4UY4

1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide

• PDB DOI: https://doi.org/10.2210/pdb4UY4/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-28 Released: 2014-09-24 
• Deposition Author(s): Talon, R., Gileadi, C., Johansson, C., Burgess-Brown, N., Shrestha, L., von Delft, F., Krojer, T., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Literature

1.86 A Structure of Human Spindlin-4 Protein in Complex with Histone H3K4Me3 Peptide

Talon, R., Gileadi, C., Johansson, C., Burgess-Brown, N., Shrestha, L., Fairhead, M., von Delft, F., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 51.35 kDa 
• Atom Count: 3,625 
• Modelled Residue Count: 423 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLIN-4	A, B	216	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q56A73 (Homo sapiens) Explore Q56A73  Go to UniProtKB:  Q56A73
PHAROS:  Q56A73 GTEx:  ENSG00000186767

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3K4ME3	C, D	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	C, D	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.072	α = 81.25
b = 51.69	β = 89.89
c = 57.141	γ = 88

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Talon, R., Gileadi, C., Johansson, C., Burgess-Brown, N., Shrestha, L., von Delft, F., Krojer, T., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Oppermann, U.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2019-05-15
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description