5V3J

mouseZFP568-ZnF1-10 in complex with DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins.

Patel, A., Yang, P., Tinkham, M., Pradhan, M., Sun, M.A., Wang, Y., Hoang, D., Wolf, G., Horton, J.R., Zhang, X., Macfarlan, T., Cheng, X.

(2018) Cell 173: 221-233.e12

  • DOI: 10.1016/j.cell.2018.02.058
  • Primary Citation of Related Structures:  
    5V3J, 5V3M, 5WJQ

  • PubMed Abstract: 

    • Tandem zinc finger (ZF) proteins are the largest and most rapidly diverging family of DNA-binding transcription regulators in mammals. ZFP568 represses a transcript of placental-specific insulin like growth factor 2 (Igf2-P0) in mice. ZFP568 binds a 24-base pair sequence-specific element upstream of Igf2-P0 via the eleven-ZF array ...

    Tandem zinc finger (ZF) proteins are the largest and most rapidly diverging family of DNA-binding transcription regulators in mammals. ZFP568 represses a transcript of placental-specific insulin like growth factor 2 (Igf2-P0) in mice. ZFP568 binds a 24-base pair sequence-specific element upstream of Igf2-P0 via the eleven-ZF array. Both DNA and protein conformations deviate from the conventional one finger-three bases recognition, with individual ZFs contacting 2, 3, or 4 bases and recognizing thymine on the opposite strand. These interactions arise from a shortened minor groove caused by an AT-rich stretch, suggesting adaptability of ZF arrays to sequence variations. Despite conservation in mammals, mutations at Igf2 and ZFP568 reduce their binding affinity in chimpanzee and humans. Our studies provide important insights into the evolutionary and structural dynamics of ZF-DNA interactions that play a key role in mammalian development and evolution.

    Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: xcheng5@mdanderson.org.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein 568E, F284Mus musculusMutation(s): 0 
Gene Names: Znf568, chato, Zfp568
UniProt
Find proteins for E9PYI1 (Mus musculus)
Explore E9PYI1 
Go to UniProtKB:  E9PYI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9PYI1
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (26-MER)A, C26Mus
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (26-MER)B, D26Mus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS
Download Ideal Coordinates CCD File 
CA [auth F],
Q [auth E]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
G [auth E],
H [auth E],
I [auth E],
AA [auth F],
BA [auth F],
G [auth E],
H [auth E],
I [auth E],
J [auth E],
K [auth E],
L [auth E],
M [auth E],
N [auth E],
O [auth E],
P [auth E],
S [auth F],
T [auth F],
U [auth F],
V [auth F],
W [auth F],
X [auth F],
Y [auth F],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
DA [auth F],
R [auth E]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.787α = 100.52
b = 65.706β = 104.25
c = 73.022γ = 97.25
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence