1MEY | pdb_00001mey

CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA

• PDB DOI: https://doi.org/10.2210/pdb1MEY/pdb
• NAKB: 1MEY

• Classification: TRANSFERASE/DNA
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1996-09-27 Released: 1997-03-12 
• Deposition Author(s): Kim, C.A., Berg, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.319 (Depositor) 
• R-Value Work: 
  0.224 (Depositor) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

A 2.2 A Resolution Crystal Structure of a Designed Zinc Finger Protein Bound to DNA

Kim, C.A., Berg, J.M.

(1996) Nat Struct Biol 3: 940-945

• PubMed: 8901872 
• DOI: https://doi.org/10.1038/nsb1196-940
• Primary Citation Related Structures: 
  1MEY


• PubMed Abstract: 
  

  Considerable recent effort has been devoted to the design and selection of sequence-specific DNA binding proteins based on tandem arrays of Cys2His2 zinc finger domains. While the DNA binding properties of these designed proteins have been studied extensively, the structural basis for site-specific binding has not been examined experimentally. Here we report the crystal structure of a complex between a protein comprised of three consensus-sequence-based zinc finger domains and an oligonucleotide corresponding to a favourable DNA binding site. This structure reveals relatively simple modular interactions and structural adaptations that compensate for differences in contact residue side-chain lengths.

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Organizational Affiliation: 
• Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.14 kDa 
• Atom Count: 2,773 
• Modeled Residue Count: 247 
• Deposited Residue Count: 313 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSENSUS ZINC FINGER	E [auth C], F, G	87	N/A	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')	A, C [auth D]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')	B, D [auth E]	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	H [auth C], I [auth C], J [auth C], K [auth F], L [auth F], M [auth F], N [auth G], O [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	P [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.319 (Depositor) 
• R-Value Work:  0.224 (Depositor) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.07	α = 90
b = 165.53	β = 90
c = 46.274	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
PROCESS	data reduction
PROCESS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-03-12 
Deposition Author(s): Kim, C.A., Berg, J.M.

Revision History  

• Version 1.0: 1997-03-12
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations