8CDN

Crystal structure of human Brachyury in complex with a single T box binding element DNA

• PDB DOI: https://doi.org/10.2210/pdb8CDN/pdb
• NAKB: 8CDN

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


• Deposited: 2023-01-31 Released: 2023-03-22 
• Deposition Author(s): Newman, J.A., Gavard, A.E., von Delft, F., Gileadi, O., Bountra, C.
• Funding Organization(s): The Mark Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.302 
• R-Value Work: 0.273 
• R-Value Observed: 0.275 

Literature

Crystal structure of human Brachyury in complex with a single T box binding element DNA

Newman, J.A., Gavard, A.E., von Delft, F., Gileadi, O., Bountra, C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.35 kDa 
• Atom Count: 1,937 
• Modelled Residue Count: 205 
• Deposited Residue Count: 216 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-box transcription factor T	A	192	Homo sapiens	Mutation(s): 0  Gene Names: TBXT, T
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens) Explore O15178  Go to UniProtKB:  O15178
PHAROS:  O15178 GTEx:  ENSG00000164458

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*TP*GP*TP*GP*AP*GP*CP*CP*T)-3')	B [auth C]	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*CP*TP*CP*AP*CP*AP*CP*CP*T)-3')	C [auth D]	12	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.302 
• R-Value Work: 0.273 
• R-Value Observed: 0.275 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.018	α = 90
b = 63.018	β = 90
c = 218.579	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Newman, J.A., Gavard, A.E., von Delft, F., Gileadi, O., Bountra, C.

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Funding Organization	Location	Grant Number
The Mark Foundation	United States	--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release