6H3R | pdb_00006h3r

Crystal structure of Smad2 without exon -MH1 bound to the CAGAC site.

• PDB DOI: https://doi.org/10.2210/pdb6H3R/pdb
• NAKB: 6H3R

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


• Deposited: 2018-07-19 Released: 2019-09-18 
• 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: 2.75 Å
• R-Value Free: 
  0.222 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-beta signaling

Aragon, E., Wang, Q., Zou, Y., Morgani, S.M., Ruiz, L., Kaczmarska, Z., Su, J., Torner, C., Tian, L., Hu, J., Shu, W., Agrawal, S., Gomes, T., Marquez, J.A., Hadjantonakis, A.-K., Macias, M.J., Massague, J.

(2020) Genes Dev 

• DOI: https://doi.org/10.1101/gad.330837.119

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.56 kDa 
• Atom Count: 2,661 
• Modeled Residue Count: 278 
• Deposited Residue Count: 314 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog	A, B	139	Homo sapiens	Mutation(s): 0  Gene Names: SMAD2
UniProt & NIH Common Fund Data Resources
Find proteins for B7Z5N5 (Homo sapiens) Explore B7Z5N5  Go to UniProtKB:  B7Z5N5
GTEx:  ENSG00000175387

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-3')	C, D	18	Homo sapiens

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.222 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.14	α = 90
b = 80.14	β = 90
c = 143.84	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-18 
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: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description