3EBJ - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN AVIAN INFLUENZA VIRUS PROTEIN

Authors :   P. Yuan, M. Bartlam, Z. Lou, S. Chen, Z. Rao, Y. Liu

Date :   27 Aug 08 (Deposition) - 10 Feb 09 (Release) - 28 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Crystal Structure, Avian Influenza, Polymerase, Pa_n, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Yuan, M. Bartlam, Z. Lou, S. Chen, J. Zhou, X. He, Z. Lv, R. Ge, X. Li, T. Deng, E. Fodor, Z. Rao, Y. Liu
Crystal Structure Of An Avian Influenza Polymerase Pa(N) Reveals An Endonuclease Active Site
Nature V. 458 909 2009
PubMed-ID: 19194458 | Reference-DOI: 10.1038/NATURE07720
(for further references see the PDB file header)

Molecule 1 - POLYMERASE ACIDIC PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-256
	Gene	:	PA
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	93838
	Synonym	:	RNA-DIRECTED RNA POLYMERASE SUBUNIT P2, PA_N

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:80 , ASP A:108 , HOH A:1001 , HOH A:1002 , HOH A:1003	BINDING SITE FOR RESIDUE MG A 999
2	AC2	SOFTWARE	GLU B:80 , LEU B:106 , ASP B:108 , HOH B:1001 , HOH B:1003 , HOH B:1021	BINDING SITE FOR RESIDUE MG B 999
3	AC3	SOFTWARE	GLU C:80 , ASP C:108 , HOH C:1001 , HOH C:1002 , HOH C:1003	BINDING SITE FOR RESIDUE MG C 999
4	AC4	SOFTWARE	GLU D:80 , ASP D:108 , GLU D:119 , HOH D:1001 , HOH D:1002 , HOH D:1003	BINDING SITE FOR RESIDUE MG D 999

(no "SS Bond" information available for 3EBJ)

Asymmetric Unit

No.	Residues
1	Lys C:139	-	Ser C:140

(no "SAP(SNP)/Variant" information available for 3EBJ)

(no "PROSITE Motif" information available for 3EBJ)

(no "Exon" information available for 3EBJ)

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:175
 aligned with PA_I96A0 | Q9Q0U9 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:200
                               1                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197
             PA_I96A0     - ---MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESTIIESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG 197
               SCOP domains d3ebja_ A: PA N-terminal domain                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh-------------------------.eee....hhhhhhhhhhhhhh............eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebj A  -2 LGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYS-------------------------RFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG 197
                                     7        17        27        37        47 |       -         -       |77        87        97       107       117       127       137       147       157       167       177       187       197
                                                                              49                        75

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with PA_I96A0 | Q9Q0U9 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:196
                             1                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189      
             PA_I96A0     - -MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESTIIESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSE 195
               SCOP domains d3ebjb_ B: PA N-terminal domain                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....---------------------..eee....hhhhhhhhhhhhhhh...........eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebj B   0 SMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFH---------------------HRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSE 195
                                     9        19        29        39        49  |      -         -    |   79        89        99       109       119       129       139       149       159       169       179       189      
                                                                               52                    74

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with PA_I96A0 | Q9Q0U9 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:200
                               1                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197
             PA_I96A0     - ---MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESTIIESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG 197
               SCOP domains d3ebjc_ C: PA N-terminal domain                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh------------------------..eee....hhhhhhhhhhhhhhh...........eee....eeeeeeee..hhhhhhhhhhhhhh....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebj C  -2 LGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYS------------------------HRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG 197
                                     7        17        27        37        47 |       -         -      | 77        87        97       107       117       127       137       147       157       167       177       187       197
                                                                              49                       74

Chain D from PDB  Type:PROTEIN  Length:175
 aligned with PA_I96A0 | Q9Q0U9 from UniProtKB/Swiss-Prot  Length:716

    Alignment length:200
                               1                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197
             PA_I96A0     - ---MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESTIIESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG 197
               SCOP domains d3ebjd_ D: PA N-terminal domain                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh-------------------------.eee....hhhhhhhhhhhhhhhh..........eee....eeeeeeee..hhhhhhhhhhhhh.....eeeeee....eee.hhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebj D  -2 LGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYS-------------------------RFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERG 197
                                     7        17        27        37        47 |       -         -       |77        87        97       107       117       127       137       147       157       167       177       187       197
                                                                              49                        75

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: 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: PA N-terminal domain (24)

Influenza A virus [TaxId: 93838] (13)

1a	d3ebja_	A:
1b	d3ebjb_	B:
1c	d3ebjc_	C:
1d	d3ebjd_	D:

(no "CATH Domain" information available for 3EBJ)

(no "Pfam Domain" information available for 3EBJ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PA_I96A0 | Q9Q0U9)

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.
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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	3ebj
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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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