2VKP - JenaLib

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Title :   CRYSTAL STRUCTURE OF BTB DOMAIN FROM BTBD6

Authors :   C. D. O. Cooper, A. C. W. Pike, E. Salah, P. Filippakopoulos, G. Bunkoczi J. M. Elkins, F. Von Delft, O. Gileadi, A. Edwards, J. Weigelt, C. H. Ar S. Knapp

Date :   21 Dec 07 (Deposition) - 12 Feb 08 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Protein-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. O. Cooper, A. C. W. Pike, E. Salah, P. Filippakopoulos, G. Bunkoczi, J. M. Elkins, F. Von Delft, O. Gileadi, A. Edwards, J. Weigelt, C. H. Arrowsmith, S. Knapp
Crystal Structure Of Btb Domain From Btbd6
To Be Published
PubMed: search

Molecule 1 - BTB/POZ DOMAIN-CONTAINING PROTEIN 6
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Fragment	:	BTB DOMAIN, RESIDUES 2-108
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LENS BTB DOMAIN PROTEIN, BTB DOMAIN PROTEIN BTBD6

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	K	1	Ligand/Ion	POTASSIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE B:74 , ASP B:75 , GLU B:105 , SER B:107 , HOH B:2068 , HOH B:2093	BINDING SITE FOR RESIDUE K B1109
2	AC2	SOFTWARE	LYS B:67 , ASP B:75	BINDING SITE FOR RESIDUE EDO B1110

(no "SS Bond" information available for 2VKP)

(no "Cis Peptide Bond" information available for 2VKP)

(no "SAP(SNP)/Variant" information available for 2VKP)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BTB	PS50097	BTB domain profile.	BTBD6_HUMAN	83-153	2	A:8-78 B:8-78

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BTB	PS50097	BTB domain profile.	BTBD6_HUMAN	83-153	4	A:8-78 B:8-78

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000392554	1b	ENSE00001512364	chr14:105715115-105715422	308	BTBD6_HUMAN	1-72	72	0	-	-
1.1e	ENST00000392554	1e	ENSE00001874698	chr14:105715494-105715584	91	BTBD6_HUMAN	72-102	31	2	A:0-27 B:0-27	28 28
1.1g	ENST00000392554	1g	ENSE00001296252	chr14:105715697-105715815	119	BTBD6_HUMAN	103-142	40	2	A:28-67 (gaps) B:28-67	40 40
1.2d	ENST00000392554	2d	ENSE00001512363	chr14:105715977-105717430	1454	BTBD6_HUMAN	142-485	344	2	A:67-108 B:67-108	42 42

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:103
 aligned with BTBD6_HUMAN | Q96KE9 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:109
                                    84        94       104       114       124       134       144       154       164       174         
          BTBD6_HUMAN    75 LMFNNELMADVHFVVGPPGATRTVPAHKYVLAVGSSVFYAMFYGDLAEVKSEIHIPDVEPAAFLILLKYMYSDEIDLEADTVLATLYAAKKYIVPALAKACVNFLETSL 183
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee......eeeeehhhhhhhhhhhhhhhhh------..eeee...hhhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------BTB  PDB: A:8-78 UniProt: 83-153                                       ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: A:0-27      Exon 1.1g  PDB: A:28-67 (gaps)          ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.2d  PDB: A:67-108 UniProt: 142-485  Transcript 1 (2)
                 2vkp A   0 SmFNNELmADVHFVVGPPGATRTVPAHKYVLAVGSSVFYAmFY------KSEIHIPDVEPAAFLILLKYmYSDEIDLEADTVLATLYAAKKYIVPALAKACVNFLETSL 108
                             |     | 9        19        29        39| |     49        59        69        79        89        99         
                             |     7-MSE                           40-MSE   49                  69-MSE                                   
                             1-MSE                                   42

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with BTBD6_HUMAN | Q96KE9 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:109
                                    84        94       104       114       124       134       144       154       164       174         
          BTBD6_HUMAN    75 LMFNNELMADVHFVVGPPGATRTVPAHKYVLAVGSSVFYAMFYGDLAEVKSEIHIPDVEPAAFLILLKYMYSDEIDLEADTVLATLYAAKKYIVPALAKACVNFLETSL 183
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -BTB-2vkpB01 B:1-108                                                                                          Pfam domains (1)
           Pfam domains (2) -BTB-2vkpB02 B:1-108                                                                                          Pfam domains (2)
         Sec.struct. author ..........eeeee......eeeeehhhhhhhhhhhhhhhhh........eeee...hhhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------BTB  PDB: B:8-78 UniProt: 83-153                                       ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1e  PDB: B:0-27      Exon 1.1g  PDB: B:28-67 UniProt: 103-142----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.2d  PDB: B:67-108 UniProt: 142-485  Transcript 1 (2)
                 2vkp B   0 SmFNNELmADVHFVVGPPGATRTVPAHKYVLAVGSSVFYAmFYGDLAEVKSEIHIPDVEPAAFLILLKYmYSDEIDLEADTVLATLYAAKKYIVPALAKACVNFLETSL 108
                             |     | 9        19        29        39|       49        59        69        79        89        99         
                             1-MSE 7-MSE                           40-MSE                       69-MSE

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 2VKP)

(no "CATH Domain" information available for 2VKP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: POZ (36)

Family: BTB (12)

Homo sapiens (Human) (12)

1a	BTB-2vkpB01	B:1-108
1b	BTB-2vkpB02	B:1-108

Asymmetric Unit(hide GO term definitions)

Chain A,B (BTBD6_HUMAN | Q96KE9)

cellular component
	GO:0000932		P-body		A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737		cytoplasm		All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Description

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Ligands, Modified Residues, Ions (3, 10)

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