8CUC | pdb_00008cuc

Crystal structure analysis of SALL4 zinc finger domain in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb8CUC/pdb
• NAKB: 8CUC

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


• Deposited: 2022-05-17 Released: 2023-05-24 
• Deposition Author(s): Seo, H.S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal Structure Analysis of SALL4 Zinc Finger domain in complex with DNA

Seo, H.S., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.22 kDa 
• Atom Count: 2,456 
• Modeled Residue Count: 209 
• Deposited Residue Count: 320 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sal-like protein 4	E, F, G, H	68	Homo sapiens	Mutation(s): 0  Gene Names: SALL4, ZNF797
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJQ4 (Homo sapiens) Explore Q9UJQ4  Go to UniProtKB:  Q9UJQ4
PHAROS:  Q9UJQ4 GTEx:  ENSG00000101115

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3')	A, C	12	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3')	B, D	12	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth E], J [auth F], K [auth F], L [auth G], M [auth G], N [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.25	α = 90
b = 70.51	β = 90
c = 112.06	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
SOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Seo, H.S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection