9YDW | pdb_00009ydw

Cryo-EM structure of single-bound FDG antibody VRC49.01 in complex with HIV-1 Env BG505 DS-SOSIP trimer

PDB DOI: https://doi.org/10.2210/pdb9YDW/pdb
EM Map EMD-72839: EMDB EMDataResource

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

Deposited: 2025-09-23 Released: 2026-08-05
Deposition Author(s): Gorman, J., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.34 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 VRC49.01 in complex with HIV-1 Env BG505 DS-SOSIP trimer

Gorman, J., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 289.2 kDa
Atom Count: 18,828
Modeled Residue Count: 2,196
Deposited Residue Count: 2,366
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.664 gp41	A, G [auth B], I	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S5
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain G [auth B] Focus chain I
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 BG505 DS-SOSIP gp120	B [auth C], H [auth D], J	481	Human immunodeficiency virus 1	Mutation(s): 4 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain B [auth C] Focus chain H [auth D] Focus chain J
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC49.01 Heavy	C [auth K], E [auth M]	125	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC49.01 Light	D [auth L], F [auth N]	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], CA [auth c], DA [auth d], EA [auth e], GA [auth g], AA [auth a], CA [auth c], DA [auth d], EA [auth e], GA [auth g], HA [auth h], JA [auth j], K [auth E], KA [auth k], LA [auth l], M [auth G], MA [auth m], N [auth H], NA [auth n], O, P, S, U, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain K [auth E] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth G] Focus chain MA [auth m] Focus chain N [auth H] Focus chain NA [auth n] Focus chain O Focus chain P Focus chain S Focus chain U Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain K [auth E] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth G] Focus chain MA [auth m] Focus chain N [auth H] Focus chain NA [auth n] Focus chain O Focus chain P Focus chain S Focus chain U Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	FA [auth f], L [auth F], V	6		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain L [auth F] Focus chain V Interactions & Density Focus chain FA [auth f] Focus chain L [auth F] Focus chain V
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q, T	9		N-Glycosylation	Interactions Focus chain Q Focus chain T Interactions & Density Focus chain Q Focus chain T
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], IA [auth i], R	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain IA [auth i] Focus chain R Interactions & Density Focus chain BA [auth b] Focus chain IA [auth i] Focus chain R
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 ZA [auth B] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UB [auth J] SDF format, chain UA [auth C] SDF format, chain TB [auth J] SDF format, chain TA [auth C] SDF format, chain SB [auth J] SDF format, chain SA [auth C] SDF format, chain RB [auth J] SDF format, chain RA [auth C] SDF format, chain QB [auth J] SDF format, chain QA [auth A] SDF format, chain PB [auth J] SDF format, chain PA [auth A] SDF format, chain OB [auth J] SDF format, chain OA [auth A] SDF format, chain NB [auth J] SDF format, chain MB [auth I] SDF format, chain LB [auth I] SDF format, chain KB [auth I] SDF format, chain JB [auth D] SDF format, chain IB [auth D] SDF format, chain HB [auth D] SDF format, chain GB [auth D] SDF format, chain FB [auth D] SDF format, chain EB [auth D] SDF format, chain DB [auth D] SDF format, chain CB [auth D] SDF format, chain BB [auth B] SDF format, chain AB [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UB [auth J] MOL2 format, chain UA [auth C] MOL2 format, chain TB [auth J] MOL2 format, chain TA [auth C] MOL2 format, chain SB [auth J] MOL2 format, chain SA [auth C] MOL2 format, chain RB [auth J] MOL2 format, chain RA [auth C] MOL2 format, chain QB [auth J] MOL2 format, chain QA [auth A] MOL2 format, chain PB [auth J] MOL2 format, chain PA [auth A] MOL2 format, chain OB [auth J] MOL2 format, chain OA [auth A] MOL2 format, chain NB [auth J] MOL2 format, chain MB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain KB [auth I] MOL2 format, chain JB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain BB [auth B] MOL2 format, chain AB [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UB [auth J] mmCIF format, chain UA [auth C] mmCIF format, chain TB [auth J] mmCIF format, chain TA [auth C] mmCIF format, chain SB [auth J] mmCIF format, chain SA [auth C] mmCIF format, chain RB [auth J] mmCIF format, chain RA [auth C] mmCIF format, chain QB [auth J] mmCIF format, chain QA [auth A] mmCIF format, chain PB [auth J] mmCIF format, chain PA [auth A] mmCIF format, chain OB [auth J] mmCIF format, chain OA [auth A] mmCIF format, chain NB [auth J] mmCIF format, chain MB [auth I] mmCIF format, chain LB [auth I] mmCIF format, chain KB [auth I] mmCIF format, chain JB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain BB [auth B] mmCIF format, chain AB [auth B]	AB [auth B] BB [auth B] CB [auth D] DB [auth D] EB [auth D] AB [auth B], BB [auth B], CB [auth D], DB [auth D], EB [auth D], FB [auth D], GB [auth D], HB [auth D], IB [auth D], JB [auth D], KB [auth I], LB [auth I], MB [auth I], NB [auth J], OA [auth A], OB [auth J], PA [auth A], PB [auth J], QA [auth A], QB [auth J], RA [auth C], RB [auth J], SA [auth C], SB [auth J], TA [auth C], TB [auth J], UA [auth C], UB [auth J], VA [auth C], WA [auth C], XA [auth C], YA [auth C], 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 D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth J] Focus chain OA [auth A] Focus chain OB [auth J] Focus chain PA [auth A] Focus chain PB [auth J] Focus chain QA [auth A] Focus chain QB [auth J] Focus chain RA [auth C] Focus chain RB [auth J] Focus chain SA [auth C] Focus chain SB [auth J] Focus chain TA [auth C] Focus chain TB [auth J] Focus chain UA [auth C] Focus chain UB [auth J] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth J] Focus chain OA [auth A] Focus chain OB [auth J] Focus chain PA [auth A] Focus chain PB [auth J] Focus chain QA [auth A] Focus chain QB [auth J] Focus chain RA [auth C] Focus chain RB [auth J] Focus chain SA [auth C] Focus chain SB [auth J] Focus chain TA [auth C] Focus chain TB [auth J] Focus chain UA [auth C] Focus chain UB [auth J] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth B]