9OMG | pdb_00009omg

Cryo-EM structure of rhesus antibody V033-a.I1 in complex with HIV Env trimer Q23.17 MD39

PDB DOI: https://doi.org/10.2210/pdb9OMG/pdb
EM Map EMD-70613: EMDB EMDataResource

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

Deposited: 2025-05-13 Released: 2025-11-05
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

Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.

Habib, R., Roark, R.S., Li, H., Connell, A.J., Hogarty, M.P., Wagh, K., Wang, S., Marchitto, L., Skelly, A.N., Carey, J.W., Sowers, K.J., Ayyanathan, K., Plante, S.J., Bibollet-Ruche, F., Park, Y., Agostino, C.J., Singh, A., Martella, C.L., Lewis, E., Rando, J.M., Chohan, N., Lora, J., Ding, W., Campion, M.S., Zhao, C., Liu, W., Li, Y., Li, X., Liang, B., Chowdhury, R.R., Amereh, K., Van Itallie, E., Sheng, Z., Ghosh, A.R., Bar, K.J., Williams, W.B., Wiehe, K., Saunders, K.O., Edwards, R.J., Cain, D.W., Lewis, M.G., Batista, F.D., Burton, D.R., Andrabi, R., Kulp, D.W., Haynes, B.F., Korber, B., Shapiro, L., Kwong, P.D., Hahn, B.H., Shaw, G.M.

(2026) Sci Immunol 11: eadz3933-eadz3933

PubMed: 41686912 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciimmunol.adz3933
Primary Citation Related Structures:
9OMG

PubMed Abstract:
Broadly neutralizing antibodies (bNAbs) are rarely elicited during HIV-1 infection. To identify obstacles to bNAb development, we longitudinally studied 122 rhesus macaques infected by 1 of 16 different simian-human immunodeficiency viruses (SHIVs). We identified the V2 apex region of the envelope (Env) as the most common bNAb target and a subset of Envs that preferentially elicited these antibodies. In 10 macaques, we delineated Env-antibody coevolution from B cell priming to bNAb development. Antibody phylogenies revealed permissive developmental pathways guided by evolving Envs that contained few mutations in or near the V2 apex C-strand, which were a sensitive indicator of apex-targeted responses. The absence of such mutations reflected a failure in bNAb priming. These results indicate that efficiency of B cell priming, and not complexities in Env-guided affinity maturation, is a primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques and identify specific HIV-1 Envs to advance as vaccine platforms.

Organizational Affiliation

Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecule Content

Total Structure Weight: 285.38 kDa
Atom Count: 16,868
Modeled Residue Count: 1,923
Deposited Residue Count: 2,324
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Env gp120	A, C, D [auth E]	469	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 16	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
HIV Env gp41 ectodomain	B, E [auth F], F [auth G]	153	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 2	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
V033-Int1 heavy chain	G [auth H]	244	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-Int1 light chain	H [auth L]	214	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
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	BA [auth b], CA [auth c], DA [auth d], EA [auth e], GA [auth g], BA [auth b], CA [auth c], DA [auth d], EA [auth e], GA [auth g], IA [auth i], J [auth I], LA [auth l], M, N, O, OA [auth o], P, PA [auth p], QA [auth q], R, S, SA [auth s], TA [auth t], U, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth 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 GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain LA [auth l] Focus chain M Focus chain N Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain TA [auth t] Focus chain U Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth 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 GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain LA [auth l] Focus chain M Focus chain N Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain TA [auth t] Focus chain U Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y]
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	AA [auth a], FA [auth f], HA [auth h], K [auth J], KA [auth k], AA [auth a], FA [auth f], HA [auth h], K [auth J], KA [auth k], L [auth K], MA [auth m], NA [auth n], Q, RA [auth r], T, UA [auth u], Z	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain K [auth J] Focus chain KA [auth k] Focus chain L [auth K] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain Q Focus chain RA [auth r] Focus chain T Focus chain UA [auth u] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain K [auth J] Focus chain KA [auth k] Focus chain L [auth K] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain Q Focus chain RA [auth r] Focus chain T Focus chain UA [auth u] 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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	V	4		N-Glycosylation	Interactions Focus chain V Interactions & Density Focus chain V
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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	JA [auth j]	5		N-Glycosylation	Interactions Focus chain JA [auth j] Interactions & Density Focus chain JA [auth j]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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