3F70 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L3MBTL2-H4K20ME1 COMPLEX

Authors :   Y. Guo, C. Qi, A. Allali-Hassani, P. Pan, H. Zhu, A. Dong, F. Mackenzie, L P. Loppnau, I. Kozieradzki, M. Vedadi, A. M. Edwards, J. Weigelt, C. Bo C. H. Arrowsmith, A. Botchkarev, R. Read, J. Min, Structural Genomic Consortium (Sgc)

Date :   07 Nov 08 (Deposition) - 06 Jan 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Mbt, Chromatin Regulator, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc-Finger, Transcription Regulator, Structural Genomics, Structural Genomics Consortium, Sgc, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Guo, N. Nady, C. Qi, A. Allali-Hassani, H. Zhu, P. Pan, M. A. Adams-Cioaba, M. F. Amaya, A. Dong, M. Vedadi, M. Schapira, R. J. Read, C. H. Arrowsmith, J. Min
Methylation-State-Specific Recognition Of Histones By The Mbt Repeat Protein L3Mbtl2.
Nucleic Acids Res. V. 37 2204 2009
PubMed-ID: 19233876 | Reference-DOI: 10.1093/NAR/GKP086

Molecule 1 - LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE 2 PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	L3MBTL2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	L(3)MBT-LIKE 2 PROTEIN, H-L(3)MBT-LIKE PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MLZ	2	Mod. Residue	N-METHYL-LYSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:82 , ASP A:546 , PHE A:570 , TRP A:573 , GLU A:608	BINDING SITE FOR RESIDUE MLZ A 20
2	AC2	SOFTWARE	ASP B:546 , TRP B:573	BINDING SITE FOR RESIDUE MLZ B 20

(no "SS Bond" information available for 3F70)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:505	-	Gln A:506
2	Pro B:226	-	Ser B:227
3	Asp B:361	-	Ser B:362
4	Lys B:501	-	Gly B:502

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015093	R	300	W	LMBL2_HUMAN	Polymorphism	2277846	A/B	R	300	W
2	UniProt	VAR_061675	V	337	A	LMBL2_HUMAN	Polymorphism	34289721	A/B	V	337	A

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

Asymmetric/Biological Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	LMBL2_HUMAN	179-283 291-391 397-500 508-604	8	A:179-283 B:179-283 A:291-386 B:291-391 A:419-500 B:408-500 A:508-604 B:508-604

(no "Exon" information available for 3F70)

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:392
 aligned with LMBL2_HUMAN | Q969R5 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:438
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601        
          LMBL2_HUMAN   172 QDALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSDAVLPSRVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYEDGDSDDDFWCHMWSPLIHPVGWSRRVGHGIKMSERRSDMAHHPTFRKIYCDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVDGGPSTDGLDWFCYHASSHAIFPATFCQKNDIELTPPKGYEAQTFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPPVAAEP 609
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3f70A01 A:172-318  [code=2.30.30.160, no name defined]                                                                                             -----------------------------------------    -----------------------                                ----3f70A03 A:423-531  [code=2.30.30.160, no n        ame defined]                                               ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh....hhhhh....hhhhhhhh....eeeee......--..eeeeeeeeee..eeeeee..........eeee.....ee..hhhhhh.........hhhhh.hhhhhhhhhhh.......hhhhhhhhhh........eeeee.......eeeeeeeeee..eeeeee..----..eeee.....eee.hhhhhhh.--------------------------------.eee..........eeeeee..eeeeeeeeeeeee....eeeeee.--------..eeee.....ee..hhhhhh...ee..........hhhhhhhhhh....hhhhh.............eeeee.......eeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh..ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------W------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------MBT  PDB: A:179-283 UniProt: 179-283                                                                     -------MBT  PDB: A:291-386 UniProt: 291-391                                                                 -----MBT  PDB: A:419-500 UniProt: 397-500                                                                    -------MBT  PDB: A:508-604 UniProt: 508-604                                                             ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f70 A 172 QDALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSDAVL--RVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYED----DDFWCHMWSPLIHPVGWSRRVGH--------------------------------RAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVD--------DWFCYHASSHAIFPATFCQKNDIELTPPKGYEAQTFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPPVAAEP 609
                                   181       191       201       211       221   |  |231       241       251       261       271       281       291       301       311       321       331       341       351       | -  |    371       381    |    -         -         -       421       431       441       451       461  |      - |     481       491       501       511       521       531       541       551       561       571       581       591       601        
                                                                               225  |                                                                                                                                359  364                   386                              419                                          464      473                                                                                                                                        
                                                                                  228

Chain B from PDB  Type:PROTEIN  Length:410
 aligned with LMBL2_HUMAN | Q969R5 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:438
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601        
          LMBL2_HUMAN   172 QDALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSDAVLPSRVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYEDGDSDDDFWCHMWSPLIHPVGWSRRVGHGIKMSERRSDMAHHPTFRKIYCDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVDGGPSTDGLDWFCYHASSHAIFPATFCQKNDIELTPPKGYEAQTFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPPVAAEP 609
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3f70B01 B:172-318  [code=2.30.30.160, no name defined]                                                                                             3f70B02 B:319-422  [code=2.30.30.160, no name defined]                                                  3f70B03 B:423-531  [code=2.30.30.160, no n        ame defined]                                               ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh.....hhhhh................eeeee..........eeeeeeeeee..eeeeee..........eeee.....ee..hhhhhh...............hhhhhhhhhhh.......hhhhhhhhh.........eeeee......eeeeeeeeeee..eeeeee.......eeeee.....ee..hhhhhhh.ee...----------------...hhhhh.....eee.........eeeeee..eeeeeeeeeeeee....eeeeee.--------..eeee.....ee..hhhhhh...ee....----..hhhhhhhhh.....hhhhh.............eeeee.......eeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh..ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------W------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------MBT  PDB: B:179-283 UniProt: 179-283                                                                     -------MBT  PDB: B:291-391 UniProt: 291-391                                                                 -----MBT  PDB: B:408-500 UniProt: 397-500                                                                    -------MBT  PDB: B:508-604 UniProt: 508-604                                                             ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f70 B 172 QDALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSDAVLPSRVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYEDGDSDDDFWCHMWSPLIHPVGWSRRVGHGIKMS----------------CDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVD--------DWFCYHASSHAIFPATFCQKNDIELTPPKG----TFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPPVAAEP 609
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391         -      |411       421       431       441       451       461  |      - |     481       491       501|    | 511       521       531       541       551       561       571       581       591       601        
                                                                                                                                                                                                                                                     391              408                                                     464      473                          502  507

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 3F70)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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)

1a	3f70A03	A:423-531
1b	3f70B03	B:423-531
1c	3f70B02	B:319-422
1d	3f70A01	A:172-318
1e	3f70B01	B:172-318

(no "Pfam Domain" information available for 3F70)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LMBL2_HUMAN | Q969R5)

molecular function
	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: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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
	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: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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MLZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:505 - Gln A:506	[ RasMol ]
		Asp B:361 - Ser B:362	[ RasMol ]
		Lys B:501 - Gly B:502	[ RasMol ]
		Pro B:226 - Ser B:227	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3f70
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LMBL2_HUMAN \| Q969R5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LMBL2_HUMAN \| Q969R5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	LMBL2_HUMAN \| Q969R5	:	2w0t 3cey

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (1, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 5)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File