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Title :   CRYSTAL STRUCTURE OF THE 3-MBT DOMAIN FROM HUMAN L3MBTL1 IN COMPLEX WITH H1.5K27ME2 AT 1.66 ANGSTROM

Authors :   H. Li, D. J. Patel

Date :   09 Oct 07 (Deposition) - 11 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Barrel, Protein-Peptide Complex, Dimethyl-Lysine, Alternative Splicing, Chromatin Regulator, Dna-Binding, Metal-Binding, Nucleus, Repressor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Transcription/Nuclear Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Li, W. Fischle, W. Wang, E. M. Duncan, L. Liang, S. Murakami-Ishibe, C. D. Allis, D. J. Patel
Structural Basis For Lower Lysine Methylation State-Specific Readout By Mbt Repeats Of L3Mbtl1 And An Engineered Phd Finger.
Mol. Cell V. 28 677 2007
PubMed-ID: 18042461 | Reference-DOI: 10.1016/J.MOLCEL.2007.10.023
(for further references see the PDB file header)

Molecule 1 - LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T3
	Expression System Strain	:	ROSSETA2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	REPEATS MBT-1, MBT-2, MBT-3; RESIDUES 197-526
	Gene	:	L3MBTL, KIAA0681, L3MBT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	L3, MBT-LIKE, L3, MBT PROTEIN HOMOLOG, H-L3, MBT PROTEIN, H-L3, MBT, L3MBTL1

Molecule 2 - HISTONE H1.5
	Chains	:	B
	Engineered	:	YES
	Fragment	:	N-TERMINAL TAIL RESIDEUS 23-27
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:278 , ASP A:459 , ARG A:461 , TRP A:486 , TYR A:490 , HOH A:589 , HOH A:635 , HOH A:829	BINDING SITE FOR RESIDUE PG4 A 1
2	AC2	SOFTWARE	THR A:232 , HIS A:233 , LYS A:235 , LYS A:509 , HOH A:776	BINDING SITE FOR RESIDUE PEG A 2

(no "SS Bond" information available for 2RHI)

(no "Cis Peptide Bond" information available for 2RHI)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051098	I	479	M	LMBL1_HUMAN	Polymorphism	6017104	A	I	479	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	LMBL1_HUMAN	206-306 314-413 422-517	3	A:206-306 A:314-413 A:422-517

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000331442	1	ENSE00001305578	chr6:27835359-27834570	790	H15_HUMAN	1-244	244	1	B:24-26	3

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:324
 aligned with LMBL1_HUMAN | Q9Y468 from UniProtKB/Swiss-Prot  Length:752

    Alignment length:324
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524    
          LMBL1_HUMAN   205 CWSWESYLEEQKAITAPVSLFQDSQAVTHNKNGFKLGMKLEGIDPQHPSMYFILTVAEVCGYRLRLHFDGYSECHDFWVNANSPDIHPAGWFEKTGHKLQPPKGYKEEEFSWSQYLRSTRAQAAPKHLFVSQSHSPPPLGFQVGMKLEAVDRMNPSLVCVASVTDVVDSRFLVHFDNWDDTYDYWCDPSSPYIHPVGWCQKQGKPLTPPQDYPDPDNFCWEKYLEETGASAVPTWAFKVRPPHSFLVNMKLEAVDRRNPALIRVASVEDVEDHRIKIHFDGWSHGYDFWIDADHPDIHPAGWCSKTGHPLQPPLGPREPSSASP 528
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2rhiA01 A:205-234,A:447-528   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2rhiA01 A:205-234,A:447-528  [code=2.30.30.160, no name defined]                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhh...........eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh.........hhhhhhhhhhhhhhh....hhhhh................eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheee......ee..hhhhhhh..ee......hhhhhhhhhhhhhhh....hhhhh............eeeee.......eeeeeeeee...eeeeee...hhhhheeee.....ee..hhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M------------------------------------------------- SAPs(SNPs)
                    PROSITE -MBT  PDB: A:206-306 UniProt: 206-306                                                                 -------MBT  PDB: A:314-413 UniProt: 314-413                                                                --------MBT  PDB: A:422-517 UniProt: 422-517                                                            ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rhi A 205 CWSWESYLEEQKAITAPVSLFQDSQAVTHNKNGFKLGMKLEGIDPQHPSMYFILTVAEVCGYRLRLHFDGYSECHDFWVNANSPDIHPAGWFEKTGHKLQPPKGYKEEEFSWSQYLRSTRAQAAPKHLFVSQSHSPPPLGFQVGMKLEAVDRMNPSLVCVASVTDVVDSRFLVHFDNWDDTYDYWCDPSSPYIHPVGWCQKQGKPLTPPQDYPDPDNFCWEKYLEETGASAVPTWAFKVRPPHSFLVNMKLEAVDRRNPALIRVASVEDVEDHRIKIHFDGWSHGYDFWIDADHPDIHPAGWCSKTGHPLQPPLGPREPSSAVD 528
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524

Chain B from PDB  Type:PROTEIN  Length:3
 aligned with H15_HUMAN | P16401 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:3
            H15_HUMAN    25 TKK  27
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
               Transcript 1 1.1 Transcript 1
                 2rhi B  24 TKk  26
                              |
                              |
                             26-MLY

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2RHI)

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.160, no name defined] (35)

Human (Homo sapiens) (27)

2rhiA01

A:205-234,A:447-528

(no "Pfam Domain" information available for 2RHI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LMBL1_HUMAN | Q9Y468)

molecular function
	GO:0032093	SAM domain binding	Interacting selectively and non-covalently with a SAM (Sterile Alpha Motif) domain, which is a 70-amino acid protein sequence that participates in protein-protein, protein-lipid, and protein-RNA interactions and is conserved from lower to higher eukaryotes.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0031493	nucleosomal histone binding	Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
	GO:0031491	nucleosome binding	Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
	GO:0045652	regulation of megakaryocyte differentiation	Any process that modulates the frequency, rate or extent of megakaryocyte differentiation.
	GO:0007088	regulation of mitotic nuclear division	Any process that modulates the frequency, rate or extent of mitosis.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	GO:0000793	condensed chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (H15_HUMAN | P16401)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0031490	chromatin DNA binding	Interacting selectively and non-covalently with DNA that is assembled into chromatin.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
biological process
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0071169	establishment of protein localization to chromatin	The directed movement of a protein to a part of a chromosome that is organized into chromatin.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0051574	positive regulation of histone H3-K9 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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2rhu	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 BOUND TO DIMETHYL-LYSINE AND IN CHIMERA WITH HISTONE H3.3(28-34)
2rhx	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 BOUND TO DIMETHYL-LYSINE
2rhy	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 BOUND TO MONOMETHYL-LYSINE
2rhz	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH D355N POINT MUTATION
2ri2	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH D355A POINT MUTATION
2ri3	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH N358Q POINT MUTATION
2ri5	CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH N358A POINT MUTATION

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 3)

Exons (1, 1)

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Gene Ontology (40, 41)

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