9NPM | pdb_00009npm

Composite map of three pairs of dimeric VRC36 Fabs bound to HIV-1 BG505.T332N DS-SOSIP.664 Env trimer

PDB DOI: https://doi.org/10.2210/pdb9NPM/pdb
EM Map EMD-49628: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-03-11 Released: 2026-08-19
Deposition Author(s): Cheng, J., Cale, E.M., Longo, N., Sutton, M.S., Lei, H., Huang, R., Morton, A.J., Lang, Z.C., Morano, N.C., Roark, R.S., Becker, J.E., Tsybovsky, Y., Li, N., Zhang, B., Du, H., Rubin, S., Shapiro, L., Pierson, T.C., Doria-Rose, N.A., Zhou, T., 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: 3.59 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

Composite map of three pairs of dimeric VRC36 Fabs bound to HIV-1 BG505.T332N DS-SOSIP.664 Env trimer

Cheng, J., Cale, E.M., Longo, N., Sutton, M.S., Lei, H., Huang, R., Morton, A.J., Lang, Z.C., Morano, N.C., Roark, R.S., Becker, J.E., Tsybovsky, Y., Li, N., Zhang, B., Du, H., Rubin, S., Shapiro, L., Pierson, T.C., Doria-Rose, N.A., Zhou, T., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 528.98 kDa
Atom Count: 35,931
Modeled Residue Count: 4,362
Deposited Residue Count: 4,500
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120	A [auth C], G [auth E], M [auth A]	473	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A [auth C] Focus chain G [auth E] Focus chain M [auth A]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp41	B [auth D], H [auth F], N [auth B]	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC36 Fab heavy chain	C [auth K] E [auth M] I [auth O] K [auth Q] O [auth G] C [auth K], E [auth M], I [auth O], K [auth Q], O [auth G], Q [auth I]	223	Homo sapiens	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
VRC36 Fab light chain	D [auth L] F [auth N] J [auth P] L [auth R] P [auth H] D [auth L], F [auth N], J [auth P], L [auth R], P [auth H], R [auth J]	214	Homo sapiens	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	DA [auth d], EA [auth e], GA [auth g], HA [auth h], OA [auth o], DA [auth d], EA [auth e], GA [auth g], HA [auth h], OA [auth o], PA [auth p], RA [auth r], S, SA [auth s], T, V, W	2		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain V Focus chain W Interactions & Density Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain V Focus chain W

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	FA [auth f], QA [auth q], U	4		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain QA [auth q] Focus chain U Interactions & Density Focus chain FA [auth f] Focus chain QA [auth q] Focus chain U

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)]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	IA [auth i], TA [auth t], X	9		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain TA [auth t] Focus chain X Interactions & Density Focus chain IA [auth i] Focus chain TA [auth t] Focus chain X

Entity ID: 8
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-(1-3)-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], KA [auth k], VA [auth v], Y, Z	8		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain KA [auth k] Focus chain VA [auth v] Focus chain Y Focus chain Z Interactions & Density Focus chain JA [auth j] Focus chain KA [auth k] Focus chain VA [auth v] Focus chain Y Focus chain Z

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-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	AA [auth a], BA [auth b], LA [auth l], MA [auth m], WA [auth w], AA [auth a], BA [auth b], LA [auth l], MA [auth m], WA [auth w], XA [auth x]	6		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain WA [auth w] Focus chain XA [auth x] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain WA [auth w] Focus chain XA [auth x]

Entity ID: 10
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	CA [auth c], NA [auth n], ZA [auth z]	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain NA [auth n] Focus chain ZA [auth z] Interactions & Density Focus chain CA [auth c] Focus chain NA [auth n] Focus chain ZA [auth z]

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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	UA [auth u]	6		N-Glycosylation	Interactions Focus chain UA [auth u] Interactions & Density Focus chain UA [auth u]

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	YA [auth y]	2		N/A	Interactions Focus chain YA [auth y] Interactions & Density Focus chain YA [auth y]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain OB [auth A] SDF format, chain NB [auth A] SDF format, chain MB [auth A] SDF format, chain LB [auth A] SDF format, chain KB [auth A] SDF format, chain JB [auth E] SDF format, chain IB [auth E] SDF format, chain HB [auth E] SDF format, chain GB [auth E] SDF format, chain FB [auth E] SDF format, chain EB [auth C] SDF format, chain DB [auth C] SDF format, chain CB [auth C] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain OB [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain HB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain EB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain OB [auth A] mmCIF format, chain NB [auth A] mmCIF format, chain MB [auth A] mmCIF format, chain LB [auth A] mmCIF format, chain KB [auth A] mmCIF format, chain JB [auth E] mmCIF format, chain IB [auth E] mmCIF format, chain HB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain EB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth E], GB [auth E], HB [auth E], IB [auth E], JB [auth E], KB [auth A], LB [auth A], MB [auth A], NB [auth A], OB [auth A]	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 C] Focus chain EB [auth C] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth A] Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth A] Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A]