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)

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
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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 EC: 3.1.31.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZF4 (Homo sapiens) Explore Q7KZF4 Go to UniProtKB: Q7KZF4
PHAROS: Q7KZF4 GTEx: ENSG00000197157
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7KZF4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
PHAROS: Q01094 GTEx: ENSG00000101412
Entity Groups
UniProt Group	Q01094
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR Query on 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

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Entry History

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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
Version 1.3: 2024-11-06
Changes: Structure summary