7SX7

Crystal structure of broadly neutralizing antibody N49P9.3-FR3-3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

• PDB DOI: https://doi.org/10.2210/pdb7SX7/pdb

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


• Deposited: 2021-11-22 Released: 2022-11-30 
• Deposition Author(s): Tolbert, W.D., Pazgier, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Crystal structure of broadly neutralizing antibody N49P9.3-FR3-3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

Tolbert, W.D., Pazgier, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 178.14 kDa 
• Atom Count: 12,727 
• Modelled Residue Count: 1,544 
• Deposited Residue Count: 1,576 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
clade A/E 93TH057 HIV-1 gp120 core	A [auth G], D [auth A]	355	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1) Explore A0A0M3KKW9  Go to UniProtKB:  A0A0M3KKW9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN	B [auth H], E [auth B]	230	Homo	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN	C [auth L], F [auth C]	203	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	EA [auth A], FA [auth A], R [auth G]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG	AA [auth A], BA [auth A], CA [auth A], DA [auth A], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G], Q [auth G], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.367	α = 90.02
b = 65.418	β = 104.85
c = 112.381	γ = 90.02

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-30 
Deposition Author(s): Tolbert, W.D., Pazgier, M.

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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 AI116274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI129769

Revision History  

• Version 1.0: 2022-11-30
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description