1OTC | PD0074 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   THE O. NOVA TELOMERE END BINDING PROTEIN COMPLEXED WITH SINGLE STRAND DNA

Authors :   M. P. Horvath, V. L. Schweiker, J. M. Bevilacqua, J. A. Ruggles, S. C. Schultz

Date :   25 Nov 98 (Deposition) - 12 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Single Strand Dna Binding Protein, Protein Dna Interactions, Protein Protein Interactions, Oligonucleotide And Oligosaccharide Binding Fold, Ob Fold, Telomeres, Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. P. Horvath, V. L. Schweiker, J. M. Bevilacqua, J. A. Ruggles, S. C. Schultz
Crystal Structure Of The Oxytricha Nova Telomere End Binding Protein Complexed With Single Strand Dna.
Cell(Cambridge, Mass. ) V. 95 963 1998
PubMed-ID: 9875850 | Reference-DOI: 10.1016/S0092-8674(00)81720-1
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(GPGPGPGPTPTPTPTPGPGPGPG)- 3')*
	Chains	:	D
	Engineered	:	YES
	Fragment	:	SINGLE STRAND DODECAMER DNA
	Synthetic	:	YES

Molecule 2 - PROTEIN (TELOMERE-BINDING PROTEIN ALPHA SUBUNIT)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	MAC-56A
	Expression System Plasmid	:	PKKT7-H
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Gene	:	MAC-56A
	Organelle	:	MACRONUCLEOUS
	Organism Scientific	:	STERKIELLA NOVA
	Organism Taxid	:	200597
	Other Details	:	ALANINE VERSION
	Synonym	:	ALPHA SUBUNIT

Molecule 3 - PROTEIN (TELOMERE-BINDING PROTEIN BETA SUBUNIT)
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	MAC-41A
	Expression System Plasmid	:	PKKT7-H
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL 28 KDA CORE DOMAIN
	Gene	:	MAC-41A
	Organelle	:	MACRONUCLEOUS
	Organism Scientific	:	STERKIELLA NOVA
	Organism Taxid	:	200597
	Other Details	:	ALANINE VERSION
	Synonym	:	BETA SUBUNIT

		1	2	3
Asymmetric/Biological Unit	:	A	B	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1OTC)

(no "Site" information available for 1OTC)

(no "SS Bond" information available for 1OTC)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:379	-	Pro A:380
2	Tyr B:47	-	Pro B:48

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TEBB_STENO_001 *	A	110	S	TEBB_STENO	---	---	B	A	110	S
2	UniProt	VAR_TEBA_STENO_002 *	A	311	S	TEBA_STENO	---	---	A	A	311	S
3	UniProt	VAR_TEBA_STENO_003 *	D	456	E	TEBA_STENO	---	---	A	D	456	E
	* ID not provided by source

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

(no "PROSITE Motif" information available for 1OTC)

(no "Exon" information available for 1OTC)

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:459
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:459
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486         
           TEBA_STENO    37 EYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
               SCOP domains d1otca1 A:37-204 Telomere end binding protein alpha subunit                                                                                                             d1otca2 A:205-328 Telomere end binding protein alpha subunit                                                                d1otca3 A:329-495 Telomere end binding protein alpha subunit                                                                                                            SCOP domains
               CATH domains 1otcA01 A:37-210 Nucleic acid-binding proteins                                                                                                                                1otcA02 A:211-326 Nucleic acid-binding proteins                                                                     1otcA03 A:327-495 Nucleic acid-binding proteins                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh..........eeeeeeee...eee...eeeeeeeee..................eeeeeee..hhh.........eeeee..eeeee..eeeeeee.....eeeee.......hhhh........................hhhhhhhhhhhhhhhhhh.....hhh...hhhhhh......eeeeeeeeee....eeeeeee.....eeeeeee...........eeee..eee.........eee.....eee.....hhhhhhhhh.....hhhhhhhh..........eee.hhh.......hhhhhh............eeeeeeeeeeee...hhhheeee.................eeeeeeeeeee..........eeeeee......hhhh..........hhhhhhhhhhhhhh......eeeeeeee..eeeee.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------E--------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otc A  37 EYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with TEBB_STENO | P16458 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:213
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
           TEBB_STENO    10 QQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQE 222
               SCOP domains d1otcb_ B: Core domain of telomere end binding protein beta subunit                                                                                                                                                   SCOP domains
               CATH domains 1otcB00 B:10-222 Telomere-binding Protein Beta Subunit; Chain                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..............eee.........eee....eeeeee....hhhhhhh.....hhh.....eee..eeeeeee............eeeeeee..eee..............hhh.hhhhhhhhhhhhhhhhhhhhhh........hhh...hhh....hhhh............................hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otc B  10 QQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQE 222
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219

Chain D from PDB  Type:DNA  Length:12
                                            
                 1otc D   1 GGGGTTTTGGGG  12
                                    10

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Single strand DNA-binding domain, SSB (96)

Protein domain: Core domain of telomere end binding protein beta subunit (14)

Oxytricha nova [TaxId: 200597] (14)

d1otcb_

Protein domain: Telomere end binding protein alpha subunit (16)

Oxytricha nova [TaxId: 200597] (16)

2a	d1otca1	A:37-204
2b	d1otca2	A:205-328
2c	d1otca3	A:329-495

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

[unclassified] (49)

1a	1otcA02	A:211-326
1b	1otcA01	A:37-210
1c	1otcA03	A:327-495

Topology: Telomere-binding Protein Beta Subunit; Chain B (14)

Homologous Superfamily: Telomere-binding Protein Beta Subunit; Chain (14)

[unclassified] (14)

1otcB00

B:10-222

(no "Pfam Domain" information available for 1OTC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TEBA_STENO | P29549)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043047	single-stranded telomeric DNA binding	Interacting selectively and non-covalently with single-stranded telomere-associated DNA.
biological process
	GO:0016233	telomere capping	A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
	GO:0000723	telomere maintenance	Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	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.

Chain B (TEBB_STENO | P16458)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	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
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	Cis Peptide Bonds
		Glu A:379 - Pro A:380	[ RasMol ]
		Tyr B:47 - Pro B:48	[ RasMol ]

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Description

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