3LWE - JenaLib

Title :   THE CRYSTAL STRUCTURE OF MPP8

Authors :   Z. Li, Z. Li, J. Ruan, C. Xu, Y. Tong, P. W. Pan, W. Tempel, L. Crombet, J. Mi

Date :   23 Feb 10 (Deposition) - 02 Mar 10 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)
Biol. Unit 4: A,B  (1x)

Keywords :   Mpp8, Structural Genomics, Structural Genomics Consortium, Sgc, Ank Repeat, Nucleus, Phosphoprotein, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Li, Z. Li, J. Ruan, C. Xu, Y. Tong, P. W. Pan, W. Tempel, L. Crombet, J. Min, J. Zang
Structural Basis For Specific Binding Of Human Mpp8 Chromodomain To Histone H3 Methylated At Lysine 9.
Plos One V. 6 25104 2011
PubMed-ID: 22022377 | Reference-DOI: 10.1371/JOURNAL.PONE.0025104

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	MPP8_HUMAN	59-109	2	A:4-54 B:4-54
2	CHROMO_1	PS00598	Chromo domain signature.	MPP8_HUMAN	76-96	2	A:21-41 B:21-41

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	MPP8_HUMAN	59-109	1	A:4-54 -
2	CHROMO_1	PS00598	Chromo domain signature.	MPP8_HUMAN	76-96	1	A:21-41 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	MPP8_HUMAN	59-109	1	- B:4-54
2	CHROMO_1	PS00598	Chromo domain signature.	MPP8_HUMAN	76-96	1	- B:21-41

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	MPP8_HUMAN	59-109	2	A:4-54 B:4-54
2	CHROMO_1	PS00598	Chromo domain signature.	MPP8_HUMAN	76-96	2	A:21-41 B:21-41

Biological Unit 4 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	MPP8_HUMAN	59-109	2	A:4-54 B:4-54
2	CHROMO_1	PS00598	Chromo domain signature.	MPP8_HUMAN	76-96	2	A:21-41 B:21-41

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:61
 aligned with MPP8_HUMAN | Q99549 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:61
                                    64        74        84        94       104       114 
           MPP8_HUMAN    55 GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAENKA 115
               SCOP domains d3lwea_ A: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee..eeeeeeee...hhhhheeeehhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CHROMO_2  PDB: A:4-54 UniProt: 59-109              ------ PROSITE (1)
                PROSITE (2) ---------------------CHROMO_1  PDB: A:21-4------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------- Transcript
                 3lwe A   0 GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAENKA  60
                                     9        19        29        39        49        59

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with MPP8_HUMAN | Q99549 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:59
                                    64        74        84        94       104         
           MPP8_HUMAN    55 GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAEN 113
               SCOP domains d3lweb_ B: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
           Pfam domains (1) ----Chromo-3lweB01 B:4-54                              ---- Pfam domains (1)
           Pfam domains (2) ----Chromo-3lweB02 B:4-54                              ---- Pfam domains (2)
         Sec.struct. author ......eeeeeeeeee..eeeeeeee...hhhhheeeehhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CHROMO_2  PDB: B:4-54 UniProt: 59-109              ---- PROSITE (1)
                PROSITE (2) ---------------------CHROMO_1  PDB: B:21-4----------------- PROSITE (2)
                 Transcript ----------------------------------------------------------- Transcript
                 3lwe B   0 GEDVFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEIHLEDCKEVLLEFRKKIAEN  58
                                     9        19        29        39        49

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MPP8_HUMAN | Q99549)

molecular function
	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: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).
biological process
	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:0044030	regulation of DNA methylation	Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	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:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	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: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.

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