9BNL | pdb_00009bnl

Cryo-EM structure of rhesus antibody 6070-a.01 in complex with HIV-1 Env trimer Q23.17 MD39

PDB DOI: https://doi.org/10.2210/pdb9BNL/pdb
EM Map EMD-44729: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Macaca mulatta
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: 3.60 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: 256.92 kDa
Atom Count: 16,749
Modelled Residue Count: 1,911
Deposited Residue Count: 2,056
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp120	A, C, D [auth E]	464	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain C Focus chain D [auth E]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein Gp41	B, E [auth F], F [auth G]	142	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain E [auth F] Focus chain F [auth G]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
6070-a.01 heavy chain	G [auth H]	131	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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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
6070-a.01 light chain	H [auth L]	107	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
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	I [auth D]	4		N-Glycosylation	Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]

Entity ID: 6
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], EA [auth e], GA [auth g], AA [auth a], BA [auth b], CA [auth c], EA [auth e], GA [auth g], IA [auth i], J [auth I], KA [auth k], L [auth K], M, MA [auth m], N, NA [auth n], O, OA [auth o], Q, QA [auth q], R, RA [auth r], T, TA [auth t], U, V, VA [auth v], W, X	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain KA [auth k] Focus chain L [auth K] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain KA [auth k] Focus chain L [auth K] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain V Focus chain VA [auth v] Focus chain W Focus chain X

Entity ID: 7
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	DA [auth d], FA [auth f], JA [auth j], K [auth J], LA [auth l], DA [auth d], FA [auth f], JA [auth j], K [auth J], LA [auth l], P, PA [auth p], S, SA [auth s], Y, Z	3		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain FA [auth f] Focus chain JA [auth j] Focus chain K [auth J] Focus chain LA [auth l] Focus chain P Focus chain PA [auth p] Focus chain S Focus chain SA [auth s] Focus chain Y Focus chain Z Interactions & Density Focus chain DA [auth d] Focus chain FA [auth f] Focus chain JA [auth j] Focus chain K [auth J] Focus chain LA [auth l] Focus chain P Focus chain PA [auth p] Focus chain S Focus chain SA [auth s] Focus chain Y Focus chain Z

Entity ID: 8
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	HA [auth h]	5		N-Glycosylation	Interactions Focus chain HA [auth h] Interactions & Density Focus chain HA [auth h]

Entity ID: 9
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	UA [auth u]	6		N-Glycosylation	Interactions Focus chain UA [auth u] Interactions & Density Focus chain UA [auth u]

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 E] SDF format, chain HB [auth E] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain KB [auth F] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain NB [auth G] SDF format, chain OB [auth G] SDF format, chain PB [auth G] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth B] 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 E] MOL2 format, chain HB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth G] MOL2 format, chain OB [auth G] MOL2 format, chain PB [auth G] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth B] 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 E] mmCIF format, chain HB [auth E] mmCIF format, chain IB [auth E] mmCIF format, chain JB [auth E] mmCIF format, chain KB [auth F] mmCIF format, chain LB [auth F] mmCIF format, chain MB [auth F] mmCIF format, chain NB [auth G] mmCIF format, chain OB [auth G] mmCIF format, chain PB [auth G] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth B]	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 E], HB [auth E], IB [auth E], JB [auth E], KB [auth F], LB [auth F], MB [auth F], NB [auth G], OB [auth G], PB [auth G], WA [auth A], XA [auth A], YA [auth A], 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 E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] 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 E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth G] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth B]