9BTJ | pdb_00009btj

Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env

PDB DOI: https://doi.org/10.2210/pdb9BTJ/pdb
EM Map EMD-44892: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Macaca mulatta, Human immunodeficiency virus 1
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: 4.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

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: 295.13 kDa
Atom Count: 17,952
Modeled Residue Count: 2,010
Deposited Residue Count: 2,353
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 6561-a.01 light chain	A [auth L]	217	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 6561-a.01 heavy chain	B [auth H]	246	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	C [auth G], E [auth A], G [auth D]	477	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for C6G0D7 (Human immunodeficiency virus type 1) Explore C6G0D7 Go to UniProtKB: C6G0D7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6G0D7
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain C [auth G] Focus chain E [auth A] Focus chain G [auth D]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	D [auth B], F [auth C], H [auth E]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for C6G0E7 (Human immunodeficiency virus type 1) Explore C6G0E7 Go to UniProtKB: C6G0E7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6G0E7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain D [auth B] Focus chain F [auth C] Focus chain H [auth E]
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	AA [auth a], BA [auth b], CA [auth c], GA [auth g], HA [auth h], AA [auth a], BA [auth b], CA [auth c], GA [auth g], HA [auth h], I [auth F], IA [auth i], JA [auth j], KA [auth k], L [auth K], LA [auth l], M, OA [auth o], Q, R, S, V, W, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth F] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain L [auth K] Focus chain LA [auth l] Focus chain M Focus chain OA [auth o] Focus chain Q Focus chain R Focus chain S Focus chain V Focus chain W 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 GA [auth g] Focus chain HA [auth h] Focus chain I [auth F] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain L [auth K] Focus chain LA [auth l] Focus chain M Focus chain OA [auth o] Focus chain Q Focus chain R Focus chain S Focus chain V Focus chain W Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	DA [auth d], J [auth I], N, NA [auth n], T	5		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain J [auth I] Focus chain N Focus chain NA [auth n] Focus chain T Interactions & Density Focus chain DA [auth d] Focus chain J [auth I] Focus chain N Focus chain NA [auth n] Focus chain T
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	K [auth J], MA [auth m], X	3		N-Glycosylation	Interactions Focus chain K [auth J] Focus chain MA [auth m] Focus chain X Interactions & Density Focus chain K [auth J] Focus chain MA [auth m] Focus chain X
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)]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	O	7		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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	P	8		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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	U	9		N-Glycosylation	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Entity ID: 11
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	EA [auth e]	4		N-Glycosylation	Interactions Focus chain EA [auth e] Interactions & Density Focus chain EA [auth e]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 12
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	FA [auth f]	6		N-Glycosylation	Interactions Focus chain FA [auth f] Interactions & Density Focus chain FA [auth f]
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 G] SDF format, chain AC [auth D] SDF format, chain BB [auth G] SDF format, chain BC [auth D] SDF format, chain CB [auth G] SDF format, chain DB [auth G] SDF format, chain DC [auth D] SDF format, chain EC [auth D] SDF format, chain FB [auth B] SDF format, chain FC [auth D] SDF format, chain GB [auth B] SDF format, chain GC [auth D] SDF format, chain HB [auth B] SDF format, chain HC [auth D] SDF format, chain IB [auth A] SDF format, chain JC [auth D] SDF format, chain KB [auth A] SDF format, chain KC [auth D] SDF format, chain LB [auth A] SDF format, chain LC [auth E] SDF format, chain MB [auth A] SDF format, chain MC [auth E] SDF format, chain NB [auth A] SDF format, chain NC [auth E] SDF format, chain OB [auth A] SDF format, chain PA [auth G] SDF format, chain PB [auth A] SDF format, chain QA [auth G] SDF format, chain QB [auth A] SDF format, chain RA [auth G] SDF format, chain RB [auth A] SDF format, chain SA [auth G] SDF format, chain SB [auth A] SDF format, chain TA [auth G] SDF format, chain UA [auth G] SDF format, chain UB [auth A] SDF format, chain VA [auth G] SDF format, chain VB [auth A] SDF format, chain WB [auth A] SDF format, chain XA [auth G] SDF format, chain XB [auth C] SDF format, chain YA [auth G] SDF format, chain YB [auth C] SDF format, chain ZA [auth G] SDF format, chain ZB [auth C] SDF format, chain WA [auth G] SDF format, chain TB [auth A] SDF format, chain JB [auth A] SDF format, chain IC [auth D] SDF format, chain EB [auth G] SDF format, chain CC [auth D] MOL2 format, chain AB [auth G] MOL2 format, chain AC [auth D] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth D] MOL2 format, chain CB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth D] MOL2 format, chain EC [auth D] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth D] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth D] MOL2 format, chain HB [auth B] MOL2 format, chain HC [auth D] MOL2 format, chain IB [auth A] MOL2 format, chain JC [auth D] MOL2 format, chain KB [auth A] MOL2 format, chain KC [auth D] MOL2 format, chain LB [auth A] MOL2 format, chain LC [auth E] MOL2 format, chain MB [auth A] MOL2 format, chain MC [auth E] MOL2 format, chain NB [auth A] MOL2 format, chain NC [auth E] MOL2 format, chain OB [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain PB [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain QB [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain RB [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain SB [auth A] MOL2 format, chain TA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain UB [auth A] MOL2 format, chain VA [auth G] MOL2 format, chain VB [auth A] MOL2 format, chain WB [auth A] MOL2 format, chain XA [auth G] MOL2 format, chain XB [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain YB [auth C] MOL2 format, chain ZA [auth G] MOL2 format, chain ZB [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain TB [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain IC [auth D] MOL2 format, chain EB [auth G] MOL2 format, chain CC [auth D] mmCIF format, chain AB [auth G] mmCIF format, chain AC [auth D] mmCIF format, chain BB [auth G] mmCIF format, chain BC [auth D] mmCIF format, chain CB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain DC [auth D] mmCIF format, chain EC [auth D] mmCIF format, chain FB [auth B] mmCIF format, chain FC [auth D] mmCIF format, chain GB [auth B] mmCIF format, chain GC [auth D] mmCIF format, chain HB [auth B] mmCIF format, chain HC [auth D] mmCIF format, chain IB [auth A] mmCIF format, chain JC [auth D] mmCIF format, chain KB [auth A] mmCIF format, chain KC [auth D] mmCIF format, chain LB [auth A] mmCIF format, chain LC [auth E] mmCIF format, chain MB [auth A] mmCIF format, chain MC [auth E] mmCIF format, chain NB [auth A] mmCIF format, chain NC [auth E] mmCIF format, chain OB [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain PB [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain QB [auth A] mmCIF format, chain RA [auth G] mmCIF format, chain RB [auth A] mmCIF format, chain SA [auth G] mmCIF format, chain SB [auth A] mmCIF format, chain TA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain UB [auth A] mmCIF format, chain VA [auth G] mmCIF format, chain VB [auth A] mmCIF format, chain WB [auth A] mmCIF format, chain XA [auth G] mmCIF format, chain XB [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain YB [auth C] mmCIF format, chain ZA [auth G] mmCIF format, chain ZB [auth C] mmCIF format, chain WA [auth G] mmCIF format, chain TB [auth A] mmCIF format, chain JB [auth A] mmCIF format, chain IC [auth D] mmCIF format, chain EB [auth G] mmCIF format, chain CC [auth D]	AB [auth G] AC [auth D] BB [auth G] BC [auth D] CB [auth G] AB [auth G], AC [auth D], BB [auth G], BC [auth D], CB [auth G], CC [auth D], DB [auth G], DC [auth D], EB [auth G], EC [auth D], FB [auth B], FC [auth D], GB [auth B], GC [auth D], HB [auth B], HC [auth D], IB [auth A], IC [auth D], JB [auth A], JC [auth D], KB [auth A], KC [auth D], LB [auth A], LC [auth E], MB [auth A], MC [auth E], NB [auth A], NC [auth E], OB [auth A], PA [auth G], PB [auth A], QA [auth G], QB [auth A], RA [auth G], RB [auth A], SA [auth G], SB [auth A], TA [auth G], TB [auth A], UA [auth G], UB [auth A], VA [auth G], VB [auth A], WA [auth G], WB [auth A], XA [auth G], XB [auth C], YA [auth G], YB [auth C], ZA [auth G], ZB [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth G] Focus chain AC [auth D] Focus chain BB [auth G] Focus chain BC [auth D] Focus chain CB [auth G] Focus chain CC [auth D] Focus chain DB [auth G] Focus chain DC [auth D] Focus chain EB [auth G] Focus chain EC [auth D] Focus chain FB [auth B] Focus chain FC [auth D] Focus chain GB [auth B] Focus chain GC [auth D] Focus chain HB [auth B] Focus chain HC [auth D] Focus chain IB [auth A] Focus chain IC [auth D] Focus chain JB [auth A] Focus chain JC [auth D] Focus chain KB [auth A] Focus chain KC [auth D] Focus chain LB [auth A] Focus chain LC [auth E] Focus chain MB [auth A] Focus chain MC [auth E] Focus chain NB [auth A] Focus chain NC [auth E] Focus chain OB [auth A] Focus chain PA [auth G] Focus chain PB [auth A] Focus chain QA [auth G] Focus chain QB [auth A] Focus chain RA [auth G] Focus chain RB [auth A] Focus chain SA [auth G] Focus chain SB [auth A] Focus chain TA [auth G] Focus chain TB [auth A] Focus chain UA [auth G] Focus chain UB [auth A] Focus chain VA [auth G] Focus chain VB [auth A] Focus chain WA [auth G] Focus chain WB [auth A] Focus chain XA [auth G] Focus chain XB [auth C] Focus chain YA [auth G] Focus chain YB [auth C] Focus chain ZA [auth G] Focus chain ZB [auth C] Interactions & Density Focus chain AB [auth G] Focus chain AC [auth D] Focus chain BB [auth G] Focus chain BC [auth D] Focus chain CB [auth G] Focus chain CC [auth D] Focus chain DB [auth G] Focus chain DC [auth D] Focus chain EB [auth G] Focus chain EC [auth D] Focus chain FB [auth B] Focus chain FC [auth D] Focus chain GB [auth B] Focus chain GC [auth D] Focus chain HB [auth B] Focus chain HC [auth D] Focus chain IB [auth A] Focus chain IC [auth D] Focus chain JB [auth A] Focus chain JC [auth D] Focus chain KB [auth A] Focus chain KC [auth D] Focus chain LB [auth A] Focus chain LC [auth E] Focus chain MB [auth A] Focus chain MC [auth E] Focus chain NB [auth A] Focus chain NC [auth E] Focus chain OB [auth A] Focus chain PA [auth G] Focus chain PB [auth A] Focus chain QA [auth G] Focus chain QB [auth A] Focus chain RA [auth G] Focus chain RB [auth A] Focus chain SA [auth G] Focus chain SB [auth A] Focus chain TA [auth G] Focus chain TB [auth A] Focus chain UA [auth G] Focus chain UB [auth A] Focus chain VA [auth G] Focus chain VB [auth A] Focus chain WA [auth G] Focus chain WB [auth A] Focus chain XA [auth G] Focus chain XB [auth C] Focus chain YA [auth G] Focus chain YB [auth C] Focus chain ZA [auth G] Focus chain ZB [auth C]