9BNK | pdb_00009bnk

Cryo-EM structure of rhesus antibody V031-a.01 in complex with HIV-1 Env BG505 DS-SOSIP

PDB DOI: https://doi.org/10.2210/pdb9BNK/pdb
EM Map EMD-44728: EMDB EMDataResource

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

Deposited: 2024-05-02 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: 3.10 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

HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene

Roark, R.S., Shapiro, L., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 279.31 kDa
Atom Count: 16,747
Modelled Residue Count: 1,966
Deposited Residue Count: 2,327
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V031-a.01 heavy chain	A [auth H]	248	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V031-a.01 light chain	B [auth L]	219	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Human immunodeficiency virus 1 envelope glycoprotein Gp120	C [auth G], E, F	473	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain C [auth G] Focus chain E Focus chain F
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp41	D [auth B], G [auth C], H [auth A]	147	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth B] Focus chain G [auth C] Focus chain H [auth A]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], I [auth D], K [auth J], N, O, AA [auth a], I [auth D], K [auth J], N, O, Q, R, S, T, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain I [auth D] Focus chain K [auth J] Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain I [auth D] Focus chain K [auth J] Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain Y Focus chain Z

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	J [auth I]	6		N-Glycosylation	Interactions Focus chain J [auth I] Interactions & Density Focus chain J [auth I]

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	L [auth K]	4		N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, U, W, X	3		N-Glycosylation	Interactions Focus chain M Focus chain U Focus chain W Focus chain X Interactions & Density Focus chain M Focus chain U Focus chain W Focus chain X

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	P, V	5		N-Glycosylation	Interactions Focus chain P Focus chain V Interactions & Density Focus chain P 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 F] SDF format, chain BA [auth G] SDF format, chain BB [auth F] SDF format, chain CA [auth G] SDF format, chain CB [auth F] SDF format, chain DA [auth G] SDF format, chain DB [auth F] SDF format, chain EA [auth G] SDF format, chain EB [auth F] SDF format, chain FA [auth G] SDF format, chain FB [auth F] SDF format, chain GA [auth G] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain IA [auth G] SDF format, chain IB [auth F] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LA [auth E] SDF format, chain LB [auth A] SDF format, chain MA [auth E] SDF format, chain MB [auth A] SDF format, chain NA [auth E] SDF format, chain NB [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth F] SDF format, chain HA [auth G] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain MB [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain NB [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth F] MOL2 format, chain HA [auth G] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain EB [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain FB [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain GB [auth F] mmCIF format, chain HB [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain IB [auth F] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth E] mmCIF format, chain LB [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain MB [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain NB [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth F] mmCIF format, chain HA [auth G]	AB [auth F] BA [auth G] BB [auth F] CA [auth G] CB [auth F] AB [auth F], BA [auth G], BB [auth F], CA [auth G], CB [auth F], DA [auth G], DB [auth F], EA [auth G], EB [auth F], FA [auth G], FB [auth F], GA [auth G], GB [auth F], HA [auth G], HB [auth F], IA [auth G], IB [auth F], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth E], LB [auth A], MA [auth E], MB [auth A], NA [auth E], NB [auth A], OA [auth E], PA [auth E], QA [auth E], RA [auth E], SA [auth E], TA [auth E], UA [auth E], VA [auth E], WA [auth E], XA [auth E], YA [auth E], ZA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth F] Focus chain BA [auth G] Focus chain BB [auth F] Focus chain CA [auth G] Focus chain CB [auth F] Focus chain DA [auth G] Focus chain DB [auth F] Focus chain EA [auth G] Focus chain EB [auth F] Focus chain FA [auth G] Focus chain FB [auth F] Focus chain GA [auth G] Focus chain GB [auth F] Focus chain HA [auth G] Focus chain HB [auth F] Focus chain IA [auth G] Focus chain IB [auth F] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth E] Focus chain LB [auth A] Focus chain MA [auth E] Focus chain MB [auth A] Focus chain NA [auth E] Focus chain NB [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth G] Focus chain BB [auth F] Focus chain CA [auth G] Focus chain CB [auth F] Focus chain DA [auth G] Focus chain DB [auth F] Focus chain EA [auth G] Focus chain EB [auth F] Focus chain FA [auth G] Focus chain FB [auth F] Focus chain GA [auth G] Focus chain GB [auth F] Focus chain HA [auth G] Focus chain HB [auth F] Focus chain IA [auth G] Focus chain IB [auth F] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth E] Focus chain LB [auth A] Focus chain MA [auth E] Focus chain MB [auth A] Focus chain NA [auth E] Focus chain NB [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth F]