1S9H - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ADENO-ASSOCIATED VIRUS TYPE 2 REP40

Authors :   J. A. James, C. R. Escalante, M. Yoon-Robarts, T. A. Edwards, R. M. Linden, A. K. Aggarwal

Date :   04 Feb 04 (Deposition) - 25 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Helicase, Aaa+ Protein, P-Loop, Walker A, Walker B, Sensor 1, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. James, C. R. Escalante, M. Yoon-Robarts, T. A. Edwards, R. M. Linden, A. K. Aggarwal
Crystal Structure Of The Sf3 Helicase From Adeno-Associated Virus Type 2
Structure V. 11 1025 2003
PubMed-ID: 12906833 | Reference-DOI: 10.1016/S0969-2126(03)00152-7
(for further references see the PDB file header)

Molecule 1 - REP 40 PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	REP
	Organism Scientific	:	ADENO-ASSOCIATED VIRUS - 2
	Organism Taxid	:	10804
	Synonym	:	DNA REPLICATION PROTEIN, NON-CAPSID PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1S9H)

(no "Site" information available for 1S9H)

(no "SS Bond" information available for 1S9H)

(no "Cis Peptide Bond" information available for 1S9H)

(no "SAP(SNP)/Variant" information available for 1S9H)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SF3_HELICASE_1	PS51206	Superfamily 3 helicase of DNA viruses domain profile.	REP68_AAV2S	308-463	3	A:308-463 B:308-463 C:308-463

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SF3_HELICASE_1	PS51206	Superfamily 3 helicase of DNA viruses domain profile.	REP68_AAV2S	308-463	1	A:308-463 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SF3_HELICASE_1	PS51206	Superfamily 3 helicase of DNA viruses domain profile.	REP68_AAV2S	308-463	1	- B:308-463 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SF3_HELICASE_1	PS51206	Superfamily 3 helicase of DNA viruses domain profile.	REP68_AAV2S	308-463	1	- - C:308-463

(no "Exon" information available for 1S9H)

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:268
 aligned with REP68_AAV2S | P03132 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:350
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490
          REP68_AAV2S   141 AGGGNKVVDECYIPNYLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARYMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
               SCOP domains d1                                                                                  s9ha_ A: Rep 40 protein helicase domain                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------------------------------------------------------------------------.hhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh..eee.................eeee........hhhhhhhhhhh..eee.......eee....eeeee......ee....ee..hhhhhhh.eeeee............hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SF3_HELICASE_1  PDB: A:308-463 UniProt: 308-463                                                                                                             --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9h A 223 AG----------------------------------------------------------------------------------MELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
                             |       -         -         -         -         -         -         -         -    |  230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490
                             |                                                                                225                                                                                                                                                                                                                                                                         
                           224

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with REP68_AAV2S | P03132 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:267
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       
          REP68_AAV2S   224 YMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
               SCOP domains d1s9hb_ B: Rep 40 protein helicase domain                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhh..eeee................eeee.....hhhhhhhhhhhhh...eeeee...eeeee....eeeee......ee....ee..hhhhhhh.eeeee............hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------SF3_HELICASE_1  PDB: B:308-463 UniProt: 308-463                                                                                                             --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9h B 224 GMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483

Chain C from PDB  Type:PROTEIN  Length:199
 aligned with REP68_AAV2S | P03132 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:350
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490
          REP68_AAV2S   141 AGGGNKVVDECYIPNYLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARYMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
               SCOP domains d1                                                                                  s9hc_ C: Rep 40 protein helicase domain                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------------------------------------------------------------------------.hhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..-------..hhhhhhhhhhhhhhhhhhhhhhhhh.................---hhhhhhhh.......------------.......ee.------------------------------........ee.....-----------------.....................hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SF3_HELICASE_1  PDB: C:308-463 UniProt: 308-463                                                                                                             --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9h C 223 AG----------------------------------------------------------------------------------MELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQ-------SNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATT---NIAEAIAHTVPFYGC------------CVDKMVIWWE------------------------------AQIDPTPVIVTSNTN-----------------LQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG 490
                             |       -         -         -         -         -         -         -         -    |  230       240       250       260       270       280      |  -    |  300       310       320       330       | - |     350     |   -       370       | -         -         -       410       420  |      -         -|      450       460       470       480       490
                           224                                                                                225                                                           287     295                                        338 342           356          369      378                            409           423               441

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 '\|'

(no "CATH Domain" information available for 1S9H)

(no "Pfam Domain" information available for 1S9H)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (REP68_AAV2S | P03132)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0039645	modulation by virus of host G1/S transition checkpoint	Any viral process that modulates the frequency, rate or extent of the host cell G1/S transition checkpoint.
	GO:0060153	modulation by virus of host cell cycle	Any viral process that modulates the rate or extent of progression through the cell cycle.
	GO:0039665	permeabilization of host organelle membrane involved in viral entry into host cell	Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
	GO:0039592	suppression by virus of G2/M transition of host mitotic cell cycle	Any viral process that decreases the rate or extent of progression from G2 phase to M phase of the host mitotic cell cycle.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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	REP68_AAV2S \| P03132	:	1u0j 4zo0 4zq9 5dcx

(no "Related Entries Specified in the PDB File" available for 1S9H)

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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