5M9O

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

• PDB DOI: https://doi.org/10.2210/pdb5M9O/pdb

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


• Deposited: 2016-11-01 Released: 2016-12-07 
• Deposition Author(s): Tallant, C., Savitsky, P., Moehlenbrink, J., Chan, C., Nunez-Alonso, G., Siejka, P., Sorrell, F.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Fedorov, O., La Thangue, N.B., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.261 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

Tallant, C., Savitsky, P., Moehlenbrink, J., Chan, C., Nunez-Alonso, G., Siejka, P., Sorrell, F.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Fedorov, O., La Thangue, N.B., Knapp, S.

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)

Macromolecule Content

• Total Structure Weight: 26.39 kDa 
• Atom Count: 1,921 
• Modelled Residue Count: 220 
• Deposited Residue Count: 233 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal nuclease domain-containing protein 1	A	224	Homo sapiens	Mutation(s): 0  Gene Names: SND1, TDRD11
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZF4 (Homo sapiens) Explore Q7KZF4  Go to UniProtKB:  Q7KZF4
GTEx:  ENSG00000197157

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E2F peptide	B	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q01094 (Homo sapiens) Explore Q01094  Go to UniProtKB:  Q01094
GTEx:  ENSG00000101412

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR	B	L-PEPTIDE LINKING	C8 H18 N4 O2		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.261 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.243	α = 90
b = 80.626	β = 90.38
c = 39.289	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Tallant, C., Savitsky, P., Moehlenbrink, J., Chan, C., Nunez-Alonso, G., Siejka, P., Sorrell, F.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Fedorov, O., La Thangue, N.B., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Derived calculations
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description