8TL2

CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-c.01 FAB

PDB DOI: https://doi.org/10.2210/pdb8TL2/pdb
EM Map EMD-41359: EMDB EMDataResource

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

Deposited: 2023-07-26 Released: 2024-08-28
Deposition Author(s): Pletnev, S., Hoyt, F., Fischer, E., Kwong, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques.

Wang, H.

To be published.

Macromolecule Content

Total Structure Weight: 329.66 kDa
Atom Count: 18,323
Modelled Residue Count: 2,187
Deposited Residue Count: 2,804
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 DS-SOSIP Surface protein gp120	A, C, E	481	Human immunodeficiency virus 1	Mutation(s): 6 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 DS-SOSIP Transmembrane protein gp41	B, D, F	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DJ85-c.01 FAB HEAVY CHAIN	G, I [auth K]	237	Homo sapiens	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
DJ85-c.01 FAB LIGHT CHAIN	H, J [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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	BA [auth Z], CA [auth b], DA [auth d], EA [auth e], FA [auth f], BA [auth Z], CA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], IA [auth i], JA [auth j], K [auth a], L [auth I], LA [auth l], M [auth J], MA [auth m], NA [auth n], O [auth N], P [auth O], R [auth Q], S [auth R], T [auth S], U [auth c], V [auth T], W [auth U], Y [auth W], Z [auth X]	2		N-Glycosylation	Interactions Focus chain BA [auth Z] Focus chain CA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K [auth a] Focus chain L [auth I] Focus chain LA [auth l] Focus chain M [auth J] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O [auth N] Focus chain P [auth O] Focus chain R [auth Q] Focus chain S [auth R] Focus chain T [auth S] Focus chain U [auth c] Focus chain V [auth T] Focus chain W [auth U] Focus chain Y [auth W] Focus chain Z [auth X] Interactions & Density Focus chain BA [auth Z] Focus chain CA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K [auth a] Focus chain L [auth I] Focus chain LA [auth l] Focus chain M [auth J] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O [auth N] Focus chain P [auth O] Focus chain R [auth Q] Focus chain S [auth R] Focus chain T [auth S] Focus chain U [auth c] Focus chain V [auth T] Focus chain W [auth U] Focus chain Y [auth W] Focus chain Z [auth X]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	HA [auth h], N [auth M], X [auth V]	3		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain N [auth M] Focus chain X [auth V] Interactions & Density Focus chain HA [auth h] Focus chain N [auth M] Focus chain X [auth V]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	AA [auth Y], KA [auth k], Q [auth P]	5		N-Glycosylation	Interactions Focus chain AA [auth Y] Focus chain KA [auth k] Focus chain Q [auth P] Interactions & Density Focus chain AA [auth Y] Focus chain KA [auth k] Focus chain Q [auth P]
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

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 E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] 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 E] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] 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 E] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] 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 E] mmCIF format, chain ZA [auth E]	AB [auth E] BB [auth E] CB [auth E] OA [auth A] PA [auth A] AB [auth E], BB [auth E], CB [auth E], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth E], ZA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] 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 E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] 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 E] Focus chain ZA [auth E]