2ZNL - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PA-PB1 COMPLEX FORM INFLUENZA VIRUS RNA POLYMERASE

Authors :   E. Obayashi, H. Yoshida, F. Kawai, N. Shibayama, A. Kawaguchi, K. Nagata, J. R. H. Tame, S. -Y. Park

Date :   28 Apr 08 (Deposition) - 02 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Influenza A Virus, Rna Polymerase, Pa, Pb1, Subunit Interaction, Phosphoprotein, Nucleotide-Binding, Nucleotidyltransferase, Rna Replication, Rna-Directed Rna Polymerase, Transferase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Obayashi, H. Yoshida, F. Kawai, N. Shibayama, A. Kawaguchi, K. Nagata, J. R. H. Tame, S. -Y. Park
The Structural Basis For An Essential Subunit Interaction In Influenza Virus Rna Polymerase
Nature V. 454 1127 2008
PubMed-ID: 18660801 | Reference-DOI: 10.1038/NATURE07225
(for further references see the PDB file header)

Molecule 1 - POLYMERASE ACIDIC PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)RILP CODONPLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 239-716
	Gene	:	PA
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	211044
	Strain	:	STRAIN A/PUERTO RICO/8/1934 H1N1
	Synonym	:	RNA-DIRECTED RNA POLYMERASE SUBUNIT P2

Molecule 2 - RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
	Chains	:	B
	EC Number	:	2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)RILP CODONPLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-81
	Gene	:	PB1
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	211044
	Strain	:	STRAIN A/PUERTO RICO/8/1934 H1N1
	Synonym	:	POLYMERASE BASIC PROTEIN 1, PB1, RNA-DIRECTED RNA POLYMERASE SUBUNIT P1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2ZNL)

(no "Site" information available for 2ZNL)

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

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

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

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

(no "Exon" information available for 2ZNL)

Asymmetric/Biological 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:421
 aligned with PA_I34A1 | P03433 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:460
                                   266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716
             PA_I34A1   257 IEPFLKTTPRPLRLPNGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLSWKQVLAELQDIENEEKIPKTKNMKKTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPELRSLASWIQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTSEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLIRSAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPKGVEESSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALS 716
               SCOP domains d2znla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Flu_PA-2znlA01 A:257-716                                                                                                                                                                                                                                                                                                                                                                                                                                                     Pfam domains
         Sec.struct. author .................................eeee........hhhhhhhhhhh....eeeeeeee.....hhhhhhhhhhhhhhhhh..-----.........hhhhhhhh.--------------------------.......hhhhhhhhhhh....................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeeeee..........eeeeeeeeee..hhhhh.......eeeeeeee.--------.eeeeeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh....eeeeee..eeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2znl A 257 IEPFLKTTPRPLRLPNGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLSWKQVLAELQDI-----IPKTKNMKKTSQLKWALG--------------------------PELRSLASWIQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTSEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDML--------SRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPKGVEESSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALS 716
                                   266       276       286       296       306       316       326       336       346 |     356       366    |    -         -         - |     406       416       426       436       446       456       466       476       486       496       506       516       526       536       546  |      - |     566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716
                                                                                                                     348   354              371                        398                                                                                                                                                    549      558

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with RDRP_I34A1 | P03431 from UniProtKB/Swiss-Prot  Length:757

    Alignment length:15
                                    10     
           RDRP_I34A1     1 MDVNPTLLFLKVPAQ  15
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains Flu_PB1-2znlB01 Pfam domains
         Sec.struct. author .ee.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2znl B   1 MDVNPTLLFLKVPAQ  15
                                    10

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Multi-domain proteins (alpha and beta) (2421)

Fold: PA C-terminal domain-like (3)

Superfamily: PA C-terminal domain-like (3)

Family: PA C-terminal domain-like (3)

Protein domain: automated matches (2)

Influenza A virus [TaxId: 211044] (1)

d2znla_

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PA_I34A1 | P03433)

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:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0075733	intracellular transport of virus	The directed movement of a virus, or part of a virus, within the host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	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:0019061	uncoating of virus	The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
	GO:0046761	viral budding from plasma membrane	A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
	GO:0019070	viral genome maturation	The processes involved in creating a mature, stable viral genome. Begins after genome replication with a newly synthesized nucleic acid and ends when the genome is ready to be packaged. Includes the addition of proteins to the newly synthesized genome, and DNA repair processes.
	GO:0019072	viral genome packaging	The encapsulation of the viral genome within the capsid.
	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.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
	GO:0019083	viral transcription	The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0031904	endosome lumen	The volume enclosed by the membrane of an endosome.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Chain B (RDRP_I34A1 | P03431)

molecular function
	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: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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0075733	intracellular transport of virus	The directed movement of a virus, or part of a virus, within the host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	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:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0019061	uncoating of virus	The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0046761	viral budding from plasma membrane	A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
	GO:0019070	viral genome maturation	The processes involved in creating a mature, stable viral genome. Begins after genome replication with a newly synthesized nucleic acid and ends when the genome is ready to be packaged. Includes the addition of proteins to the newly synthesized genome, and DNA repair processes.
	GO:0019072	viral genome packaging	The encapsulation of the viral genome within the capsid.
	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.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
	GO:0019083	viral transcription	The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0031904	endosome lumen	The volume enclosed by the membrane of an endosome.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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	2znl
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	2.7.7.48
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UniProtKB/Swiss-Prot
	PA_I34A1 \| P03433	:	4yyl 4zhz 4zi0 4zqq 5fdd 5fdg 5i13 5jht 5jhv
	RDRP_I34A1 \| P03431	:	2ztt 3a1g

(no "Related Entries Specified in the PDB File" available for 2ZNL)

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