8U1D

Cryo-EM structure of vaccine-elicited CD4 binding site antibody DH1285 bound to HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env Local Refinement

• PDB DOI: https://doi.org/10.2210/pdb8U1D/pdb
• EM Map EMD-41810: EMDB EMDataResource

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


• Deposited: 2023-08-31 Released: 2024-01-03 
• Deposition Author(s): Thakur, B., Stalls, V.D., Acharya, P.
• 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: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Rhesus macaque vaccine elicited antibody DH1285 Fab bound to the one of the gp120 promoter of CH505M5chimer.6R.SOSIP.664v4.1 Env

Thakur, B., Acharya, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 124.53 kDa 
• Atom Count: 5,109 
• Modelled Residue Count: 650 
• Deposited Residue Count: 1,123 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A	647	Human immunodeficiency virus 1	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1285 Heavy Chain	B [auth I]	243	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1285 Light Chain	C [auth J]	233	Macaca mulatta	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [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: 4.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): Thakur, B., Stalls, V.D., Acharya, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI145687
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144371

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release