9YEM | pdb_00009yem

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

PDB DOI: https://doi.org/10.2210/pdb9YEM/pdb
EM Map EMD-72855: EMDB EMDataResource

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

Deposited: 2025-09-24 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: 3.81 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: 394.79 kDa
Atom Count: 26,232
Modeled Residue Count: 3,120
Deposited Residue Count: 3,291
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], M [auth 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 M [auth I]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.664 gp120	B [auth C], H [auth D], N [auth J]	480	Human immunodeficiency virus 1	Mutation(s): 0 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 N [auth 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] I [auth E] K [auth G] O C [auth K], E [auth M], I [auth E], K [auth G], O, Q	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] J [auth F] L [auth H] P D [auth L], F [auth N], J [auth F], L [auth H], P, R	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], EA [auth e], FA [auth f], GA [auth g], AA [auth a], CA [auth c], EA [auth e], FA [auth f], GA [auth g], HA [auth h], KA [auth k], MA [auth m], OA [auth o], PA [auth p], QA [auth q], RA [auth r], S, U, UA [auth u], V, W, X	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain U Focus chain UA [auth u] Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain U Focus chain UA [auth u] Focus chain V Focus chain W Focus chain X

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	DA [auth d], NA [auth n], T	6		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain NA [auth n] Focus chain T Interactions & Density Focus chain DA [auth d] Focus chain NA [auth n] Focus chain T

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	BA [auth b], IA [auth i], LA [auth l], SA [auth s], VA [auth v], BA [auth b], IA [auth i], LA [auth l], SA [auth s], VA [auth v], Y	9		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain IA [auth i] Focus chain LA [auth l] Focus chain SA [auth s] Focus chain VA [auth v] Focus chain Y Interactions & Density Focus chain BA [auth b] Focus chain IA [auth i] Focus chain LA [auth l] Focus chain SA [auth s] Focus chain VA [auth v] Focus chain Y

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	JA [auth j], TA [auth t], Z	3		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain TA [auth t] Focus chain Z Interactions & Density Focus chain JA [auth j] Focus chain TA [auth t] Focus chain Z

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 C] SDF format, chain AC [auth J] SDF format, chain BB [auth C] SDF format, chain BC [auth J] SDF format, chain CB [auth C] SDF format, chain CC [auth J] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain KB [auth D] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain NB [auth D] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain QB [auth D] SDF format, chain RB [auth D] SDF format, chain SB [auth I] SDF format, chain TB [auth I] SDF format, chain UB [auth I] SDF format, chain VB [auth J] SDF format, chain WA [auth A] SDF format, chain WB [auth J] SDF format, chain XA [auth A] SDF format, chain XB [auth J] SDF format, chain YA [auth A] SDF format, chain YB [auth J] SDF format, chain ZA [auth C] SDF format, chain ZB [auth J] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth J] MOL2 format, chain BB [auth C] MOL2 format, chain BC [auth J] MOL2 format, chain CB [auth C] MOL2 format, chain CC [auth J] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain QB [auth D] MOL2 format, chain RB [auth D] MOL2 format, chain SB [auth I] MOL2 format, chain TB [auth I] MOL2 format, chain UB [auth I] MOL2 format, chain VB [auth J] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth J] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth J] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth J] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth J] mmCIF format, chain AB [auth C] mmCIF format, chain AC [auth J] mmCIF format, chain BB [auth C] mmCIF format, chain BC [auth J] mmCIF format, chain CB [auth C] mmCIF format, chain CC [auth J] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain NB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain QB [auth D] mmCIF format, chain RB [auth D] mmCIF format, chain SB [auth I] mmCIF format, chain TB [auth I] mmCIF format, chain UB [auth I] mmCIF format, chain VB [auth J] mmCIF format, chain WA [auth A] mmCIF format, chain WB [auth J] mmCIF format, chain XA [auth A] mmCIF format, chain XB [auth J] mmCIF format, chain YA [auth A] mmCIF format, chain YB [auth J] mmCIF format, chain ZA [auth C] mmCIF format, chain ZB [auth J]	AB [auth C] AC [auth J] BB [auth C] BC [auth J] CB [auth C] AB [auth C], AC [auth J], BB [auth C], BC [auth J], CB [auth C], CC [auth J], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth B], IB [auth B], JB [auth B], KB [auth D], LB [auth D], MB [auth D], NB [auth D], OB [auth D], PB [auth D], QB [auth D], RB [auth D], SB [auth I], TB [auth I], UB [auth I], VB [auth J], WA [auth A], WB [auth J], XA [auth A], XB [auth J], YA [auth A], YB [auth J], ZA [auth C], ZB [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain AC [auth J] Focus chain BB [auth C] Focus chain BC [auth J] Focus chain CB [auth C] Focus chain CC [auth J] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QB [auth D] Focus chain RB [auth D] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain UB [auth I] Focus chain VB [auth J] Focus chain WA [auth A] Focus chain WB [auth J] Focus chain XA [auth A] Focus chain XB [auth J] Focus chain YA [auth A] Focus chain YB [auth J] Focus chain ZA [auth C] Focus chain ZB [auth J] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth J] Focus chain BB [auth C] Focus chain BC [auth J] Focus chain CB [auth C] Focus chain CC [auth J] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QB [auth D] Focus chain RB [auth D] Focus chain SB [auth I] Focus chain TB [auth I] Focus chain UB [auth I] Focus chain VB [auth J] Focus chain WA [auth A] Focus chain WB [auth J] Focus chain XA [auth A] Focus chain XB [auth J] Focus chain YA [auth A] Focus chain YB [auth J] Focus chain ZA [auth C] Focus chain ZB [auth J]