8TO7

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

PDB DOI: https://doi.org/10.2210/pdb8TO7/pdb
EM Map EMD-41438: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-03 Released: 2024-08-07
Deposition Author(s): Roark, R.S., Hoyt, F., Hansen, B., Fischer, E., 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: 3.39 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: 381.12 kDa
Atom Count: 20,361
Modelled Residue Count: 2,442
Deposited Residue Count: 3,273
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein gp120	A [auth E], E [auth D], I [auth F]	481	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: 17	Glycosylation Focus chain A [auth E] Focus chain E [auth D] Focus chain I [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	B, F [auth A], J [auth C]	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 B Focus chain F [auth A] Focus chain J [auth C]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HERH-b*01 heavy chain	C [auth H], G, K [auth I]	238	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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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HERH-b*01 light chain	D [auth L], H [auth J], L [auth K]	219	Macaca mulatta	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], M, Q, R, V, AA [auth a], M, Q, R, V, W	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain M Focus chain Q Focus chain R Focus chain V Focus chain W Interactions & Density Focus chain AA [auth a] Focus chain M Focus chain Q Focus chain R Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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, O, S, T, X N, O, S, T, X, Y	2		N-Glycosylation	Interactions Focus chain N Focus chain O Focus chain S Focus chain T Focus chain X Focus chain Y Interactions & Density Focus chain N Focus chain O Focus chain S Focus chain T Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
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	P, U, Z	5		N-Glycosylation	Interactions Focus chain P Focus chain U Focus chain Z Interactions & Density Focus chain P Focus chain U Focus chain Z
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 D] SDF format, chain BA [auth E] SDF format, chain BB [auth D] SDF format, chain CA [auth E] SDF format, chain CB [auth D] SDF format, chain DA [auth E] SDF format, chain DB [auth A] SDF format, chain EA [auth E] SDF format, chain EB [auth A] SDF format, chain FA [auth E] SDF format, chain FB [auth F] SDF format, chain GA [auth E] SDF format, chain GB [auth F] SDF format, chain HA [auth E] SDF format, chain HB [auth F] SDF format, chain IA [auth E] SDF format, chain IB [auth F] SDF format, chain JA [auth E] SDF format, chain JB [auth F] SDF format, chain KA [auth E] SDF format, chain KB [auth F] SDF format, chain LA [auth E] SDF format, chain LB [auth F] SDF format, chain MA [auth E] SDF format, chain MB [auth F] SDF format, chain NA [auth E] 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 PB [auth F] SDF format, chain QA [auth D] SDF format, chain QB [auth F] SDF format, chain RA [auth D] SDF format, chain RB [auth F] SDF format, chain SA [auth D] SDF format, chain SB [auth C] SDF format, chain TA [auth D] SDF format, chain TB [auth C] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth A] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth F] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth F] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth F] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth F] MOL2 format, chain MA [auth E] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth E] 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 PB [auth F] MOL2 format, chain QA [auth D] MOL2 format, chain QB [auth F] MOL2 format, chain RA [auth D] MOL2 format, chain RB [auth F] MOL2 format, chain SA [auth D] MOL2 format, chain SB [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth A] mmCIF format, chain EA [auth E] mmCIF format, chain EB [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth F] mmCIF format, chain GA [auth E] mmCIF format, chain GB [auth F] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth F] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth F] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth F] mmCIF format, chain KA [auth E] mmCIF format, chain KB [auth F] mmCIF format, chain LA [auth E] mmCIF format, chain LB [auth F] mmCIF format, chain MA [auth E] mmCIF format, chain MB [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain NB [auth F] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth F] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth F] mmCIF format, chain QA [auth D] mmCIF format, chain QB [auth F] mmCIF format, chain RA [auth D] mmCIF format, chain RB [auth F] mmCIF format, chain SA [auth D] mmCIF format, chain SB [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth C] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	AB [auth D] BA [auth E] BB [auth D] CA [auth E] CB [auth D] AB [auth D], BA [auth E], BB [auth D], CA [auth E], CB [auth D], DA [auth E], DB [auth A], EA [auth E], EB [auth A], FA [auth E], FB [auth F], GA [auth E], GB [auth F], HA [auth E], HB [auth F], IA [auth E], IB [auth F], JA [auth E], JB [auth F], KA [auth E], KB [auth F], LA [auth E], LB [auth F], MA [auth E], MB [auth F], NA [auth E], NB [auth F], OA [auth B], OB [auth F], PA [auth B], PB [auth F], QA [auth D], QB [auth F], RA [auth D], RB [auth F], SA [auth D], SB [auth C], TA [auth D], TB [auth C], UA [auth D], VA [auth D], WA [auth D], XA [auth D], YA [auth D], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BA [auth E] Focus chain BB [auth D] Focus chain CA [auth E] Focus chain CB [auth D] Focus chain DA [auth E] Focus chain DB [auth A] Focus chain EA [auth E] Focus chain EB [auth A] Focus chain FA [auth E] Focus chain FB [auth F] Focus chain GA [auth E] Focus chain GB [auth F] Focus chain HA [auth E] Focus chain HB [auth F] Focus chain IA [auth E] Focus chain IB [auth F] Focus chain JA [auth E] Focus chain JB [auth F] Focus chain KA [auth E] Focus chain KB [auth F] Focus chain LA [auth E] Focus chain LB [auth F] Focus chain MA [auth E] Focus chain MB [auth F] Focus chain NA [auth E] Focus chain NB [auth F] Focus chain OA [auth B] Focus chain OB [auth F] Focus chain PA [auth B] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain RB [auth F] Focus chain SA [auth D] Focus chain SB [auth C] Focus chain TA [auth D] Focus chain TB [auth C] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth E] Focus chain BB [auth D] Focus chain CA [auth E] Focus chain CB [auth D] Focus chain DA [auth E] Focus chain DB [auth A] Focus chain EA [auth E] Focus chain EB [auth A] Focus chain FA [auth E] Focus chain FB [auth F] Focus chain GA [auth E] Focus chain GB [auth F] Focus chain HA [auth E] Focus chain HB [auth F] Focus chain IA [auth E] Focus chain IB [auth F] Focus chain JA [auth E] Focus chain JB [auth F] Focus chain KA [auth E] Focus chain KB [auth F] Focus chain LA [auth E] Focus chain LB [auth F] Focus chain MA [auth E] Focus chain MB [auth F] Focus chain NA [auth E] Focus chain NB [auth F] Focus chain OA [auth B] Focus chain OB [auth F] Focus chain PA [auth B] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain RB [auth F] Focus chain SA [auth D] Focus chain SB [auth C] Focus chain TA [auth D] Focus chain TB [auth C] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]