3MLP | pdb_00003mlp

Early B-cell Factor 1 (Ebf1) bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb3MLP/pdb
• NAKB: 3MLP

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-04-17 Released: 2010-12-01 
• Deposition Author(s): Treiber, N., Treiber, T., Zocher, G., Grosschedl, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins

Treiber, N., Treiber, T., Zocher, G., Grosschedl, R.

(2010) Genes Dev 24: 2270-2275

• PubMed: 20876732 
• DOI: https://doi.org/10.1101/gad.1976610
• Primary Citation Related Structures: 
  3MLN, 3MLO, 3MLP


• PubMed Abstract: 
  

  Early B-cell factor 1 (Ebf1) is a key transcriptional determinant of B-lymphocyte differentiation whose DNA-binding domain has no sequence similarity to other transcription factor families. Here we report the crystal structure of an Ebf1 dimer bound to its palindromic recognition site. The DNA-binding domain adopts a pseudoimmunoglobulin-like fold with novel topology, but is structurally similar to the Rel homology domains of NFAT and NF-κB. Ebf1 contacts the DNA with two loop-based modules and a unique Zn coordination motif whereby each Ebf1 monomer interacts with both palindromic half-sites. This unusual mode of DNA recognition generates an extended contact area that may be crucial for the function of Ebf1 in chromatin.

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Organizational Affiliation: 
• Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, 79108 Freiburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 210.22 kDa 
• Atom Count: 11,961 
• Modeled Residue Count: 1,358 
• Deposited Residue Count: 1,696 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor COE1	A, B, E, F	402	Mus musculus	Mutation(s): 1  Gene Names: Ebf1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07802 (Mus musculus) Explore Q07802  Go to UniProtKB:  Q07802
IMPC:  MGI:95275

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')	C, D, G, H	22	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	J [auth A], K [auth A], M [auth B], O [auth E], Q [auth F]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	I [auth A], L [auth B], N [auth E], P [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.49	α = 88.99
b = 78.69	β = 90
c = 103.57	γ = 77.81

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Treiber, N., Treiber, T., Zocher, G., Grosschedl, R.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-12
  Changes: Refinement description
• Version 1.3: 2015-12-23
  Changes: Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description