3FEO

The crystal structure of MBTD1

• PDB DOI: https://doi.org/10.2210/pdb3FEO/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-30 Released: 2009-01-06 
• Deposition Author(s): Amaya, M.F., Eryilmaz, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.274 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 

Literature

Structural studies of a four-MBT repeat protein MBTD1.

Eryilmaz, J., Pan, P., Amaya, M.F., Allali-Hassani, A., Dong, A., Adams-Cioaba, M.A., Mackenzie, F., Vedadi, M., Min, J.

(2009) PLoS One 4: e7274-e7274

• PubMed: 19841675 
• DOI: https://doi.org/10.1371/journal.pone.0007274
• Primary Citation of Related Structures:  
  3FEO


• PubMed Abstract: 
  

  The Polycomb group (PcG) of proteins is a family of important developmental regulators. The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes. MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein. MBTD1 contains four MBT repeats.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

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: 99.13 kDa 
• Atom Count: 6,279 
• Modelled Residue Count: 804 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MBT domain-containing protein 1	A, B	437	Homo sapiens	Mutation(s): 0  Gene Names: MBTD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05BQ5 (Homo sapiens) Explore Q05BQ5  Go to UniProtKB:  Q05BQ5
PHAROS:  Q05BQ5 GTEx:  ENSG00000011258

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.274 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.31	α = 90
b = 100.904	β = 90
c = 135.303	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Amaya, M.F., Eryilmaz, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description