1PHJ | PD0444 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GG(3DR) GTTTTGGGG

Authors :   D. L. Theobald, S. C. Schultz

Date :   29 May 03 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   D. L. Theobald, S. C. Schultz
Nucleotide Shuffling And Ssdna Recognition In Oxytricha Nova Telomere End-Binding Protein Complexes
Embo J. V. 22 4314 2003
PubMed-ID: 12912928 | Reference-DOI: 10.1093/EMBOJ/CDG415
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPGPGPGPTPTPTPTPGPGPGPGPT)-3'**
	Chains	:	G, H
	Engineered	:	YES
	Other Details	:	3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES.
	Synthetic	:	YES

*Molecule 2 - 5'-D(GPGP(3DR)PGPTPTPTPTPGPGPGPG)-3'*
	Chains	:	D
	Engineered	:	YES
	Mutation	:	YES
	Other Details	:	3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, G TO 3DR SUBSTITUTION.
	Synthetic	:	YES

Molecule 3 - TELOMERE-BINDING PROTEIN ALPHA SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKKT7
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAC-56A AND MAC-56K AND MAC-56S
	Organism Scientific	:	STERKIELLA NOVA
	Organism Taxid	:	200597
	Synonym	:	TELOMERE-BINDING PROTEIN 56 KDA SUBUNIT, TEBP ALPHA

Molecule 4 - TELOMERE-BINDING PROTEIN BETA SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKKT7
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 9-224
	Gene	:	MAC-41A AND MAC-41S
	Organism Scientific	:	STERKIELLA NOVA
	Organism Taxid	:	200597
	Synonym	:	TELOMERE-BINDING PROTEIN 41 KDA SUBUNIT, TEBP BETA

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	D	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(no "Site" information available for 1PHJ)

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

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 1PHJ)

(no "Exon" information available for 1PHJ)

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:449
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:458
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484        
           TEBA_STENO    35 KYEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTK 492
               SCOP domains d1phja1 A:35-204 Telomere end binding protein alpha s     ubunit                                                                                                          d1phja2 A:205-328 Telomere end binding protein alpha subunit                                                                d1phja3 A:329-492 Telomere end binding protein alpha subunit                                                                                                         SCOP domains
               CATH domains --1phjA01 A:37-210 Nucleic acid-binding proteins                                                                                                                                1phjA02 A:211-326 Nucleic acid-binding proteins                                                                     1phjA03 A:327-492 Nucleic acid-binding proteins                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeee...ee.....eeeeeeee........-----.....eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.........hhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhh...eeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeeeee........eeeeeeeeeeeee...hhhhhhhhhhh...hhhhhhhhhh......ee..ee.hhhh.....hhhhhhhh...hhhhhh..eeeeeeeeeeee..hhhh.eeeee....eee...----..eeeeeeeeeeehhhhh...eeeeeeee...................hhhhhhhhhhhhhhhh...eeeeeeeeee..eeeee.ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1phj A  35 KYEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQ-----DASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLK----KGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTK 492
                                    44        54        64        74        84  |     94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394      |  - |     414       424       434       444       454       464       474       484        
                                                                               87    93                                                                                                                                                                                                                                                                                                                 401  406

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with TEBB_STENO | P16458 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:215
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
           TEBB_STENO    10 QQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQEKG 224
               SCOP domains d1phjb_ B: Core domain of telomere end binding protein beta subunit                                                                                                                                                     SCOP domains
               CATH domains 1phjB00 B:10-224 Telomere-binding Protein Beta Subunit; Chain                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh........hhhhh..eeeeeee.....eee...eee.eeehhhhhhhhhhhh...hhhhh...eeeeeeeeeeeee............eeeeeeeeeeeee...........ee...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh......hhhh.eee........................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1phj B  10 QQSAFKQLYTELFNNEGDFSKVSSNLKKPLKCYVKESYPHFLVTDGYFFVAPYFTKEAVNEFHAKFPNVNIVDLTDKVIVINNWSLELRRVNSAEVFTSYANLEARLIVHSFKPNLQERLNPTRYPVNLFRDDEFKTTIQHFRHTALQAAINKTVKGDNLVDISKVADAAGKKGKVDAGIVKASASKGDEFSDFSFKEGNTATLKIADIFVQEKG 224
                                    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
                                            
                 1phj D   1 GGxGTTTTGGGG  12
                              |     10  
                              3-3DR

Chain G from PDB  Type:DNA  Length:12
                                            
                 1phj G   1 GGGGTTTTGGGG  12
                                    10

Chain H from PDB  Type:DNA  Length:12
                                            
                 1phj H   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)

d1phjb_

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

Oxytricha nova [TaxId: 200597] (16)

2a	d1phja1	A:35-204
2b	d1phja2	A:205-328
2c	d1phja3	A:329-492

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	1phjA02	A:211-326
1b	1phjA01	A:37-210
1c	1phjA03	A:327-492

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

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

[unclassified] (14)

1phjB00

B:10-224

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

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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	Sites
(no "Sites" information available for 1phj)

	Cis Peptide Bonds
		Glu A:379 - Pro A:380	[ RasMol ]
		Tyr B:47 - Pro B:48	[ RasMol ]

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1jb7	SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH COGNATE SSDNA GGGGTTTTGGGG
1k8g	35 KDA N-TERMINAL FRAGMENT OF ALPHA SUBUNIT ALONE COMPLEXED WITH TTGGGG
1kix	DIMER OF ALPHA SUBUNIT ALONE COMPLEXED WITH TTTTGGGG
1otc	SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH COGNATE SSDNA GGGGTTTTGGGG
1pa6	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG
1ph1	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGGGT
1ph2	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG
1ph3	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGTG
1ph4	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG
1ph5	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG(3DR)GG
1ph6	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG
1ph7	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGIGG
1ph8	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGCGG
1ph9	CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 13)

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