9BNM | pdb_00009bnm

Cryo-EM structure of rhesus antibody 44715-a.01 in complex with HIV-1 Env BG505 DS-SOSIP

PDB DOI: https://doi.org/10.2210/pdb9BNM/pdb
EM Map EMD-44730: EMDB EMDataResource

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

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: 3.97 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: 282.11 kDa
Atom Count: 16,450
Modelled Residue Count: 1,917
Deposited Residue Count: 2,348
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp120	A, B, C	476	Human immunodeficiency virus 1	Mutation(s): 4 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 A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
47715-a.01 heavy chain	D [auth H]	245	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
44715-a.01 light chain	E [auth L]	219	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp41	F [auth X], G [auth Y], H [auth Z]	152	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: 1	Glycosylation Focus chain G [auth Y] Focus chain H [auth Z]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], I [auth D], J [auth E], JA [auth j], K [auth F], M [auth I], MA [auth m], N [auth J], NA [auth n], O [auth K], OA [auth o], PA [auth p], Q [auth N], R [auth O], S [auth P], T [auth Q], U [auth R], W [auth T], X [auth U], Y [auth V]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth D] Focus chain J [auth E] Focus chain JA [auth j] Focus chain K [auth F] Focus chain M [auth I] Focus chain MA [auth m] Focus chain N [auth J] Focus chain NA [auth n] Focus chain O [auth K] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth N] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain U [auth R] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth D] Focus chain J [auth E] Focus chain JA [auth j] Focus chain K [auth F] Focus chain M [auth I] Focus chain MA [auth m] Focus chain N [auth J] Focus chain NA [auth n] Focus chain O [auth K] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth N] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain U [auth R] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V]

Entity ID: 6
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	IA [auth i], L [auth G], LA [auth l], Z [auth W]	3		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain L [auth G] Focus chain LA [auth l] Focus chain Z [auth W] Interactions & Density Focus chain IA [auth i] Focus chain L [auth G] Focus chain LA [auth l] Focus chain Z [auth W]

Entity ID: 7
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 [auth M]	5		N-Glycosylation	Interactions Focus chain P [auth M] Interactions & Density Focus chain P [auth M]

Entity ID: 8
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	V [auth S]	4		N-Glycosylation	Interactions Focus chain V [auth S] Interactions & Density Focus chain V [auth S]

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	KA [auth k]	7		N-Glycosylation	Interactions Focus chain KA [auth k] Interactions & Density Focus chain KA [auth k]

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 B] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth Y] SDF format, chain IB [auth Z] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain SA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth Y] MOL2 format, chain IB [auth Z] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain SA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth Y] mmCIF format, chain IB [auth Z] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain SA [auth A]	AB [auth B] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth B], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth Y], IB [auth Z], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth Y] Focus chain IB [auth Z] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth Y] Focus chain IB [auth Z] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]