain L [auth K] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X
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	DA [auth d], FA [auth f], JA [auth j], K [auth J], LA [auth l], DA [auth d], FA [auth f], JA [auth j], K [auth J], LA [auth l], P, PA [auth p], S, SA [auth s], Y, Z	3		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain FA [auth f] Focus chain JA [auth j] Focus chain K [auth J] Focus chain LA [auth l] Focus chain P Focus chain PA [auth p] Focus chain S Focus chain SA [auth s] Focus chain Y Focus chain Z Interactions & Density Focus chain DA [auth d] Focus chain FA [auth f] Focus chain JA [auth j] Focus chain K [auth J] Focus chain LA [auth l] Focus chain P Focus chain PA [auth p] Focus chain S Focus chain SA [auth s] Focus chain Y Focus chain Z
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	HA [auth h]	5		N-Glycosylation	Interactions Focus chain HA [auth h] Interactions & Density Focus chain HA [auth h]
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-(1-3)-[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	UA [auth u]	6		N-Glycosylation	Interactions Focus chain UA [auth u] Interactions & Density Focus chain UA [auth u]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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 B] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth E] SDF format, chain HB [auth E] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain KB [auth F] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain NB [auth G] SDF format, chain OB [auth G] SDF format, chain PB [auth G] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth E] MOL2 format, chain HB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth G] MOL2 format, chain OB [auth G] MOL2 format, chain PB [auth G] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth E] mmCIF format, chain HB [auth E] mmCIF format, chain IB [auth E] mmCIF format, chain JB [auth E] mmCIF format, chain KB [auth F] mmCIF format, chain LB [auth F] mmCIF format, chain MB [auth F] mmCIF format, chain NB [auth G] mmCIF format, chain OB [auth G] mmCIF format, chain PB [auth G] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth B]	AB [auth B] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth B], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth E], HB [auth E], IB [auth E], JB [auth E], KB [auth F], LB [auth F], MB [auth F], NB [auth G], OB [auth G], PB [auth G], WA [auth A], XA [auth A], YA [auth A], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth B]