3CEY - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L3MBTL2

Authors :   N. Nady, Y. Guo, P. Pan, A. Allali-Hassani, C. Qi, H. Zhu, A. Dong, F. Mack L. Crombet, P. Loppnau, I. Kozieradzki, M. Vedadi, A. M. Edwards, J. We C. Bountra, C. H. Arrowsmith, A. Bochkarev, R. Read, J. Min, Structura Genomics Consortium (Sgc)

Date :   29 Feb 08 (Deposition) - 06 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Mbt, Structural Genomics, Structural Genomics Consortium, Sgc, Chromatin Regulator, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc-Finger, Transcription Regulator (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
	Fragment	:	UNP RESIDUES 170-625
	Gene	:	L3MBTL2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	L3, MBT-LIKE 2 PROTEIN, H-L3, MBT-LIKE PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3CEY)

(no "Site" information available for 3CEY)

Asymmetric Unit

No.	Residues
1	A:451	-	A:462
2	B:451	-	B:462

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

Asymmetric 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)

Biological Unit 1 (2, 2)

								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	R	300	W
2	UniProt	VAR_061675	V	337	A	LMBL2_HUMAN	Polymorphism	34289721	A	V	337	A

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

Biological Unit 2 (2, 2)

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

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

Biological Unit 3 (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 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:291-390 B:291-389 A:408-500 B:408-500 A:508-604 B:508-604

Biological Unit 1 (1, 4)

	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	4	A:179-283 - A:291-390 - A:408-500 - A:508-604 -

Biological Unit 2 (1, 4)

	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	4	- B:179-283 - B:291-389 - B:408-500 - B:508-604

Biological Unit 3 (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:291-390 B:291-389 A:408-500 B:408-500 A:508-604 B:508-604

(no "Exon" information available for 3CEY)

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:390
 aligned with LMBL2_HUMAN | Q969R5 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:433
                                   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 QDALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSDAVLPSRVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYEDGDSDDDFWCHMWSPLIHPVGWSRRVGHGIKMSERRSDMAHHPTFRKIYCDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVDGGPSTDGLDWFCYHASSHAIFPATFCQKNDIELTPPKGYEAQTFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPP 604
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ceyA01 A:172-318  [code=2.30.30.160, no name defin     ed]                                                                                        3ceyA02 A:319-422  [code=2.30.30.160, no    name defined]                                               3ceyA03 A:423-528  [code=2.30.30.160, no n        ame defined]                                                 ----------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh....hhhhh....hhhhh.......eeeee...-----..eeeeeeeeee..eeeeee..........eeee.....ee..hhhhhh...............hhhhhhhhhhh.......hhhhhhhhhh........eeeeee..eeeeeeeeeeeeee..eeeeee..---..eeeee.....ee..hhhhhhh.ee..-----------------...hhhhh.....eee.........eeeeee..eeeeeeeeeeeee....eeeeee.--------..eeee.....eee.hhhhhhh..ee...-----..hhhhhhhhh.....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:291-390 UniProt: 291-391                                                                 -----MBT  PDB: A:408-500 UniProt: 397-500                                                                    -------MBT  PDB: A:508-604 UniProt: 508-604                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cey A 172 QDALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSD-----RVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYED---DDDFWCHMWSPLIHPVGWSRRVGHGIKM-----------------CDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVD--------DWFCYHASSHAIFPATFCQKNDIELTPPK-----TFNWENYLEKTKSKAAPSRLFN-----HGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPP 604
                                   181       191       201       211       221|     |231       241       251       261       271       281       291       301       311       321       331       341       351       | - |     371       381        |-         -      |411       421       431       441       451       461  |      - |     481       491       501     | 511       521      |  -  |    541       551       561       571       581       591       601   
                                                                            222   228                                                                                                                                359 363                        390               408                                                     464      473                         501   507                  528   534

Chain B from PDB  Type:PROTEIN  Length:396
 aligned with LMBL2_HUMAN | Q969R5 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:433
                                   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602   
          LMBL2_HUMAN   173 DALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSDAVLPSRVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYEDGDSDDDFWCHMWSPLIHPVGWSRRVGHGIKMSERRSDMAHHPTFRKIYCDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVDGGPSTDGLDWFCYHASSHAIFPATFCQKNDIELTPPKGYEAQTFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPPV 605
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ceyB01 B:173-318  [code=2.30.30.160, no name defi     ned]                                                                                       3ceyB02 B:319-422  [code=2.30.30.160, no    name defined]                                               3ceyB03 B: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.....hhhhheeee.....ee..hhhhhh.........hhhhh.hhhhhhhhhhh.......hhhhhhhhhh........eeeeee..eeeeeeeeeeeeee..eeeeee..---..eeeee.....eee.hhhhhhh.ee.------------------...hhhhh....eee..........eeeeee..eeeeeeeeeeeee....eeeeee.--------..eeee.....ee..hhhhhhh..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:291-389 UniProt: 291-391                                                                 -----MBT  PDB: B:408-500 UniProt: 397-500                                                                    -------MBT  PDB: B:508-604 UniProt: 508-604                                                             - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cey B 173 DALVLGFDWGKFLKDHSYKAAPVSCFKHVPLYDQWEDVMKGMKVEVLNSD-----RVYWIASVIQTAGYRVLLRYEGFENDASHDFWCNLGTVDVHPIGWCAINSKILVPPRTIHAKFTDWKGYLMKRLVGSRTLPVDFHIKMVESMKYPFRQGMRLEVVDKSQVSRTRMAVVDTVIGGRLRLLYED---DDDFWCHMWSPLIHPVGWSRRVGHGIK------------------CDAVPYLFKKVRAVYTEGGWFEEGMKLEAIDPLNLGNICVATVCKVLLDGYLMICVD--------DWFCYHASSHAIFPATFCQKNDIELTPPKGY---TFNWENYLEKTKSKAAPSRLFNMDCPNHGFKVGMKLEAVDLMEPRLICVATVKRVVHRLLSIHFDGWDSEYDQWVDCESPDIYPVGWCELTGYQLQPPV 605
                                   182       192       202       212       222     | 232       242       252       262       272       282       292       302       312       322       332       342       352      |  -|      372       382      |  -         -     | 412       422       432       442       452       462 |       -|      482       492       502|   |  512       522       532       542       552       562       572       582       592       602   
                                                                           222   228                                                                                                                                359 363                       389                408                                                     464      473                           503 507

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 3CEY)

Asymmetric 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	3ceyB03	B:423-531
1b	3ceyA03	A:423-528
1c	3ceyA02	A:319-422
1d	3ceyB02	B:319-422
1e	3ceyB01	B:173-318
1f	3ceyA01	A:172-318

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

Asymmetric 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.

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	3cey
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	LMBL2_HUMAN \| Q969R5
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	LMBL2_HUMAN \| Q969R5	:	2w0t 3f70

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Ligands, Modified Residues, Ions (0, 0)

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