1KIX | PD0278 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   DIMERIC STRUCTURE OF THE O. NOVA TELOMERE END BINDING PROTEIN ALPHA SUBUNIT WITH BOUND SSDNA

Authors :   O. B. Peersen, J. A. Ruggles, S. C. Schultz

Date :   03 Dec 01 (Deposition) - 22 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Telomere Binding Protein, Dna-Protein Interactions, Single Stranded Dna, Ssdna, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. B. Peersen, J. A. Ruggles, S. C. Schultz
Dimeric Structure Of The Oxytricha Nova Telomere End-Binding Protein Alpha-Subunit Bound To Ssdna.
Nat. Struct. Biol. V. 9 182 2002
PubMed-ID: 11836536
(for further references see the PDB file header)

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

Molecule 2 - 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
	Organism Scientific	:	STERKIELLA NOVA
	Organism Taxid	:	200597
	Other Details	:	ALANINE VERSION
	Synonym	:	ALPHA, MACRONUCLEAR ALPHA PROTEIN (ALANINE VERSION), MAC-56A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:438 , GLY A:440 , ALA A:441 , ASN A:442 , LYS A:489 , ASP A:490 , HOH A:565	BINDING SITE FOR RESIDUE SO4 A 901
2	AC2	SOFTWARE	ARG A:154 , GLN A:351 , ASN A:425	BINDING SITE FOR RESIDUE SO4 A 902

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

Asymmetric Unit

No.	Residues
1	Glu A:379	-	Pro A:380

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TEBA_STENO_002 *	A	311	S	TEBA_STENO	---	---	A	A	311	S
2	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)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TEBA_STENO_002 *	A	311	S	TEBA_STENO	---	---	A	A	311	S
2	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 1KIX)

(no "Exon" information available for 1KIX)

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
	(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:446
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:460
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHSVEVASLKKNVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
               SCOP domains d1kixa1 A:36-204 Telomere end binding protein alpha subunit                                                                                                              d1kixa2 A:205-318 Telomere end binding protein alpha subunit                                                                d1kixa3 A:329-495 Telomere end binding protein alpha subunit                                                                                                            SCOP domains
               CATH domains -1kixA01 A:37-210 Nucleic acid-binding proteins                                                                                                                                1kixA02 A:211-331 Nucleic acid-binding proteins                                                                          1kixA03 A:332-495 Nucleic acid-binding proteins                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......eeeeeeeeee...eeee..eeeeeeeee.............hhhhheeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee..............----.....ee.......hhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhh.....eeeeeeeeeeeeee..eeeeeee.....eeeeeee...........eeeeeeeee........eeeeeeeeeeeee...hhhhhhhhhhh.....----------.......eee.hhhh.....hhhhhhhhhhhh.......eeeeeeeeeeee..hhhh.eeeee....eee..........eeeeeeeeee..........eeeeee...................hhhhhhhhhhhhhhhhh....eeeeeee....eeee.eee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------E--------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kix A  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQ----DTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDDHS----------SLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDRKTKKSSSLKGASGKGDNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHKNADARKKLEDSAELLTKFNSYVDAVVERRNGFYLIKDTKLIY 495
                                    45        55        65        75        85        95       105       115       125       135       145       155       | -  |    175       185       195       205       215       225       235       245       255       265       275       285       295       305       315  |      -   |   335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
                                                                                                                                                         163  168                                                                                                                                                   318        329

Chain D from PDB  Type:DNA  Length:7
                                       
                 1kix D   2 TTTGGGG   8

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(

)

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: Telomere end binding protein alpha subunit (16)

Oxytricha nova [TaxId: 200597] (16)

1a	d1kixa1	A:36-204
1b	d1kixa2	A:205-318
1c	d1kixa3	A:329-495

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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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	1kixA02	A:211-331
1b	1kixA03	A:332-495
1c	1kixA01	A:37-210

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

Asymmetric 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.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Glu A:379 - Pro A:380	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1kix
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1jb7	ALPHA:BETA:SSDNA TERNARY COMPLEX WITH G-QUARTET STRUCTURE
1k8g	ALPHA N-TERMINAL DOMAIN WITH AND WITHOUT BOUND SSDNA
1otc	ALPHA:BETA:SSDNA TERNARY COMPLEX

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

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