2W69 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   INFLUENZA POLYMERASE FRAGMENT

Authors :   A. Dias, D. Bouvier, T. Crepin, A. A. Mccarthy, D. J. Hart, F. Baudin, S. Cusack, R. W. H. Ruigrok

Date :   17 Dec 08 (Deposition) - 03 Feb 09 (Release) - 06 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Rna-Dependent, Rna Polymerase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dias, D. Bouvier, T. Crepin, A. A. Mccarthy, D. J. Hart, F. Baudin, S. Cusack, R. W. H. Ruigrok
The Cap-Snatching Endonuclease Of Influenza Virus Polymerase Resides In The Pa Subunit
Nature V. 458 914 2009
PubMed-ID: 19194459 | Reference-DOI: 10.1038/NATURE07745

Molecule 1 - POLYMERASE ACIDIC PROTEIN
	Chains	:	A, B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIL CODONPLUS
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 1-209
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	11320
	Strain	:	A/VICTORIA/3/1975
	Synonym	:	INFLUENZA POLYMERASE PA SUBUNIT, RNA-DIRECTED RNA POLYMERASE SUBUNIT P2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	MN	5	Ligand/Ion	MANGANESE (II) ION
2	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:80 , ASP A:108 , MN A:302 , HOH A:2064 , HOH A:2065 , GLU D:59	BINDING SITE FOR RESIDUE MN A 301
02	AC2	SOFTWARE	HIS A:41 , ASP A:108 , GLU A:119 , ILE A:120 , MN A:301 , GLU D:59	BINDING SITE FOR RESIDUE MN A 302
03	AC3	SOFTWARE	ARG A:84 , LEU A:106 , SER D:60 , VAL D:62	BINDING SITE FOR RESIDUE SO4 A 401
04	AC4	SOFTWARE	ARG A:179 , TRP A:188 , ARG A:192	BINDING SITE FOR RESIDUE SO4 A 402
05	AC5	SOFTWARE	GLU A:59 , GLU B:80 , LEU B:106 , ASP B:108 , HOH B:2069	BINDING SITE FOR RESIDUE MN B 301
06	AC6	SOFTWARE	SER A:60 , ILE A:61 , VAL A:62 , VAL A:63 , ARG B:84 , PHE B:105 , LEU B:106 , HOH B:2070 , HOH B:2071 , HOH B:2072	BINDING SITE FOR RESIDUE SO4 B 401
07	AC7	SOFTWARE	ARG B:179 , TRP B:188 , ARG B:192	BINDING SITE FOR RESIDUE SO4 B 402
08	AC8	SOFTWARE	ARG B:192 , GLN B:193	BINDING SITE FOR RESIDUE SO4 B 403
09	AC9	SOFTWARE	GLU D:80 , ASP D:108 , HOH D:2013	BINDING SITE FOR RESIDUE MN D 301
10	BC1	SOFTWARE	GLU B:59 , HIS D:41 , ASP D:108 , GLU D:119 , ILE D:120	BINDING SITE FOR RESIDUE MN D 302
11	BC2	SOFTWARE	SER B:60 , ILE B:61 , VAL B:62 , VAL B:63 , ARG D:84 , PHE D:105 , LEU D:106 , HOH D:2014	BINDING SITE FOR RESIDUE SO4 D 401
12	BC3	SOFTWARE	ARG D:179 , TRP D:188 , ARG D:192	BINDING SITE FOR RESIDUE SO4 D 402
13	BC4	SOFTWARE	ARG D:125 , GLU D:126 , ILE D:129 , ARG D:192	BINDING SITE FOR RESIDUE SO4 D 403

(no "SS Bond" information available for 2W69)

(no "Cis Peptide Bond" information available for 2W69)

(no "SAP(SNP)/Variant" information available for 2W69)

(no "PROSITE Motif" information available for 2W69)

(no "Exon" information available for 2W69)

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:194
 aligned with PA_I75A3 | P31343 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:197
                             1                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       
             PA_I75A3     - -MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINEQGESIVVELDDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSENTHIHIFSFTGEGMATKADYTLDEESRARIKTRLFTIRQEMANRGLWDSFRQSER 196
               SCOP domains d2w69a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........hhhhh......-...eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhh....--.eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w69 A   0 AMEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINEQGESIVVELDDPNAL-KHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKS--THIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMANRGLWDSFRQSER 196
                                     9        19        29        39        49        59        69 | |    79        89        99       109       119       129       139|  |   149       159       169       179       189       
                                                                                                  71 |                                                                140  |                                                     
                                                                                                    73                                                                   143

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with PA_I75A3 | P31343 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:197
                             1                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       
             PA_I75A3     - -MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINEQGESIVVELDDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSENTHIHIFSFTGEGMATKADYTLDEESRARIKTRLFTIRQEMANRGLWDSFRQSER 196
               SCOP domains d2w69b_ B: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...........hhhhh..........eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhh......eeeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w69 B   0 AMEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINEQGESIVVELDDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSENTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMANRGLWDSFRQSER 196
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain D from PDB  Type:PROTEIN  Length:183
 aligned with PA_I75A3 | P31343 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:197
                             1                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       
             PA_I75A3     - -MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINEQGESIVVELDDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSENTHIHIFSFTGEGMATKADYTLDEESRARIKTRLFTIRQEMANRGLWDSFRQSER 196
               SCOP domains d2w69d_ D: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Flu_PA-2w69D01 D:21-196                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) ---------------------Flu_PA-2w69D02 D:21-196                                                                                                                                                          Pfam domains (2)
           Pfam domains (3) ---------------------Flu_PA-2w69D03 D:21-196                                                                                                                                                          Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.............-----------..eee....hhhhhhhhhhhhhhhhh.........eee....eeeeeeee..hhhhhhhhhhh...---.eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w69 D   0 AMEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINEQGESIV-----------HRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIK---THIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMANRGLWDSFRQSER 196
                                     9        19        29        39        49        59  |      -    |   79        89        99       109       119       129       139   |   149       159       169       179       189       
                                                                                         62          74                                                              139 143

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: PA N-terminal domain (25)

Protein domain: automated matches (1)

Influenza A virus [TaxId: 11320] (1)

1a	d2w69a_	A:
1b	d2w69b_	B:
1c	d2w69d_	D:

(no "CATH Domain" information available for 2W69)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Flu_PA] (5)

Family: Flu_PA (5)

Influenza A virus (strain A/Victoria/3/1975 H3N2) (1)

1a	Flu_PA-2w69D01	D:21-196
1b	Flu_PA-2w69D02	D:21-196
1c	Flu_PA-2w69D03	D:21-196

Asymmetric Unit(hide GO term definitions)

Chain A,B,D (PA_I75A3 | P31343)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	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:0075526	cap snatching	A transcription initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs.
	GO:0039523	suppression by virus of host RNA polymerase II activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host RNA polymerase II activity.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	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.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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	2w69
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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