6F59

Crystal structure of human Brachyury (T) G177D variant in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb6F59/pdb
• NAKB: 6F59

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


• Deposited: 2017-12-01 Released: 2017-12-13 
• Deposition Author(s): Newman, J.A., Gavard, A.E., Krojer, T., Shrestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.252 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Crystal structure of human Brachyury (T) G177D variant in complex with DNA

Newman, J.A., Gavard, A.E., Krojer, T., Shrestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 60.27 kDa 
• Atom Count: 4,105 
• Modelled Residue Count: 415 
• Deposited Residue Count: 436 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Brachyury protein	C [auth A], D [auth B]	192	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens) Explore O15178  Go to UniProtKB:  O15178
PHAROS:  O15178 GTEx:  ENSG00000164458

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	A [auth C], B [auth D]	26	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.252 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.27	α = 90
b = 75.27	β = 90
c = 288.468	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Newman, J.A., Gavard, A.E., Krojer, T., Shrestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description