7N9U | pdb_00007n9u

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

• PDB DOI: https://doi.org/10.2210/pdb7N9U/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Lama glama
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-18 Released: 2022-06-22 
• Deposition Author(s): Gerber, E.E., Digianantonio, K.M., Tripler, T.N., Smaga, S.S., Summers, B.J., Xiong, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Models: experimental

Literature

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

Gerber, E.E., Digianantonio, K.M., Tripler, T.N., Smaga, S.S., Summers, B.J., Xiong, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 111.73 kDa 
• Atom Count: 7,616 
• Modelled Residue Count: 992 
• Deposited Residue Count: 1,023 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	223	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12493  Go to UniProtKB:  P12493

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	D, E, F	118	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.698	α = 90
b = 143.57	β = 90
c = 228.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Gerber, E.E., Digianantonio, K.M., Tripler, T.N., Smaga, S.S., Summers, B.J., Xiong, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P50GM082251
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F32 GM131426 01A1

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary