3OB9 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   STRUCTURE OF THE HUMAN MSL3 CHROMO-BARREL DOMAIN AT 2.5 ANGSTROM RESOLUTION

Authors :   S. A. Moore, Y. Ferhatoglu

Date :   06 Aug 10 (Deposition) - 13 Oct 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

Keywords :   Chromodomain, Chromo-Barrel, Chromo, Methyllysine Binding, Histone Tail, Nucleosome Recognition, Histone H4K20Me1, Nucleus, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Moore, Y. Ferhatoglu
Structure Of The Human Msl3 Chromo-Barrel Domain At 2. 5 Angstrom Resolution
J. Biol. Chem. 2010
PubMed: search

Molecule 1 - MALE-SPECIFIC LETHAL 3-LIKE 1 (DROSOPHILA), ISOFORM CRA_C
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P3
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	GLUTATHIONE S. TRANSFERASE FUSION
	Fragment	:	HMSL3 (UNP RESIDUES 2 TO 93)
	Gene	:	HCG_401190, MSL3, MSL3L1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN MSL3

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 20)

No.	Name	Count	Type	Full Name
1	NHE	3	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2	SO4	17	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	NHE	1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	NHE	1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 7)

No.	Name	Count	Type	Full Name
1	NHE	-1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	NHE	1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	NHE	-1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:55 , ASN A:57 , GLY A:58	BINDING SITE FOR RESIDUE SO4 A 320
02	AC2	SOFTWARE	GLU A:78 , ARG A:81	BINDING SITE FOR RESIDUE SO4 A 340
03	AC3	SOFTWARE	ARG A:28	BINDING SITE FOR RESIDUE SO4 A 345
04	AC4	SOFTWARE	LYS A:10 , LEU A:73 , ARG A:74 , ASN A:79 , SO4 C:355	BINDING SITE FOR RESIDUE SO4 A 375
05	AC5	SOFTWARE	GLU A:21 , LYS A:26 , TYR A:31 , PHE A:56 , TRP A:59 , TRP A:63 , LYS D:48	BINDING SITE FOR RESIDUE NHE A 540
06	AC6	SOFTWARE	LYS B:10 , ARG B:80 , ARG B:84	BINDING SITE FOR RESIDUE SO4 B 310
07	AC7	SOFTWARE	LYS B:8 , ARG B:81 , ARG B:84 , ARG B:88 , LYS D:8	BINDING SITE FOR RESIDUE SO4 B 315
08	AC8	SOFTWARE	ARG B:47 , HIS B:55 , ASN B:57 , GLY B:58	BINDING SITE FOR RESIDUE SO4 B 325
09	AC9	SOFTWARE	ASN A:60 , ARG A:61 , GLU B:21 , TYR B:31 , PHE B:56 , TRP B:59 , TRP B:63	BINDING SITE FOR RESIDUE NHE B 520
10	BC1	SOFTWARE	GLU C:5	BINDING SITE FOR RESIDUE SO4 C 350
11	BC2	SOFTWARE	LYS A:10 , ARG A:74 , SO4 A:375 , HIS C:12	BINDING SITE FOR RESIDUE SO4 C 355
12	BC3	SOFTWARE	ARG C:28 , HOH C:98	BINDING SITE FOR RESIDUE SO4 C 360
13	BC4	SOFTWARE	HIS C:55 , ASN C:57 , GLY C:58	BINDING SITE FOR RESIDUE SO4 C 365
14	BC5	SOFTWARE	ALA C:27 , ARG C:28 , ALA D:27 , ARG D:28	BINDING SITE FOR RESIDUE SO4 C 370
15	BC6	SOFTWARE	LYS C:10 , LEU C:73 , ARG C:74 , ASN C:79	BINDING SITE FOR RESIDUE SO4 C 380
16	BC7	SOFTWARE	LYS C:26 , ALA C:27 , LYS C:48 , ARG D:28	BINDING SITE FOR RESIDUE SO4 C 385
17	BC8	SOFTWARE	LYS D:10 , LEU D:73 , ARG D:74 , ASN D:79	BINDING SITE FOR RESIDUE SO4 D 330
18	BC9	SOFTWARE	ASP D:32 , ARG D:80 , GLN D:83	BINDING SITE FOR RESIDUE NHE D 500
19	CC1	SOFTWARE	LYS A:42 , LYS E:10 , LEU E:73 , ARG E:74 , ASN E:79	BINDING SITE FOR RESIDUE SO4 E 335
20	CC2	SOFTWARE	ASN E:60 , TRP E:63	BINDING SITE FOR RESIDUE SO4 E 390

(no "SS Bond" information available for 3OB9)

(no "Cis Peptide Bond" information available for 3OB9)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069061	S	2	T	MS3L1_HUMAN	Polymorphism	150938844	D	S	2	T

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

Biological Unit 1 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

Biological Unit 2 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

Biological Unit 3 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069061	S	2	T	MS3L1_HUMAN	Polymorphism	150938844	D	S	2	T

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

Biological Unit 5 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

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

(no "PROSITE Motif" information available for 3OB9)

(no "Exon" information available for 3OB9)

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:89
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:89
                                    14        24        34        44        54        64        74        84         
           MS3L1_HUMAN    5 EGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVAR 93
               SCOP domains d3ob9a_ A: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3ob9 A  5 EGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVAR 93
                                    14        24        34        44        54        64        74        84

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:87
                                    15        25        35        45        55        65        75        85       
           MS3L1_HUMAN    6 GMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
               SCOP domains d3ob9b_ B: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.........eeeeeeeeeeee.......eeeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  3ob9 B  6 GMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
                                    15        25        35        45        55        65        75        85

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:88
                                    14        24        34        44        54        64        74        84        
           MS3L1_HUMAN    5 EGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
               SCOP domains d3ob9c_ C: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  3ob9 C  5 EGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
                                    14        24        34        44        54        64        74        84

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:93
                             1                                                                                           
                             |       9        19        29        39        49        59        69        79        89   
           MS3L1_HUMAN    - -MSASEGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
               SCOP domains d3ob9d_ D: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --T------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3ob9 D  0 GSSASEGMKFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
                                     9        19        29        39        49        59        69        79        89

Chain E from PDB  Type:PROTEIN  Length:79
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:85
                                    17        27        37        47        57        67        77        87     
           MS3L1_HUMAN    8 KFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
               SCOP domains d3ob9e_ E: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.........eeeeeeeeeee.------..eeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3ob9 E  8 KFKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVG------KIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
                                    17        27        37   |     -|       57        67        77        87     
                                                            41     48

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Chromo domain-like (82)

Family: automated matches (10)

Protein domain: automated matches (10)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d3ob9a_	A:
1b	d3ob9b_	B:
1c	d3ob9c_	C:
1d	d3ob9d_	D:
1e	d3ob9e_	E:

(no "CATH Domain" information available for 3OB9)

(no "Pfam Domain" information available for 3OB9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (MS3L1_HUMAN | Q8N5Y2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
biological process
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0006342	chromatin silencing	Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
	GO:0043968	histone H2A acetylation	The modification of histone H2A by the addition of an acetyl group.
	GO:0043984	histone H4-K16 acetylation	The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	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:0072487	MSL complex	A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residue at position 16. In human, it contains the catalytic subunit MOF, and MSL1, MSL2 and MSL3.
	GO:0035267	NuA4 histone acetyltransferase complex	A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
	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.

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	Cis Peptide Bonds
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	3ob9
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(no "Related Entries Specified in the PDB File" available for 3OB9)

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