8J70 | pdb_00008j70

Native SAND domain of protein SP140 with DNA

• PDB DOI: https://doi.org/10.2210/pdb8J70/pdb
• NAKB: 8J70

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-04-26 Released: 2024-05-01 
• Deposition Author(s): Li, H.T., Liu, W.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for Speckled protein SP140 bivalent recognition of histone H3 and DNA.

Li, H.T., Liu, W.Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 30.7 kDa 
• Atom Count: 1,984 
• Modeled Residue Count: 196 
• Deposited Residue Count: 224 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear body protein SP140	A, B	99	Homo sapiens	Mutation(s): 0  Gene Names: SP140, LYSP100
UniProt & NIH Common Fund Data Resources
Find proteins for Q13342 (Homo sapiens) Explore Q13342  Go to UniProtKB:  Q13342
PHAROS:  Q13342 GTEx:  ENSG00000079263

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')	C, D	13	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SEY	E [auth A]	selenourea C H4 N2 Se IYKVLICPFCEZOF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.629	α = 90
b = 119.071	β = 90
c = 64.679	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Li, H.T., Liu, W.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release