8TJS

CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO GPZ6-a.01 FAB

PDB DOI: https://doi.org/10.2210/pdb8TJS/pdb
EM Map EMD-41310: EMDB EMDataResource

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

Deposited: 2023-07-24 Released: 2024-07-31
Deposition Author(s): Morano, N.C., Becker, J.E., Shapiro, L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.31 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

CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO GPZ6-a.01 FAB

Morano, N.C., Becker, J.E., Shapiro, L.

To be published.

Macromolecule Content

Total Structure Weight: 306.43 kDa
Atom Count: 20,193
Modelled Residue Count: 2,448
Deposited Residue Count: 2,598
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 gp160	A [auth G], C [auth N], E [auth O]	480	Human immunodeficiency virus 1	Mutation(s): 0 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: 13	Glycosylation Focus chain A [auth G] Focus chain C [auth N] Focus chain E [auth O]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B, D [auth H], F [auth I]	153	Human immunodeficiency virus 1	Mutation(s): 2 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: 3	Glycosylation Focus chain B Focus chain D [auth H] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody GPZ6-a.01 Heavy Chain	G [auth Q], I [auth P], K [auth R]	126	Macaca	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
Antibody GPZ6-a.01 Light Chain	H [auth T], J [auth S], L [auth U]	107	Macaca	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
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	M [auth A], P [auth E], S [auth F]	6		N/A	Interactions Focus chain M [auth A] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain M [auth A] Focus chain P [auth E] Focus chain S [auth F]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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	N [auth C], O [auth D], Q [auth J], R [auth L], T [auth K], N [auth C], O [auth D], Q [auth J], R [auth L], T [auth K], U [auth M]	2		N/A	Interactions Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth J] Focus chain R [auth L] Focus chain T [auth K] Focus chain U [auth M] Interactions & Density Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth J] Focus chain R [auth L] Focus chain T [auth K] Focus chain U [auth M]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AA [auth G] SDF format, chain AB [auth H] SDF format, chain BA [auth G] SDF format, chain BB [auth O] SDF format, chain CA [auth G] SDF format, chain CB [auth O] SDF format, chain DA [auth G] SDF format, chain DB [auth O] SDF format, chain EA [auth G] SDF format, chain EB [auth O] SDF format, chain FA [auth G] SDF format, chain FB [auth O] SDF format, chain GA [auth G] SDF format, chain GB [auth O] SDF format, chain HA [auth G] SDF format, chain HB [auth O] SDF format, chain IA [auth B] SDF format, chain IB [auth O] SDF format, chain JA [auth B] SDF format, chain JB [auth O] SDF format, chain KA [auth B] SDF format, chain KB [auth O] SDF format, chain LA [auth N] SDF format, chain LB [auth O] SDF format, chain MA [auth N] SDF format, chain MB [auth O] SDF format, chain NA [auth N] SDF format, chain NB [auth O] SDF format, chain OA [auth N] SDF format, chain OB [auth I] SDF format, chain PA [auth N] SDF format, chain PB [auth I] SDF format, chain QA [auth N] SDF format, chain QB [auth I] SDF format, chain RA [auth N] SDF format, chain SA [auth N] SDF format, chain TA [auth N] SDF format, chain UA [auth N] SDF format, chain V [auth G] SDF format, chain VA [auth N] SDF format, chain W [auth G] SDF format, chain WA [auth N] SDF format, chain X [auth G] SDF format, chain XA [auth N] SDF format, chain Y [auth G] SDF format, chain YA [auth H] SDF format, chain Z [auth G] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth G] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain BB [auth O] MOL2 format, chain CA [auth G] MOL2 format, chain CB [auth O] MOL2 format, chain DA [auth G] MOL2 format, chain DB [auth O] MOL2 format, chain EA [auth G] MOL2 format, chain EB [auth O] MOL2 format, chain FA [auth G] MOL2 format, chain FB [auth O] MOL2 format, chain GA [auth G] MOL2 format, chain GB [auth O] MOL2 format, chain HA [auth G] MOL2 format, chain HB [auth O] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth O] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth O] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth O] MOL2 format, chain LA [auth N] MOL2 format, chain LB [auth O] MOL2 format, chain MA [auth N] MOL2 format, chain MB [auth O] MOL2 format, chain NA [auth N] MOL2 format, chain NB [auth O] MOL2 format, chain OA [auth N] MOL2 format, chain OB [auth I] MOL2 format, chain PA [auth N] MOL2 format, chain PB [auth I] MOL2 format, chain QA [auth N] MOL2 format, chain QB [auth I] MOL2 format, chain RA [auth N] MOL2 format, chain SA [auth N] MOL2 format, chain TA [auth N] MOL2 format, chain UA [auth N] MOL2 format, chain V [auth G] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth G] MOL2 format, chain WA [auth N] MOL2 format, chain X [auth G] MOL2 format, chain XA [auth N] MOL2 format, chain Y [auth G] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain ZA [auth H]	AA [auth G] AB [auth H] BA [auth G] BB [auth O] CA [auth G] AA [auth G], AB [auth H], BA [auth G], BB [auth O], CA [auth G], CB [auth O], DA [auth G], DB [auth O], EA [auth G], EB [auth O], FA [auth G], FB [auth O], GA [auth G], GB [auth O], HA [auth G], HB [auth O], IA [auth B], IB [auth O], JA [auth B], JB [auth O], KA [auth B], KB [auth O], LA [auth N], LB [auth O], MA [auth N], MB [auth O], NA [auth N], NB [auth O], OA [auth N], OB [auth I], PA [auth N], PB [auth I], QA [auth N], QB [auth I], RA [auth N], SA [auth N], TA [auth N], UA [auth N], V [auth G], VA [auth N], W [auth G], WA [auth N], X [auth G], XA [auth N], Y [auth G], YA [auth H], Z [auth G], ZA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain AB [auth H] Focus chain BA [auth G] Focus chain BB [auth O] Focus chain CA [auth G] Focus chain CB [auth O] Focus chain DA [auth G] Focus chain DB [auth O] Focus chain EA [auth G] Focus chain EB [auth O] Focus chain FA [auth G] Focus chain FB [auth O] Focus chain GA [auth G] Focus chain GB [auth O] Focus chain HA [auth G] Focus chain HB [auth O] Focus chain IA [auth B] Focus chain IB [auth O] Focus chain JA [auth B] Focus chain JB [auth O] Focus chain KA [auth B] Focus chain KB [auth O] Focus chain LA [auth N] Focus chain LB [auth O] Focus chain MA [auth N] Focus chain MB [auth O] Focus chain NA [auth N] Focus chain NB [auth O] Focus chain OA [auth N] Focus chain OB [auth I] Focus chain PA [auth N] Focus chain PB [auth I] Focus chain QA [auth N] Focus chain QB [auth I] Focus chain RA [auth N] Focus chain SA [auth N] Focus chain TA [auth N] Focus chain UA [auth N] Focus chain V [auth G] Focus chain VA [auth N] Focus chain W [auth G] Focus chain WA [auth N] Focus chain X [auth G] Focus chain XA [auth N] Focus chain Y [auth G] Focus chain YA [auth H] Focus chain Z [auth G] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth G] Focus chain AB [auth H] Focus chain BA [auth G] Focus chain BB [auth O] Focus chain CA [auth G] Focus chain CB [auth O] Focus chain DA [auth G] Focus chain DB [auth O] Focus chain EA [auth G] Focus chain EB [auth O] Focus chain FA [auth G] Focus chain FB [auth O] Focus chain GA [auth G] Focus chain GB [auth O] Focus chain HA [auth G] Focus chain HB [auth O] Focus chain IA [auth B] Focus chain IB [auth O] Focus chain JA [auth B] Focus chain JB [auth O] Focus chain KA [auth B] Focus chain KB [auth O] Focus chain LA [auth N] Focus chain LB [auth O] Focus chain MA [auth N] Focus chain MB [auth O] Focus chain NA [auth N] Focus chain NB [auth O] Focus chain OA [auth N] Focus chain OB [auth I] Focus chain PA [auth N] Focus chain PB [auth I] Focus chain QA [auth N] Focus chain QB [auth I] Focus chain RA [auth N] Focus chain SA [auth N] Focus chain TA [auth N] Focus chain UA [auth N] Focus chain V [auth G] Focus chain VA [auth N] Focus chain W [auth G] Focus chain WA [auth N] Focus chain X [auth G] Focus chain XA [auth N] Focus chain Y [auth G] Focus chain YA [auth H] Focus chain Z [auth G] Focus chain ZA [auth H]