9OMG | pdb_00009omg

Cryo-EM structure of rhesus antibody V033-a.I1 in complex with HIV Env trimer Q23.17 MD39

• PDB DOI: https://doi.org/10.2210/pdb9OMG/pdb
• EM Map EMD-70613: EMDB EMDataResource

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


• Deposited: 2025-05-13 Released: 2025-11-05 
• Deposition Author(s): Roark, R.S., Shapiro, L., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV-1 V2 apex broadly neutralizing antibody development

Habib, R., Roark, R.S., Kwong, P.D., Shaw, G.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A3B3C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 285.38 kDa 
• Atom Count: 16,868 
• Modeled Residue Count: 1,923 
• Deposited Residue Count: 2,324 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Env gp120	A, C, D [auth E]	469	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 16

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Env gp41 ectodomain	B, E [auth F], F [auth G]	153	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V033-Int1 heavy chain	G [auth H]	244	Macaca mulatta	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V033-Int1 light chain	H [auth L]	214	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	I [auth D]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

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	BA [auth b], CA [auth c], DA [auth d], EA [auth e], GA [auth g], IA [auth i], J [auth I], LA [auth l], M, N, O, OA [auth o], P, PA [auth p], QA [auth q], R, S, SA [auth s], TA [auth t], U, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

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], FA [auth f], HA [auth h], K [auth J], KA [auth k], L [auth K], MA [auth m], NA [auth n], Q, RA [auth r], T, UA [auth u], Z	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	V	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Entity ID: 9
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	JA [auth j]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AB [auth A], BB [auth A], CB [auth B], DB [auth B], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth E], JB [auth E], KB [auth E], LB [auth F], MB [auth F], NB [auth G], OB [auth G], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Roark, R.S., Shapiro, L., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release