Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.00 kDa 
• Atom Count: 2730 
• Residue Count: 280 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1OZJ

Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution

• DOI: 10.2210/pdb1OZJ/pdb
• NDB: PD0409

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


• Deposited: 2003-04-09 Released: 2004-03-23 
• Deposition Author(s): Chai, J., Wu, J.-W., Yan, N., Massague, J., Pavletich, N.P., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.270 
• R-Value Work: 0.210 

Literature

Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding.

Chai, J., Wu, J.-W., Yan, N., Massague, J., Pavletich, N.P., Shi, Y.

(2003) J Biol Chem 278: 20327-20331

• PubMed: 12686552 
• DOI: 10.1074/jbc.C300134200
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The Smad family of proteins mediates transforming growth factor-beta signaling from cell membrane to the nucleus. In the nucleus, Smads serve as transcription factors by directly binding to specific DNA sequences and regulating the expression of ligand-response genes. A previous structural analysis, at 2.8-A resolution, revealed a novel DNA-binding mode for the Smad MH1 domain but did not allow accurate assignment of the fines features of protein-DNA interactions. The crystal structure of a Smad3 MH1 domain bound to a palindromic DNA sequence, determined at 2.4-A resolution, reveals a surprisingly important role for water molecules. The asymmetric placement of the DNA-binding motif (a conserved 11-residue beta-hairpin) in the major groove of DNA is buttressed by seven well ordered water molecules. These water molecules make specific hydrogen bonds to the DNA bases, the DNA phosphate backbones, and several critical Smad3 residues. In addition, the MH1 domain is found to contain a bound zinc atom using four invariant residues among Smad proteins, three cysteines and one histidine. Removal of the zinc atom results in compromised DNA binding activity. These results define the Smad MH1 domain as a zinc-coordinating module that exhibits unique DNA binding properties.

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Organizational Affiliation: 

Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, New Jersey 08544, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
SMAD 3	A, B	144	Homo sapiens	Mutation(s): 0  Gene Names: MADH3 OR SMAD3 OR MAD3, SMAD3, MADH3
Find proteins for P84022 (Homo sapiens) Go to UniProtKB:  P84022
NIH Common Fund Data Resources
PHAROS  P84022 GTEx  ENSG00000166949

Entity ID: 1
Molecule	Chains	Length	Organism
Smad binding element	C	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
Smad binding element	D	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.270 
• R-Value Work: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.6	α = 90
b = 60.4	β = 102
c = 71.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-09 
• Released Date: 2004-03-23 
Deposition Author(s): Chai, J., Wu, J.-W., Yan, N., Massague, J., Pavletich, N.P., Shi, Y.

Revision History 

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection