2IO4 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PCNA12 DIMER FROM SULFOLOBUS SOLFATARICUS.

Authors :   V. Hlinkova, H. Ling

Date :   09 Oct 06 (Deposition) - 08 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Pcna12 Heterodimer, Protein-Protein Interaction, Pcna123 Heterotrimer, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Hlinkova, G. Xing, J. Bauer, Y. J. Shin, I. Dionne, K. R. Rajashankar S. D. Bell, H. Ling
Structures Of Monomeric, Dimeric And Trimeric Pcna: Pcna-Ring Assembly And Opening.
Acta Crystallogr. , Sect. D V. 64 941 2008
PubMed-ID: 18703842 | Reference-DOI: 10.1107/S0907444908021665

Molecule 1 - DNA POLYMERASE SLIDING CLAMP B
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET33B
	Expression System Strain	:	BL 21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCNB, PCNA-2
	Mutation	:	YES
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	P2
	Synonym	:	PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG B, PCNA B

Molecule 2 - DNA POLYMERASE SLIDING CLAMP C
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL 21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PCNC, PCNA-2
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	P2
	Synonym	:	PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG C, PCNA C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 3 (1, 10)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	10	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:145 , ASP B:149 , ASP D:145 , ASP D:149 , HOH D:266	BINDING SITE FOR RESIDUE CA B 701
2	AC2	SOFTWARE	LYS A:44 , PRO A:228	BINDING SITE FOR RESIDUE MPD A 250
3	AC3	SOFTWARE	ASP B:142 , ASP B:145 , GLU B:146 , HOH B:751 , HOH B:752 , GLU D:146	BINDING SITE FOR RESIDUE MPD B 301
4	AC4	SOFTWARE	ASP B:21 , ASN B:204 , LYS B:207 , ASP D:21 , GLU D:200 , ASN D:204	BINDING SITE FOR RESIDUE MPD B 401
5	AC5	SOFTWARE	ARG B:44 , TYR B:240	BINDING SITE FOR RESIDUE MPD B 501
6	AC6	SOFTWARE	GLY B:151 , GLU B:152 , ILE B:168 , GLY B:169 , ASP B:170 , HOH B:712 , ARG D:210	BINDING SITE FOR RESIDUE MPD B 601

(no "SS Bond" information available for 2IO4)

Asymmetric Unit

No.	Residues
1	Lys A:185	-	Pro A:186
2	Gly C:108	-	Ala C:109
3	Lys C:185	-	Pro C:186

(no "SAP(SNP)/Variant" information available for 2IO4)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA2_SULSO	33-56	2	B:34-57 D:34-57

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA2_SULSO	33-56	1	B:34-57 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA2_SULSO	33-56	1	- D:34-57

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA2_SULSO	33-56	4	B:34-57 D:34-57

(no "Exon" information available for 2IO4)

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:249
 aligned with PCNA1_SULSO | P57766 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          PCNA1_SULSO     1 MFKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh.....eeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeehhhhhhhhhhh.....eeeeeee...eeeeeeee.....eeeeeee.eee.............eeeeehhhhhhhhhhhhhhhh.eeeeeee..eeeeee......eeeeeee..ee.eeee....eeeeehhhhhhhhhh.......eeeee.....eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2io4 A   1 MVKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with PCNA2_SULSO | Q97Z84 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:246
                             1                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239      
          PCNA2_SULSO     - -MKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRAD 245
               SCOP domains d2io4b1 B:1-127 automated matches                                                                                              d2io4b2 B:128-246 automated matches                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh....eeeeeee..eeeeeee.....eeeeeeee.hhh..eee....eeeeeehhhhhhhhh......eeeeee...eeeeeee....eeeeee.................eeeeeehhhhhhhhhhhh....eeeeeee..eeeeeee....eeeeee........eeee...eeeeehhhhhhhhhhhhh..eeeeeee..eeeeeeee.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: B:34-57    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2io4 B   1 MMKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRAD 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain C from PDB  Type:PROTEIN  Length:249
 aligned with PCNA1_SULSO | P57766 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          PCNA1_SULSO     1 MFKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh.....eeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeehhhhhhhhhhh.....eeeeeeee..eeeeeeee......eeeeee.eee.............eeeeehhhhhhhhhhhhhhhh.eeeeee....eeeee.....eeeeeeee..ee.eeee....eeeeehhhhhhhhhh.......eeeee.....eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2io4 C   1 MVKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain D from PDB  Type:PROTEIN  Length:243
 aligned with PCNA2_SULSO | Q97Z84 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                             1                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
          PCNA2_SULSO     - -MKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRA 244
               SCOP domains d2io4d1 D:1-127 automated matches                                                                                              d2io4d2 D:128-245 automated matches                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh.eeeeee...eeeeeee.....eeeeeeee...eeeeee....eeeeeehhhhhhhhh......eeeeee...eeeeeee...eeeeeee..........--.....eeeeeehhhhhhhhhhhh....eeeeeee..eeeeeee....eeeeee........eeee...eeeeehhhhhhhhhhhhh..eeeeee.....eeeeee.hhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: D:34-57    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2io4 D   1 MMKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPP--NLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRA 245
                                    10        20        30        40        50        60        70        80        90       100       110       120  |  | 130       140       150       160       170       180       190       200       210       220       230       240     
                                                                                                                                                    123  |                                                                                                                       
                                                                                                                                                       126

Legend:		→ Mismatch	(orange background)
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	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: Alpha and beta proteins (a+b) (23004)

Fold: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: automated matches (17)

Protein domain: automated matches (17)

Sulfolobus solfataricus [TaxId: 273057] (3)

1a	d2io4b1	B:1-127
1b	d2io4b2	B:128-246
1c	d2io4d1	D:1-127
1d	d2io4d2	D:128-245

(no "CATH Domain" information available for 2IO4)

(no "Pfam Domain" information available for 2IO4)

Asymmetric Unit(hide GO term definitions)

Chain A,C (PCNA1_SULSO | P57766)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030337	DNA polymerase processivity factor activity	An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006272	leading strand elongation	The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
	GO:0043626	PCNA complex	A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation.

Chain B,D (PCNA2_SULSO | Q97Z84)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030337	DNA polymerase processivity factor activity	An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006272	leading strand elongation	The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
	GO:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
	GO:0043626	PCNA complex	A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation.

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	Cis Peptide Bonds
		Gly C:108 - Ala C:109	[ RasMol ]
		Lys A:185 - Pro A:186	[ RasMol ]
		Lys C:185 - Pro C:186	[ RasMol ]

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	PCNA2_SULSO \| Q97Z84
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UniProtKB/Swiss-Prot
	PCNA1_SULSO \| P57766	:	2hii 2hik 2ix2 2izo 2nti 3fds
	PCNA2_SULSO \| Q97Z84	:	2hii 2hik 2ix2 2izo 2nti 3fds

2ijx	CRYSTAL STRUCTURE OF PCNA3 FROM SULFOLOBUS SOLFATARICUS.
2ix2	CRYSTAL STRUCTURE OF PCNA123 HETEROTRIMER FORM SULFOLOBUS SOLFATARICUS.
2izo	CRYSTAL STRUCTURE OF PCNA12 DIMER WITH FEN1 FROM SULFOLOBUS SOLFATARICUS.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (6, 12)

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Related Entries Specified in the PDB File