5M9N

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

• PDB DOI: https://doi.org/10.2210/pdb5M9N/pdb

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


• Deposited: 2016-11-01 Released: 2016-11-16 
• Deposition Author(s): Tallant, C., Savitsky, P., Moehlenbrink, J., Chan, C., Nunez-Alonso, G., Newman, J.A., 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: 1.95 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

Tallant, C., Savitsky, P., Moehlenbrink, J., Chan, C., Nunez-Alonso, G., Newman, J.A., 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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 50.77 kDa 
• Atom Count: 3,249 
• Modelled Residue Count: 404 
• Deposited Residue Count: 457 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tudor domain-containing protein 1	A, B	220	Homo sapiens	Mutation(s): 0  Gene Names: TDRD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXT4 (Homo sapiens) Explore Q9BXT4  Go to UniProtKB:  Q9BXT4
PHAROS:  Q9BXT4 GTEx:  ENSG00000095627

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E2F peptide	C	17	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q01094 (Homo sapiens) Explore Q01094  Go to UniProtKB:  Q01094
PHAROS:  Q01094 GTEx:  ENSG00000101412

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2MR	F [auth B]	N3, N4-DIMETHYLARGININE C8 H18 N4 O2 HVPFXCBJHIIJGS-LURJTMIESA-N
EDO	D [auth A], E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.91	α = 64.94
b = 52.962	β = 88.85
c = 59.619	γ = 67.67

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Tallant, C., Savitsky, P., Moehlenbrink, J., Chan, C., Nunez-Alonso, G., Newman, J.A., 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: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary