8TO9

Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP

PDB DOI: https://doi.org/10.2210/pdb8TO9/pdb
EM Map EMD-41440: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-03 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: 4.03 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: 303.48 kDa
Atom Count: 18,788
Modelled Residue Count: 2,249
Deposited Residue Count: 2,547
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A, B, C	463	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNM-f*01 heavy chain	D, E, H	126	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNM-f*01 light chain	F, G, K [auth L]	107	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	I, J, L [auth Z]	153	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain I Focus chain J Focus chain L [auth Z]
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 a], BA [auth b], DA [auth d], M [auth K], O [auth N], AA [auth a], BA [auth b], DA [auth d], M [auth K], O [auth N], P [auth O], Q [auth P], R [auth Q], S [auth R], U [auth T], V [auth U], W [auth V], X [auth W], Y [auth X]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain M [auth K] Focus chain O [auth N] Focus chain P [auth O] Focus chain Q [auth P] Focus chain R [auth Q] Focus chain S [auth R] Focus chain U [auth T] Focus chain V [auth U] Focus chain W [auth V] Focus chain X [auth W] Focus chain Y [auth X] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain M [auth K] Focus chain O [auth N] Focus chain P [auth O] Focus chain Q [auth P] Focus chain R [auth Q] Focus chain S [auth R] Focus chain U [auth T] Focus chain V [auth U] Focus chain W [auth V] Focus chain X [auth W] Focus chain Y [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	CA [auth c], N [auth M], T [auth S], Z [auth Y]	3		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain N [auth M] Focus chain T [auth S] Focus chain Z [auth Y] Interactions & Density Focus chain CA [auth c] Focus chain N [auth M] Focus chain T [auth S] Focus chain Z [auth Y]
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 AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] 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 A] SDF format, chain GB [auth C] SDF format, chain HA [auth A] SDF format, chain HB [auth C] SDF format, chain IA [auth A] SDF format, chain IB [auth C] SDF format, chain JA [auth A] SDF format, chain JB [auth C] SDF format, chain KA [auth A] SDF format, chain KB [auth C] SDF format, chain LA [auth A] SDF format, chain LB [auth C] SDF format, chain MA [auth A] SDF format, chain MB [auth C] SDF format, chain NA [auth A] SDF format, chain NB [auth C] SDF format, chain OA [auth A] SDF format, chain OB [auth C] SDF format, chain PA [auth A] SDF format, chain PB [auth C] SDF format, chain QA [auth A] SDF format, chain QB [auth C] SDF format, chain RA [auth B] SDF format, chain RB [auth I] SDF format, chain SA [auth B] SDF format, chain SB [auth J] SDF format, chain TA [auth B] SDF format, chain TB [auth Z] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] 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 A] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth I] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth J] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth Z] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EA [auth A] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], IB [auth C], JA [auth A], JB [auth C], KA [auth A], KB [auth C], LA [auth A], LB [auth C], MA [auth A], MB [auth C], NA [auth A], NB [auth C], OA [auth A], OB [auth C], PA [auth A], PB [auth C], QA [auth A], QB [auth C], RA [auth B], RB [auth I], SA [auth B], SB [auth J], TA [auth B], TB [auth Z], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain NA [auth A] Focus chain NB [auth C] Focus chain OA [auth A] Focus chain OB [auth C] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain RA [auth B] Focus chain RB [auth I] Focus chain SA [auth B] Focus chain SB [auth J] Focus chain TA [auth B] Focus chain TB [auth Z] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain IB [auth C] Focus chain JA [auth A] Focus chain JB [auth C] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain NA [auth A] Focus chain NB [auth C] Focus chain OA [auth A] Focus chain OB [auth C] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain RA [auth B] Focus chain RB [auth I] Focus chain SA [auth B] Focus chain SB [auth J] Focus chain TA [auth B] Focus chain TB [auth Z] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]