8TNU

Cryo-EM structure of TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP

PDB DOI: https://doi.org/10.2210/pdb8TNU/pdb
EM Map EMD-41426: EMDB EMDataResource

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

Deposited: 2023-08-02 Released: 2024-08-07
Deposition Author(s): Roark, R.S., Morano, N.C., Shapiro, L.S., 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: 3.36 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., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 376.54 kDa
Atom Count: 24,893
Modelled Residue Count: 3,039
Deposited Residue Count: 3,219
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNM-b*01 heavy chain	A [auth B], D [auth J], F [auth H]	226	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNM-b*01 light chain	B [auth C], E [auth K], G [auth L]	213	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	C [auth Z], K [auth X], L [auth Y]	153	Human immunodeficiency virus 1	Mutation(s): 0 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: 3	Glycosylation Focus chain C [auth Z] Focus chain K [auth X] Focus chain L [auth Y]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 DS-SOSIP Surface protein gp120	H [auth G], I [auth E], J [auth F]	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: 16	Glycosylation Focus chain H [auth G] Focus chain I [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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], EA [auth e], FA [auth f], HA [auth h], BA [auth b], CA [auth c], EA [auth e], FA [auth f], HA [auth h], M [auth A], N [auth D], O [auth I], P [auth M], Q [auth N], R [auth O], S [auth P], T [auth Q], V [auth S], W [auth T], X [auth U], Y [auth V]	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain M [auth A] Focus chain N [auth D] Focus chain O [auth I] Focus chain P [auth M] Focus chain Q [auth N] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain M [auth A] Focus chain N [auth D] Focus chain O [auth I] Focus chain P [auth M] Focus chain Q [auth N] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	U [auth R], Z [auth W]	5		N-Glycosylation	Interactions Focus chain U [auth R] Focus chain Z [auth W] Interactions & Density Focus chain U [auth R] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	AA [auth a], DA [auth d], GA [auth g], IA [auth i]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain IA [auth i] Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain IA [auth i]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 JA [auth Z] SDF format, chain LB [auth F] SDF format, chain UA [auth E] SDF format, chain ZA [auth E] 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 FB [auth E] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain IB [auth F] SDF format, chain JB [auth F] SDF format, chain KA [auth Z] SDF format, chain KB [auth F] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain MB [auth F] SDF format, chain NA [auth G] SDF format, chain NB [auth F] SDF format, chain OA [auth G] SDF format, chain OB [auth F] SDF format, chain PA [auth G] SDF format, chain PB [auth F] SDF format, chain QA [auth G] SDF format, chain QB [auth X] SDF format, chain RA [auth G] SDF format, chain RB [auth X] SDF format, chain SA [auth G] SDF format, chain SB [auth Y] SDF format, chain TA [auth G] SDF format, chain TB [auth Y] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain YA [auth E] MOL2 format, chain JA [auth Z] MOL2 format, chain LB [auth F] MOL2 format, chain UA [auth E] MOL2 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 DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain IB [auth F] MOL2 format, chain JB [auth F] MOL2 format, chain KA [auth Z] MOL2 format, chain KB [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain OB [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain PB [auth F] MOL2 format, chain QA [auth G] MOL2 format, chain QB [auth X] MOL2 format, chain RA [auth G] MOL2 format, chain RB [auth X] MOL2 format, chain SA [auth G] MOL2 format, chain SB [auth Y] MOL2 format, chain TA [auth G] MOL2 format, chain TB [auth Y] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E]	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], FB [auth E], GB [auth F], HB [auth F], IB [auth F], JA [auth Z], JB [auth F], KA [auth Z], KB [auth F], LA [auth G], LB [auth F], MA [auth G], MB [auth F], NA [auth G], NB [auth F], OA [auth G], OB [auth F], PA [auth G], PB [auth F], QA [auth G], QB [auth X], RA [auth G], RB [auth X], SA [auth G], SB [auth Y], TA [auth G], TB [auth Y], UA [auth E], VA [auth E], WA [auth E], XA [auth E], 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 DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JA [auth Z] Focus chain JB [auth F] Focus chain KA [auth Z] Focus chain KB [auth F] Focus chain LA [auth G] Focus chain LB [auth F] Focus chain MA [auth G] Focus chain MB [auth F] Focus chain NA [auth G] Focus chain NB [auth F] Focus chain OA [auth G] Focus chain OB [auth F] Focus chain PA [auth G] Focus chain PB [auth F] Focus chain QA [auth G] Focus chain QB [auth X] Focus chain RA [auth G] Focus chain RB [auth X] Focus chain SA [auth G] Focus chain SB [auth Y] Focus chain TA [auth G] Focus chain TB [auth Y] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] 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 DB [auth E] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JA [auth Z] Focus chain JB [auth F] Focus chain KA [auth Z] Focus chain KB [auth F] Focus chain LA [auth G] Focus chain LB [auth F] Focus chain MA [auth G] Focus chain MB [auth F] Focus chain NA [auth G] Focus chain NB [auth F] Focus chain OA [auth G] Focus chain OB [auth F] Focus chain PA [auth G] Focus chain PB [auth F] Focus chain QA [auth G] Focus chain QB [auth X] Focus chain RA [auth G] Focus chain RB [auth X] Focus chain SA [auth G] Focus chain SB [auth Y] Focus chain TA [auth G] Focus chain TB [auth Y] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]