2GLI | pdb_00002gli

FIVE-FINGER GLI/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb2GLI/pdb
• NAKB: 2GLI

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


• Deposited: 1993-11-09 Released: 1993-11-09 
• Deposition Author(s): Pavletich, N.P., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers.

Pavletich, N.P., Pabo, C.O.

(1993) Science 261: 1701-1707

• PubMed: 8378770 
• DOI: https://doi.org/10.1126/science.8378770
• Primary Citation of Related Structures:  
  2GLI


• PubMed Abstract: 
  

  Zinc finger proteins, of the type first discovered in transcription factor IIIA (TFIIIA), are one of the largest and most important families of DNA-binding proteins. The crystal structure of a complex containing the five Zn fingers from the human GLI oncogene and a high-affinity DNA binding site has been determined at 2.6 A resolution. Finger one does not contact the DNA. Fingers two through five bind in the major groove and wrap around the DNA, but lack the simple, strictly periodic arrangement observed in the Zif268 complex. Fingers four and five of GLI make extensive base contacts in a conserved nine base-pair region, and this section of the DNA has a conformation intermediate between B-DNA and A-DNA. Analyzing the GLI complex and comparing it with Zif268 offers new perspectives on Zn finger-DNA recognition.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.37 kDa 
• Atom Count: 2,174 
• Modelled Residue Count: 197 
• Deposited Residue Count: 197 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (FIVE-FINGER GLI)	C [auth A]	155	Homo sapiens	Mutation(s): 0  Gene Names: GLI ONCOGENE
UniProt & NIH Common Fund Data Resources
Find proteins for P08151 (Homo sapiens) Explore P08151  Go to UniProtKB:  P08151
PHAROS:  P08151 GTEx:  ENSG00000111087

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*CP*GP*TP*CP*TP*TP*GP*GP*GP*TP*GP*GP*TP*CP*CP*AP*CP*G)-3')	A [auth C]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*TP*GP*GP*AP*CP*CP*AP*CP*CP*CP*AP*AP*GP*AP*CP*GP*AP*A)-3')	B [auth D]	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149	α = 90
b = 50.2	β = 90
c = 45.4	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-11-09 
Deposition Author(s): Pavletich, N.P., Pabo, C.O.

Revision History  

• Version 1.0: 1993-11-09
  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