3UT1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE 3-MBT REPEAT DOMAIN OF L3MBTL3

Authors :   N. Zhong, W. Tempel, A. K. Wernimont, S. Graslund, C. H. Arrowsmith, A. M C. Bountra, J. Weigelt, P. J. Brown, Structural Genomics Consortiu

Date :   24 Nov 11 (Deposition) - 28 Dec 11 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Chromatin Modification, Transcription Repression, Mbt Repeat, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Zhong, W. Tempel, A. K. Wernimont, S. Graslund, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, P. J. Brown
Crystal Structure Of The 3-Mbt Repeat Domain Of L3Mbtl3
To Be Published
PubMed: search

Molecule 1 - LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE PROTEIN 3
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BL21-V2R-PRARE2
	Expression System Strain	:	PET28-SBP-TEV
	Expression System Taxid	:	511693
	Fragment	:	UNP RESIDUES 228-551
	Gene	:	L3MBTL3, KIAA1798, MBT1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	H-L(3)MBT-LIKE PROTEIN 3, L(3)MBT-LIKE PROTEIN 3, MBT-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	CO	5	Ligand/Ion	COBALT (II) ION
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	UNX	12	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 26)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	UNX	24	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:63 , HOH A:93 , HOH A:94 , HIS A:422 , HIS A:503	BINDING SITE FOR RESIDUE CO A 1
2	AC2	SOFTWARE	HOH A:100 , HIS A:404 , ASN A:407	BINDING SITE FOR RESIDUE CO A 2
3	AC3	SOFTWARE	HIS A:432	BINDING SITE FOR RESIDUE CO A 3
4	AC4	SOFTWARE	HIS A:330	BINDING SITE FOR RESIDUE CO A 4
5	AC5	SOFTWARE	HIS A:277	BINDING SITE FOR RESIDUE CO A 5
6	AC6	SOFTWARE	PRO A:355 , ASP A:381 , ASN A:384 , PHE A:387 , CYS A:389 , PHE A:405 , TRP A:408 , TYR A:412	BINDING SITE FOR RESIDUE EPE A 552

(no "SS Bond" information available for 3UT1)

(no "Cis Peptide Bond" information available for 3UT1)

(no "SAP(SNP)/Variant" information available for 3UT1)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	LMBL3_HUMAN	232-332 340-439 448-543	3	A:232-332 A:340-439 A:448-543

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MBT	PS51079	MBT repeat profile.	LMBL3_HUMAN	232-332 340-439 448-543	6	A:232-332 A:340-439 A:448-543

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.5c	ENST00000368136	5c	ENSE00002182355	chr6:130341702-130341813	112	LMBL3_HUMAN	-	0	0	-	-
1.6	ENST00000368136	6	ENSE00001409294	chr6:130343372-130343450	79	LMBL3_HUMAN	-	0	0	-	-
1.7	ENST00000368136	7	ENSE00001411632	chr6:130363830-130363946	117	LMBL3_HUMAN	1-34	34	0	-	-
1.8	ENST00000368136	8	ENSE00000975595	chr6:130370427-130370538	112	LMBL3_HUMAN	35-72	38	0	-	-
1.9b	ENST00000368136	9b	ENSE00001084666	chr6:130370901-130370975	75	LMBL3_HUMAN	72-97	26	0	-	-
1.10b	ENST00000368136	10b	ENSE00000975596	chr6:130372394-130372553	160	LMBL3_HUMAN	97-150	54	0	-	-
1.11b	ENST00000368136	11b	ENSE00000975597	chr6:130374004-130374136	133	LMBL3_HUMAN	150-194	45	0	-	-
1.12b	ENST00000368136	12b	ENSE00000975598	chr6:130376316-130376400	85	LMBL3_HUMAN	195-223	29	0	-	-
1.13	ENST00000368136	13	ENSE00002162936	chr6:130378551-130378642	92	LMBL3_HUMAN	223-253	31	1	A:231-253	23
1.14	ENST00000368136	14	ENSE00002186523	chr6:130381181-130381285	105	LMBL3_HUMAN	254-288	35	1	A:254-288	35
1.15	ENST00000368136	15	ENSE00002186040	chr6:130387498-130387633	136	LMBL3_HUMAN	289-334	46	1	A:289-334	46
1.16b	ENST00000368136	16b	ENSE00000975602	chr6:130389475-130389566	92	LMBL3_HUMAN	334-364	31	1	A:334-364	31
1.17b	ENST00000368136	17b	ENSE00000975603	chr6:130392121-130392272	152	LMBL3_HUMAN	365-415	51	1	A:365-415	51
1.18	ENST00000368136	18	ENSE00002154851	chr6:130399703-130399779	77	LMBL3_HUMAN	415-441	27	1	A:415-441	27
1.19	ENST00000368136	19	ENSE00002160966	chr6:130404765-130404850	86	LMBL3_HUMAN	441-469	29	1	A:441-469 (gaps)	29
1.20	ENST00000368136	20	ENSE00002177917	chr6:130407285-130407395	111	LMBL3_HUMAN	470-506	37	1	A:470-506	37
1.21b	ENST00000368136	21b	ENSE00000975607	chr6:130413890-130414004	115	LMBL3_HUMAN	507-545	39	1	A:507-545	39
1.22	ENST00000368136	22	ENSE00000975608	chr6:130415410-130415512	103	LMBL3_HUMAN	545-579	35	1	A:545-545	1
1.23	ENST00000368136	23	ENSE00000975609	chr6:130425571-130425720	150	LMBL3_HUMAN	579-629	51	0	-	-
1.24	ENST00000368136	24	ENSE00000975610	chr6:130442024-130442103	80	LMBL3_HUMAN	629-656	28	0	-	-
1.25	ENST00000368136	25	ENSE00000975611	chr6:130454597-130454766	170	LMBL3_HUMAN	656-712	57	0	-	-
1.26	ENST00000368136	26	ENSE00000975612	chr6:130454988-130455050	63	LMBL3_HUMAN	713-733	21	0	-	-
1.27d	ENST00000368136	27d	ENSE00002176826	chr6:130460755-130462584	1830	LMBL3_HUMAN	734-780	47	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:313
 aligned with LMBL3_HUMAN | Q96JM7 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:315
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540     
          LMBL3_HUMAN   231 AWCWASYLEEEKAVAVPAKLFKEHQSFPYNKNGFKVGMKLEGVDPEHQSVYCVLTVAEVCGYRIKLHFDGYSDCYDFWVNADALDIHPVGWCEKTGHKLHPPKGYKEEEFNWQTYLKTCKAQAAPKSLFENQNITVIPSGFRVGMKLEAVDKKNPSFICVATVTDMVDNRFLVHFDNWDESYDYWCEASSPHIHPVGWCKEHRRTLITPPGYPNVKHFSWDKYLEETNSLPAPARAFKVKPPHGFQKKMKLEVVDKRNPMFIRVATVADTDDHRVKVHFDGWNNCYDYWIDADSPDIHPVGWCSKTGHPLQPPLS 545
               SCOP domains d3ut1a1 A:231-339 automated matches                                                                          d3ut1a2 A:340-447 automated matches                                                                         d3ut1a3 A:448-545 automated matches                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhh.................eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh..ee..........hhhhhhhhh.....hhhhh................eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheee......ee..hhhhhh...ee.....--....hhhhhhhhh.....hhhhh............eeeee.......eeeeeeeee...eeeeee...hhhhheeee.....ee..hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -MBT  PDB: A:232-332 UniProt: 232-332                                                                 -------MBT  PDB: A:340-439 UniProt: 340-439                                                                --------MBT  PDB: A:448-543 UniProt: 448-543                                                            -- PROSITE
           Transcript 1 (1) Exon 1.13 [INCOMPLETE] Exon 1.14  PDB: A:254-288          Exon 1.15  PDB: A:289-334 UniProt: 289-334    ------------------------------Exon 1.17b  PDB: A:365-415 UniProt: 365-415        -------------------------Exon 1.19 UniProt: 441-469   Exon 1.20  PDB: A:470-506            Exon 1.21b  PDB: A:507-545              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.16b  PDB: A:334-364     --------------------------------------------------Exon 1.18  PDB: A:415-441  -------------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 3ut1 A 231 AWCWASYLEEEKAVAVPAKLFKEHQSFPYNKNGFKVGMKLEGVDPEHQSVYCVLTVAEVCGYRIKLHFDGYSDCYDFWVNADALDIHPVGWCEKTGHKLHPPKGYKEEEFNWQTYLKTCKAQAAPKSLFENQNITVIPSGFRVGMKLEAVDKKNPSFICVATVTDMVDNRFLVHFDNWDESYDYWCEASSPHIHPVGWCKEHRRTLITPPGY--VKHFSWDKYLEETNSLPAPARAFKVKPPHGFQKKMKLEVVDKRNPMFIRVATVADTDDHRVKVHFDGWNNCYDYWIDADSPDIHPVGWCSKTGHPLQPPLS 545
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440 |  |  450       460       470       480       490       500       510       520       530       540     
                                                                                                                                                                                                                                             442  |                                                                                                    
                                                                                                                                                                                                                                                445

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Tudor/PWWP/MBT (72)

Family: automated matches (24)

Protein domain: automated matches (24)

Human (Homo sapiens) [TaxId: 9606] (20)

1a	d3ut1a1	A:231-339
1b	d3ut1a2	A:340-447
1c	d3ut1a3	A:448-545

(no "CATH Domain" information available for 3UT1)

(no "Pfam Domain" information available for 3UT1)

Asymmetric Unit(hide GO term definitions)

Chain A (LMBL3_HUMAN | Q96JM7)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0043249	erythrocyte maturation	A developmental process, independent of morphogenetic (shape) change, that is required for an erythrocyte to attain its fully functional state.
	GO:0030851	granulocyte differentiation	The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
	GO:0030225	macrophage differentiation	The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
	GO:0030099	myeloid cell differentiation	The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
	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: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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	3ut1
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	LMBL3_HUMAN \| Q96JM7	:	1wjq 1wjs 4fl6 4l59

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (10, 10)

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