Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.24 kDa 
• Atom Count: 1590 
• Modelled Residue Count: 177 
• Deposited Residue Count: 178 
• Unique protein chains: 1

6USI

Barrier-to-autointegration factor soaked in 1,6-hexanediol: 1 of 14 in MSCS set

• PDB DOI: 10.2210/pdb6USI/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-26 Released: 2020-10-07 
• Deposition Author(s): Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.208 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

Literature

Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor.

Agarwal, S., Smith, M., De La Rosa, I., Verba, K.A., Swartz, P., Segura-Totten, M., Mattos, C.

(2020) Acta Crystallogr D Struct Biol 76: 1001-1014

• PubMed: 33021502 
• DOI: 10.1107/S2059798320011341
• Primary Citation of Related Structures:  
  6UNT, 6URE, 6URJ, 6URK, 6URL, 6URN, 6URR, 6URZ, 6US0, 6US1, 6US7, 6USB, 6USD, 6USI


• PubMed Abstract: 
  

The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.

---

Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Barrier-to-autointegration factor	A, B	89	Homo sapiens	Mutation(s): 0  Gene Names: BANF1, BAF, BCRG1
UniProt & NIH Common Fund Data Resources
Find proteins for O75531 (Homo sapiens) Explore O75531  Go to UniProtKB:  O75531
PHAROS:  O75531 GTEx:  ENSG00000175334

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH (Subject of Investigation/LOI)	C [auth A], D [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.208 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.65	α = 90
b = 41.65	β = 90
c = 214.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-10-26 
• Released Date: 2020-10-07 
Deposition Author(s): Agarwal, S., Smith, M., De La Rosa, I., Kliment, A.V., Swartz, P., Segura-Totten, M., Mattos, C.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Database references