8TJR

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

PDB DOI: https://doi.org/10.2210/pdb8TJR/pdb
EM Map EMD-41309: EMDB EMDataResource

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

Deposited: 2023-07-24 Released: 2024-07-31
Deposition Author(s): Morano, N.C., Hoyt, F., Hansen, B., Fischer, 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: 3.29 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 HERH-c.01 FAB

Morano, N.C., Hoyt, F., Hansen, B., Fischer, E., Shapiro, L.

To be published.

Macromolecule Content

Total Structure Weight: 276.96 kDa
Atom Count: 18,283
Modelled Residue Count: 2,196
Deposited Residue Count: 2,336
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody HERH-a.01 Heavy Chain	A [auth J], G [auth H]	114	Macaca	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody HERH-a.01 Light Chain	B [auth K], H [auth L]	112	Macaca	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
Envelope glycoprotein gp160	C [auth A], E [auth B], I [auth C]	475	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 C [auth A] Focus chain E [auth B] Focus chain I [auth C]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	D, F [auth E], J [auth F]	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 D Focus chain F [auth E] Focus chain J [auth F]
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	K [auth P], N [auth U], Q [auth X]	6		N/A	Interactions Focus chain K [auth P] Focus chain N [auth U] Focus chain Q [auth X] Interactions & Density Focus chain K [auth P] Focus chain N [auth U] Focus chain Q [auth X]
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	L [auth Q], M [auth R], O [auth V], P [auth W], R [auth Y], L [auth Q], M [auth R], O [auth V], P [auth W], R [auth Y], S [auth Z]	2		N/A	Interactions Focus chain L [auth Q] Focus chain M [auth R] Focus chain O [auth V] Focus chain P [auth W] Focus chain R [auth Y] Focus chain S [auth Z] Interactions & Density Focus chain L [auth Q] Focus chain M [auth R] Focus chain O [auth V] Focus chain P [auth W] Focus chain R [auth Y] Focus chain S [auth Z]
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 A] SDF format, chain AB [auth C] SDF format, chain BA [auth A] SDF format, chain BB [auth C] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain FA [auth A] SDF format, chain FB [auth C] SDF format, chain GA [auth D] SDF format, chain GB [auth C] SDF format, chain HA [auth D] SDF format, chain HB [auth C] SDF format, chain IA [auth D] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain MB [auth F] SDF format, chain NA [auth B] SDF format, chain NB [auth F] SDF format, chain OA [auth B] SDF format, chain OB [auth F] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth E] SDF format, chain X [auth A] SDF format, chain XA [auth E] SDF format, chain Y [auth A] SDF format, chain YA [auth E] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth F] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C]	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth D], GB [auth C], HA [auth D], HB [auth C], IA [auth D], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth F], NA [auth B], NB [auth F], OA [auth B], OB [auth F], PA [auth B], QA [auth B], RA [auth B], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth E], X [auth A], XA [auth E], Y [auth A], YA [auth E], Z [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth D] Focus chain GB [auth C] Focus chain HA [auth D] Focus chain HB [auth C] Focus chain IA [auth D] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth F] Focus chain NA [auth B] Focus chain NB [auth F] Focus chain OA [auth B] Focus chain OB [auth F] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth E] Focus chain X [auth A] Focus chain XA [auth E] Focus chain Y [auth A] Focus chain YA [auth E] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth D] Focus chain GB [auth C] Focus chain HA [auth D] Focus chain HB [auth C] Focus chain IA [auth D] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth F] Focus chain NA [auth B] Focus chain NB [auth F] Focus chain OA [auth B] Focus chain OB [auth F] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth E] Focus chain X [auth A] Focus chain XA [auth E] Focus chain Y [auth A] Focus chain YA [auth E] Focus chain Z [auth A] Focus chain ZA [auth C]