3H6Z | pdb_00003h6z

Crystal Structure of the Four MBT Repeats of Drosophila melanogaster Sfmbt in Complex with Peptide RHR (me)K VLR

PDB DOI: https://doi.org/10.2210/pdb3H6Z/pdb

Classification: TRANSCRIPTION
Organism(s): Drosophila melanogaster, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-24 Released: 2009-06-16
Deposition Author(s): Grimm, C., Mueller, C.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.221 (Depositor), 0.224 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt

Grimm, C., Matos, R., Ly-Hartig, N., Steuerwald, U., Lindner, D., Rybin, V., Muller, J., Muller, C.W.

(2009) EMBO J 28: 1965-1977

PubMed: 19494831 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/emboj.2009.147
Primary Citation Related Structures:
3H6Z

PubMed Abstract:
Polycomb group (PcG) proteins repress transcription by modifying chromatin structure in target genes. dSfmbt is a subunit of the Drosophila melanogaster PcG protein complex PhoRC and contains four malignant brain tumour (MBT) repeats involved in the recognition of various mono- and dimethylated histone peptides. Here, we present the crystal structure of the four-MBT-repeat domain of dSfmbt in complex with a mono-methylated histone H4 peptide. Only a single histone peptide binds to the four-MBT-repeat domain. Mutational analyses show high-affinity binding with low peptide sequence selectivity through combinatorial interaction of the methyl-lysine with an aromatic cage and positively charged flanking residues with the surrounding negatively charged surface of the fourth MBT repeat. dSfmbt directly interacts with the PcG protein Scm, a related MBT-repeat protein with similar methyl-lysine binding activity. dSfmbt and Scm co-occupy Polycomb response elements of target genes in Drosophila and they strongly synergize in the repression of these target genes, suggesting that the combined action of these two MBT proteins is crucial for Polycomb silencing.

Organizational Affiliation

European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France.

Macromolecule Content

Total Structure Weight: 103.75 kDa
Atom Count: 7,115
Modeled Residue Count: 874
Deposited Residue Count: 906
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein Sfmbt	A, C [auth B]	447	Drosophila melanogaster	Mutation(s): 3 Gene Names: Sfmbt
UniProt
Find proteins for Q9VK33 (Drosophila melanogaster) Explore Q9VK33 Go to UniProtKB: Q9VK33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VK33
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
'HR(MLZ)VLR	B [auth L], D [auth M]	6	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E [auth C], F [auth D], G [auth E], H [auth F]	2		N/A	Interactions Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Interactions & Density Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ Query on MLZ	B [auth L], D [auth M]	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	E [auth C], F [auth D], G [auth E], H [auth F]	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Interactions & Density Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.254 (Depositor), 0.254 (DCC)
R-Value Work: 0.221 (Depositor), 0.224 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.8	α = 90
b = 97.04	β = 90
c = 214.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Grimm, C.

Mueller, C.W.

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2019-08-28
Changes: Data collection, Derived calculations, Source and taxonomy
Version 1.3: 2019-10-16
Changes: Data collection, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-11-10
Changes: Database references, Structure summary