1K8G | PD0266 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF OXYTRICHA NOVA TELOMERE END BINDING PROTEIN ALPHA SUBUNIT BOTH UNCOMPLEXED AND COMPLEXED WITH TELOMERIC SSDNA

Authors :   S. Classen, J. A. Ruggles, S. C. Schultz

Date :   24 Oct 01 (Deposition) - 20 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,E  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Protein-Dna Complex, Telomeres, Sequence Specific Ssdna Binding Protein, Ob Folds, Structure, Protein Single Strand Dna Interactions, 3'-Dna End Binding Protein, Telomere End Binding Protein, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Classen, J. A. Ruggles, S. C. Schultz
Crystal Structure Of The N-Terminal Domain Of Oxytricha Nova Telomere End-Binding Protein Alpha Subunit Both Uncomplexed And Complexed With Telomeric Ssdna.
J. Mol. Biol. V. 314 1113 2001
PubMed-ID: 11743727 | Reference-DOI: 10.1006/JMBI.2000.5191
(for further references see the PDB file header)

*Molecule 1 - 5'-D(TPTPGPGPGPG)-3'**
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TELOMERE-BINDING PROTEIN ALPHA SUBUNIT
	Chains	:	A, B, C
	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	:	N-TERMINAL 35KDA SSDNA BINDING DOMAIN
	Organism Scientific	:	STERKIELLA NOVA
	Organism Taxid	:	200597
	Other Details	:	ALANINE VERSION
	Synonym	:	ALPHA, MACRONUCLEAR ALPHA PROTEIN (ALANINE VERSION), MAC-56A

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B			E
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 2)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:204 , LYS A:304 , LYS C:216	BINDING SITE FOR RESIDUE SO4 A 321
2	AC2	SOFTWARE	TYR A:36 , HIS A:123 , ARG A:124 , SER A:145	BINDING SITE FOR RESIDUE SO4 A 322
3	AC3	SOFTWARE	LYS A:216 , TYR B:203 , SER B:204	BINDING SITE FOR RESIDUE SO4 B 321
4	AC4	SOFTWARE	HIS B:123 , ARG B:124 , SER B:176	BINDING SITE FOR RESIDUE SO4 B 322
5	AC5	SOFTWARE	LYS B:216 , SER C:202 , TYR C:203 , SER C:204 , LYS C:304 , HOH C:362	BINDING SITE FOR RESIDUE SO4 C 321
6	AC6	SOFTWARE	HIS C:123 , ARG C:124 , SER C:145 , SER C:176 , HOH C:384	BINDING SITE FOR RESIDUE SO4 C 322

(no "SS Bond" information available for 1K8G)

(no "Cis Peptide Bond" information available for 1K8G)

Asymmetric Unit (1, 3)

								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/B/C	A	311	S
	* ID not provided by source

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

Biological Unit 1 (1, 1)

								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
	* ID not provided by source

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TEBA_STENO_002 *	A	311	S	TEBA_STENO	---	---	B	A	311	S
	* ID not provided by source

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TEBA_STENO_002 *	A	311	S	TEBA_STENO	---	---	C	A	311	S
	* ID not provided by source

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

(no "PROSITE Motif" information available for 1K8G)

(no "Exon" information available for 1K8G)

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:269
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:280
                                    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
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQD 315
               SCOP domains d1k8ga1 A:36-204 Telomere end bi    nding protein al       pha subunit                                                                                                   d1k8ga2 A:205-315 Telomere end binding protein alpha subunit                                                    SCOP domains
               CATH domains -1k8gA01 A:37-210 Nucleic acid-b    inding proteins                                                                                                                            1k8gA02 A:211-315 Nucleic acid-binding proteins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeee......----.eeeeeee........-------...eeeeee..hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.......hhhhhhhhhhhhhhhhhhhhhh.........hhhhh.....eeeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeeee.................eeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8g A  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKT----YICSLKIVDPTLYLKQ-------SDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQD 315
                                    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
                                                          67   72             87      95

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:281
                                    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 
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
               SCOP domains d1k8gb1 B:36-204 Telomere end binding protein alpha s      ubunit                                                                                                        d1k8gb2 B:205-316 Telomere end binding protein alpha subunit                                                     SCOP domains
               CATH domains -1k8gB01 B:37-210 Nucleic acid-binding proteins                                                                                                                                1k8gB02 B:211-316 Nucleic acid-binding proteins                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee............eeeeeeeeee...eeee..eeeeeeeee.........------...eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.........hhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhh...eeeeeeeeeeeeee..eeeeeee.....eeeeeee...........eeeeeeeee........eee.....eeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8g B  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQ------SDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
                                    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 
                                                                               88     95

Chain C from PDB  Type:PROTEIN  Length:278
 aligned with TEBA_STENO | P29549 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:281
                                    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 
           TEBA_STENO    36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
               SCOP domains d1k8gc1 C:36-204 Telomere end binding protein alpha sub   unit                                                                                                           d1k8gc2 C:205-316 Telomere end binding protein alpha subunit                                                     SCOP domains
               CATH domains 1k8gC01 C:36-210 Nucleic acid-binding proteins                                                                                                                                 1k8gC02 C:211-316 Nucleic acid-binding proteins                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......eeeeeeeeee...eeee..eeeeeeeee...........---....eeeeeee.hhhhh....ee..eeeeeeeeeeee..eeeeeee.....eeeee.....hhhhhhhh..........ee.......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....eeeeeeeeeeee....eeeeeee.....eeeeeee...........eeeeeee..................eeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8g C  36 YEYVELAKASLTSAQPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKG---ASDYATLVLYAKRFEDLPIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISILQNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELDEYTNELKLKDASGQVFYTLSLKLKFPHVRTGEVVRIRSATYDETSTQKKVLILSHYSNIITFIQSSKLAKELRAKIQDD 316
                                    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 
                                                                                 90  94

Chain D from PDB  Type:DNA  Length:4
                                    
                 1k8g D   5 GGGG   8

Chain E from PDB  Type:DNA  Length:4
                                    
                 1k8g E   5 GGGG   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	d1k8ga1	A:36-204
1b	d1k8ga2	A:205-315
1c	d1k8gb1	B:36-204
1d	d1k8gb2	B:205-316
1e	d1k8gc1	C:36-204
1f	d1k8gc2	C:205-316

Asymmetric 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	1k8gA02	A:211-315
1b	1k8gA01	A:37-210
1c	1k8gB01	B:37-210
1d	1k8gC01	C:36-210
1e	1k8gB02	B:211-316
1f	1k8gC02	C:211-316

(no "Pfam Domain" information available for 1K8G)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k8g)

Biological Units
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	1k8g
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1jb7	DNA G-QUARTETS IN A 1.86 A RESOLUTION STRUCTURE OF AN OXYTRICHA NOVA TELOMERIC PROTEIN-DNA COMPLEX
1otc	THE O. NOVA TELOMERE END BINDING PROTEIN COMPLEXED WITH SINGLE STRAND DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

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