6FZT

Crystal structure of Smad8_9-MH1 bound to the GGCGC site.

• PDB DOI: https://doi.org/10.2210/pdb6FZT/pdb
• NAKB: 6FZT

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


• Deposited: 2018-03-15 Released: 2019-10-02 
• Deposition Author(s): Kaczmarska, Z., Marquez, J.A., Macias, M.J.
• Funding Organization(s): European Commission, Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes

Ruiz, L., Kaczmarska, Z., Gomes, T., Aragon, E., Torner, C., Freier, R., Baginski, B., Martin-Malpartida, P., Marquez, J.A., Cordeiro, T.N., Pluta, R., Macias, M.J.

(2021) Computational And Structural Biotechnology Journal 19

• DOI: https://doi.org/10.1016/j.csbj.2020.12.044

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 42.42 kDa 
• Atom Count: 2,848 
• Modelled Residue Count: 289 
• Deposited Residue Count: 312 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog 9	A, B	140	Homo sapiens	Mutation(s): 0  Gene Names: SMAD9, MADH6, MADH9, SMAD8
UniProt & NIH Common Fund Data Resources
Find proteins for O15198 (Homo sapiens) Explore O15198  Go to UniProtKB:  O15198
PHAROS:  O15198 GTEx:  ENSG00000120693

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3')	C, D	16	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.433	α = 90
b = 79.509	β = 90
c = 88.372	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Kaczmarska, Z., Marquez, J.A., Macias, M.J.

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Funding Organization	Location	Grant Number
European Commission	Germany	EMBL_291772
European Commission	Spain	IRBPostPro2.0_600404
Ministry of Economy and Competitiveness	Spain	BFU2014-53787-P
European Commission	France	653706

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2020-10-07
  Changes: Derived calculations, Refinement description
• Version 1.2: 2021-01-20
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description