8TKC

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

PDB DOI: https://doi.org/10.2210/pdb8TKC/pdb
EM Map EMD-41346: EMDB EMDataResource

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

Deposited: 2023-07-25 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: 3.10 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

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

Wang, H.

To be published.

Macromolecule Content

Total Structure Weight: 378.49 kDa
Atom Count: 20,064
Modelled Residue Count: 2,421
Deposited Residue Count: 3,264
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 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
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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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DJ85-b.01 FAB HEAVY CHAIN	G, I, K	240	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-b.01 FAB LIGHT CHAIN	H, J, L	214	Homo sapiens	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth Y], BA [auth Z], DA [auth d], EA [auth e], FA [auth f], AA [auth Y], BA [auth Z], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], KA [auth k], LA [auth l], M [auth a], N [auth M], NA [auth n], O [auth N], OA [auth o], PA [auth p], Q [auth P], R [auth Q], T [auth S], U [auth T], V [auth U], W [auth c], X [auth V], Y [auth W]	2		N-Glycosylation	Interactions Focus chain AA [auth Y] Focus chain BA [auth Z] 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 IA [auth i] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth a] Focus chain N [auth M] Focus chain NA [auth n] Focus chain O [auth N] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth P] Focus chain R [auth Q] Focus chain T [auth S] Focus chain U [auth T] Focus chain V [auth U] Focus chain W [auth c] Focus chain X [auth V] Focus chain Y [auth W] Interactions & Density Focus chain AA [auth Y] Focus chain BA [auth Z] 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 IA [auth i] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth a] Focus chain N [auth M] Focus chain NA [auth n] Focus chain O [auth N] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth P] Focus chain R [auth Q] Focus chain T [auth S] Focus chain U [auth T] Focus chain V [auth U] Focus chain W [auth c] Focus chain X [auth V] Focus chain Y [auth W]
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	JA [auth j], P [auth O], Z [auth X]	3		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain P [auth O] Focus chain Z [auth X] Interactions & Density Focus chain JA [auth j] Focus chain P [auth O] Focus chain Z [auth X]
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	CA [auth b], MA [auth m], S [auth R]	5		N-Glycosylation	Interactions Focus chain CA [auth b] Focus chain MA [auth m] Focus chain S [auth R] Interactions & Density Focus chain CA [auth b] Focus chain MA [auth m] Focus chain S [auth R]
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 DB [auth E] SDF format, chain EB [auth E] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C]	AB [auth E] BB [auth E] CB [auth E] DB [auth E] EB [auth E] AB [auth E], BB [auth E], CB [auth E], DB [auth E], EB [auth E], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	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 DB [auth E] Focus chain EB [auth E] 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 C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] 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 C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]