NMR paper Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.

		BioNMR > Educational resources > Journal club
[NMR paper] Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

10-17-2013, 04:57 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.

Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.

Related Articles Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.

PLoS One. 2013;8(10):e77020

Authors: Lemak A, Yee A, Wu H, Yap D, Zeng H, Dombrovski L, Houliston S, Aparicio S, Arrowsmith CH

Abstract
Mixed Lineage Leukemia 5 (MLL5) is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. In addition to its catalytic domain, MLL5 contains a PHD finger domain, a protein module that is often involved in binding to the N-terminus of histone H3. Here we report the NMR solution structure of the MLL5 PHD domain showing a variant of the canonical PHD fold that combines conserved H3 binding features from several classes of other PHD domains (including an aromatic cage) along with a novel C-terminal ?-helix, not previously seen. We further demonstrate that the PHD domain binds with similar affinity to histone H3 tail peptides di- and tri-methylated at lysine 4 (H3K4me2 and H3K4me3), the former being the putative product of the MLL5 catalytic reaction. This work establishes the PHD domain of MLL5 as a bone fide 'reader' domain of H3K4 methyl marks suggesting that it may guide the spreading or further methylation of this site on chromatin.

PMID: 24130829 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR structure note: solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger NMR structure note: solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger NMR structure note: solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger Content Type Journal Article Category NMR structure note Pages 1-7 DOI 10.1007/s10858-012-9654-1 Authors	nmrlearner	Journal club	0	07-20-2012 11:13 PM
[NMR paper] Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Related Articles Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Protein Expr Purif. 2006 Jan;45(1):99-106 Authors: Chen X, Tong X, Xie Y, Wang Y, Ma J, Gao D, Wu H, Chen H The human hepatitis B virus enhancer II...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a muta Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis. Related Articles Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis. Proteins. 2005 May 1;59(2):347-55 Authors: le Maire A, Weber T, Saunier S, Broutin I, Antignac C, Ducruix A, Dardel F Human nephrocystin is a protein associated with juvenile NPH, an autosomal recessive, inherited kidney disease responsible for chronic renal failure in children. It...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Solution NMR structure of the C-terminal domain of the human protein DEK. Solution NMR structure of the C-terminal domain of the human protein DEK. Related Articles Solution NMR structure of the C-terminal domain of the human protein DEK. Protein Sci. 2004 Aug;13(8):2252-9 Authors: Devany M, Kotharu NP, Matsuo H The chromatin-associated protein DEK was first identified as a fusion protein in patients with a subtype of acute myelogenous leukemia. It has since become associated with diverse human ailments ranging from cancers to autoimmune diseases. Despite much research effort, the biochemical basis for these...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] NMR solution structure of the inserted domain of human leukocyte function associated NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. Related Articles NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. J Mol Biol. 2000 Feb 4;295(5):1251-64 Authors: Legge GB, Kriwacki RW, Chung J, Hommel U, Ramage P, Case DA, Dyson HJ, Wright PE The interaction between the leukocyte function-associated antigen-1 (LFA-1) and the intercellular adhesion molecule is thought to be mediated primarily via the inserted domain (I-domain) in the alpha-subunit. The...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin. Related Articles NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin. J Biol Chem. 2000 Jan 14;275(2):1089-94 Authors: Huang W, Dolmer K, Liao X, Gettins PG Human alpha(2)-macroglobulin-proteinase complexes bind to their receptor, the low density lipoprotein receptor-related protein (LRP), through a discrete 138-residue C-terminal receptor binding domain (RBD), which also binds to the beta-amyloid peptide. We have used NMR...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] High-resolution solution NMR structure of the minimal active domain of the human immu High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. Related Articles High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. Biochemistry. 1998 Dec 22;37(51):17704-13 Authors: Kodera Y, Sato K, Tsukahara T, Komatsu H, Maeda T, Kohno T The retroviral nucleocapsid (NC) protein is a multifunctional protein essential for RNA genome packaging and viral infectivity. The NC protein, NCp8, of the...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] The structure of the human retinoic acid receptor-beta DNA-binding domain determined The structure of the human retinoic acid receptor-beta DNA-binding domain determined by NMR. Related Articles The structure of the human retinoic acid receptor-beta DNA-binding domain determined by NMR. Nucleic Acids Symp Ser. 1992;(27):65-6 Authors: Katahira M, Knegtel R, Schilthius J, Boelens R, Eib D, van der Saag P, Kaptein R The solution structure of the DNA-binding domain (DBD) of the human retinoic acid receptor-beta (hRAR-beta) has been determined by nuclear magnetic resonance (NMR) spectroscopy and distance geometry (DG). The...	nmrlearner	Journal club	0	08-21-2010 11:41 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off