3K81 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE CENTRAL INTERACTION PROTEIN FROM THE TRYPANOSOMA BRUCEI EDITOSOME IN COMPLEX WITH SINGLE DOMAIN ANTIBODIES

Authors :   Y. -J. Park, W. Hol

Date :   13 Oct 09 (Deposition) - 17 Nov 10 (Release) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

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

Keywords :   Krepa6, Vhh, Single Domain Antibody, Immune System, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Wu, Y. J. Park, E. Pardon, S. Turley, A. Hayhurst, J. Deng, J. Steyaert, W. G. Hol
Structures Of A Key Interaction Protein From The Trypanosom Brucei Editosome In Complex With Single Domain Antibodies.
J. Struct. Biol. V. 174 124 2011
PubMed-ID: 20969962 | Reference-DOI: 10.1016/J.JSB.2010.10.007

Molecule 1 - MP18 RNA EDITING COMPLEX PROTEIN
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSF
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	KREPA6
	Gene	:	KREPA6, TB10.70.2090
	Organism Scientific	:	TRYPANOSOMA BRUCEI
	Organism Taxid	:	5691

Molecule 2 - SINGLE STRAND ANTIBODY VHH DOMAIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSF
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SINGLE DOMAIN ANTIBODY VHH
	Organism Scientific	:	LAMA GLAMA
	Organism Taxid	:	9844

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3K81)

(no "Site" information available for 3K81)

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:95
2	B:22	-	B:95

Asymmetric/Biological Unit

No.	Residues
1	Ser C:108	-	Cys C:109
2	Pro C:122	-	Pro C:123
3	Glu D:62	-	Val D:63
4	Pro D:122	-	Pro D:123
5	Ser A:25	-	Gly A:26
6	Ile A:27	-	Thr A:28
7	Glu A:54	-	Gly A:55
8	Glu B:54	-	Gly B:55
9	Gln B:100	-	Thr B:101

(no "SAP(SNP)/Variant" information available for 3K81)

(no "PROSITE Motif" information available for 3K81)

(no "Exon" information available for 3K81)

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:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.........eeeeee...........eeeeee.....eeeeeee.....eee........eeeee....eeeeeee.......eeeeee..hhhhh...........eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3k81 A   2 VQPQESGGGLAQAGGSLRLSCVVSGITFASEAWGWYRRAPGKQRELIAAINNEGRTNYVDSVKGRFTVSRDNAKNVMYLQMNSLKPEDTAVYYCNANLQTGTLSGARLYWGQGTQVTV 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............ee...ee..........eeeeee.....eee....................ee.......ee.eeee.......eeeeeee.................eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k81 B   2 VQPQESGGGLAQAGGSLRLSCVVSGITFASEAWGWYRRAPGKQRELIAAINNEGRTNYVDSVKGRFTVSRDNAKNVMYLQMNSLKPEDTAVYYCNANLQTGTLSGARLYWGQGTQVTVSS 121
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:105
 aligned with Q38B90_TRYB2 | Q38B90 from UniProtKB/TrEMBL  Length:164

    Alignment length:113
                                    29        39        49        59        69        79        89        99       109       119       129   
         Q38B90_TRYB2    20 KSVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHG 132
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....ee....ee..eeeee...--------.....eeeeeee.hhhhhhhhhhhh....eeee..eeeee............eeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3k81 C  20 KSVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSI--------VVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHG 132
                                    29        39        49    |    -   |    69        79        89        99       109       119       129   
                                                             54       63

Chain D from PDB  Type:PROTEIN  Length:106
 aligned with Q38B90_TRYB2 | Q38B90 from UniProtKB/TrEMBL  Length:164

    Alignment length:111
                                    30        40        50        60        70        80        90       100       110       120       130 
         Q38B90_TRYB2    21 SVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIH 131
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.....ee..ee.eeeeeeeee...-----....eeeeeeeee.hhhhhhhhhhhh....eeeeeeeeeee............eeeeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3k81 D  21 SVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDT-----EVVVEKDHHTIRCFGELFSAEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIH 131
                                    30        40        50     |   - |      70        80        90       100       110       120       130 
                                                              56    62

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 3K81)

(no "CATH Domain" information available for 3K81)

(no "Pfam Domain" information available for 3K81)

Asymmetric/Biological Unit(hide GO term definitions)

Chain C,D (Q38B90_TRYB2 | Q38B90)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0031019	mitochondrial mRNA editing complex	An mRNA editing complex found in the mitochondrion. The best characterized example is that of Trypanosoma brucei, which catalyzes the insertion and deletion of uridylates.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3k81)

	Sites
(no "Sites" information available for 3k81)

	Cis Peptide Bonds
		Gln B:100 - Thr B:101	[ RasMol ]
		Glu A:54 - Gly A:55	[ RasMol ]
		Glu B:54 - Gly B:55	[ RasMol ]
		Glu D:62 - Val D:63	[ RasMol ]
		Ile A:27 - Thr A:28	[ RasMol ]
		Pro C:122 - Pro C:123	[ RasMol ]
		Pro D:122 - Pro D:123	[ RasMol ]
		Ser A:25 - Gly A:26	[ RasMol ]
		Ser C:108 - Cys C:109	[ RasMol ]

Jmol
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	3k81
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	Q38B90_TRYB2 \| Q38B90	:	3k7u 3k80 3stb 4dni

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (7, 7)

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