9YMK | pdb_00009ymk

RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab

PDB DOI: https://doi.org/10.2210/pdb9YMK/pdb
EM Map EMD-73109: EMDB EMDataResource

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

Deposited: 2025-10-10 Released: 2026-07-08
Deposition Author(s): Sewall, L.M., Ozorowski, G., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Vaccination elicits HIV broadly neutralizing antibodies in primates

Steichen, J.M., Madden, P.J., Flynn, C.T., Phulera, S., Shil, M., Kalyuzhniy, O., Liguori, A., Kifude, C., Sewall, L.M., Cottrell, C.A., Ma, K.M., Baboo, S., Diedrich, J.K., McKenney, K., deCamp, A.C., Carnathan, D.G., Phung, I., Ramezani-Rad, P., Marina-Zarate, E., Freeman, B., Xie, Z., Lee, J.H., Sincomb, T., Phelps, N., Lu, D., Goodwin, D., Tingle, R., Adachi, Y., Alavi, N., Tran, J., Tran, A.S., Nascimento, A., Sovie, C., Bader, D.L.V., Voic, H., Zhou, X., Pixton, G., Walsh, A., Melo, M.B., Schiffner, T., Batista, F.D., Burton, D.R., Irvine, D.J., Paulson, J.C., Yates, J.R., Ozorowski, G., Ward, A.B., Silvestri, G., Crotty, S., Schief, W.R.

(2026) Nature

DOI: https://doi.org/10.1038/s41586-026-10837-5

Macromolecule Content

Total Structure Weight: 529.69 kDa
Atom Count: 25,272
Modeled Residue Count: 3,081
Deposited Residue Count: 4,671
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 Fab heavy chain	A [auth G], G [auth J], M [auth O]	229	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 light chain	B [auth I], H [auth M], N [auth Q]	215	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 MD39 SOSIP gp120	C [auth A], I [auth C], O [auth E]	513	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: 15	Glycosylation Focus chain C [auth A] Focus chain I [auth C] Focus chain O [auth E]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 MD39 SOSIP gp41	D [auth B], J [auth D], P [auth F]	153	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 B] Focus chain J [auth D] Focus chain P [auth F]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RVz20_wk72_08 Fab heavy chain	E [auth H], K, Q [auth P]	230	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RVz20_wk72_08 light chain	F [auth L], L [auth N], R	217	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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	CA [auth c], S, X	7		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain S Focus chain X Interactions & Density Focus chain CA [auth c] Focus chain S Focus chain X

Entity ID: 8
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	DA [auth d], T, Y	9		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain T Focus chain Y Interactions & Density Focus chain DA [auth d] Focus chain T Focus chain Y

Entity ID: 9
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], EA [auth e], GA [auth g], U, W, BA [auth b], EA [auth e], GA [auth g], U, W, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain U Focus chain W Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain U Focus chain W Focus chain Z

Entity ID: 10
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], V	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain FA [auth f] Focus chain V Interactions & Density Focus chain AA [auth a] Focus chain FA [auth f] Focus chain V

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 C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HA [auth A] SDF format, chain HB [auth E] SDF format, chain IA [auth A] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain KA [auth A] SDF format, chain KB [auth E] SDF format, chain LA [auth A] SDF format, chain LB [auth E] SDF format, chain MA [auth A] SDF format, chain MB [auth E] SDF format, chain NA [auth A] SDF format, chain NB [auth E] SDF format, chain OA [auth A] SDF format, chain OB [auth E] SDF format, chain PA [auth A] SDF format, chain PB [auth F] SDF format, chain QA [auth A] SDF format, chain QB [auth F] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain JA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth E] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth E] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth E] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth E] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth F] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth F] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain JA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth E] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth E] mmCIF format, chain JB [auth E] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth E] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth E] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth E] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth E] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth E] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth F] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth F] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain JA [auth A]	AB [auth C] BB [auth C] CB [auth C] DB [auth D] EB [auth D] AB [auth C], BB [auth C], CB [auth C], DB [auth D], EB [auth D], FB [auth E], GB [auth E], HA [auth A], HB [auth E], IA [auth A], IB [auth E], JA [auth A], JB [auth E], KA [auth A], KB [auth E], LA [auth A], LB [auth E], MA [auth A], MB [auth E], NA [auth A], NB [auth E], OA [auth A], OB [auth E], PA [auth A], PB [auth F], QA [auth A], QB [auth F], RA [auth B], SA [auth B], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth A] Focus chain HB [auth E] Focus chain IA [auth A] Focus chain IB [auth E] Focus chain JA [auth A] Focus chain JB [auth E] Focus chain KA [auth A] Focus chain KB [auth E] Focus chain LA [auth A] Focus chain LB [auth E] Focus chain MA [auth A] Focus chain MB [auth E] Focus chain NA [auth A] Focus chain NB [auth E] Focus chain OA [auth A] Focus chain OB [auth E] Focus chain PA [auth A] Focus chain PB [auth F] Focus chain QA [auth A] Focus chain QB [auth F] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth A] Focus chain HB [auth E] Focus chain IA [auth A] Focus chain IB [auth E] Focus chain JA [auth A] Focus chain JB [auth E] Focus chain KA [auth A] Focus chain KB [auth E] Focus chain LA [auth A] Focus chain LB [auth E] Focus chain MA [auth A] Focus chain MB [auth E] Focus chain NA [auth A] Focus chain NB [auth E] Focus chain OA [auth A] Focus chain OB [auth E] Focus chain PA [auth A] Focus chain PB [auth F] Focus chain QA [auth A] Focus chain QB [auth F] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]