2QUD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PP7 COAT PROTEIN DIMER

Authors :   J. A. Chao

Date :   04 Aug 07 (Deposition) - 18 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Bacteriophage, Rna-Protein Complex, Capsid Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Chao, Y. Patskovsky, S. C. Almo, R. H. Singer
Structural Basis For The Coevolution Of A Viral Rna-Protein Complex.
Nat. Struct. Mol. Biol. V. 15 103 2008
PubMed-ID: 18066080 | Reference-DOI: 10.1038/NSMB1327

Molecule 1 - COAT PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET22HT
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PP7 COAT PROTEIN
	Organism Scientific	:	PSEUDOMONAS PHAGE PP7
	Organism Taxid	:	12023

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:23 , ARG A:24 , GLN A:25 , ALA A:42 , SER A:43 , LEU A:44 , HOH A:195 , HOH A:238 , HOH A:278	BINDING SITE FOR RESIDUE GOL A 128

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

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

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

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

(no "Exon" information available for 2QUD)

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:125
 aligned with COAT_BPPP7 | P03630 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:131
                                1                                                                                                                              
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126 
           COAT_BPPP7     - ----SKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDCSTSVCGELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVVQATSEDLVVNLVPLGR 127
               SCOP domains d2quda_ A: automated matches                                                                                                        SCOP domains
               CATH domains 2qudA00 A:-3-127 MS2 Viral Coat Protein                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeeeeee....eeee..........eeeeeeee.....eeeeeeeeeeeee....------...eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qud A  -3 GGSMSKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDSG------LPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR 127
                                     6        16        26        36        46        56        66 |      76        86        96       106       116       126 
                                                                                                  68     75

Chain A from PDB  Type:PROTEIN  Length:125
 aligned with Q38062_BPPP7 | Q38062 from UniProtKB/TrEMBL  Length:128

    Alignment length:131
                               1                                                                                                                               
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127 
         Q38062_BPPP7     - ---MSKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDCSTSVCGELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR 128
               SCOP domains d2quda_ A: automated matches                                                                                                        SCOP domains
               CATH domains 2qudA00 A:-3-127 MS2 Viral Coat Protein                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeeeeee....eeee..........eeeeeeee.....eeeeeeeeeeeee....------...eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qud A  -3 GGSMSKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDSG------LPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR 127
                                     6        16        26        36        46        56        66 |      76        86        96       106       116       126 
                                                                                                  68     75

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with COAT_BPPP7 | P03630 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           COAT_BPPP7     1 SKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDCSTSVCGELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVVQATSEDLVVNLVPLGR 127
               SCOP domains d2qudb_ B: automated matches                                                                                                    SCOP domains
               CATH domains 2qudB00 B:1-127 MS2 Viral Coat Protein                                                                                          CATH domains
           Pfam domains (1) Phage_coat-2qudB01 B:1-127                                                                                                      Pfam domains (1)
           Pfam domains (2) Phage_coat-2qudB02 B:1-127                                                                                                      Pfam domains (2)
         Sec.struct. author ..eeeeee..eeeeeeeeee...eeeee..........eeeeeeee.....eeeeeeeeeeeee.----------..eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qud B   1 SKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVV----------PKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR 127
                                    10        20        30        40        50        60    |    -     |  80        90       100       110       120       
                                                                                           65         76

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q38062_BPPP7 | Q38062 from UniProtKB/TrEMBL  Length:128

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
         Q38062_BPPP7     2 SKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDCSTSVCGELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR 128
               SCOP domains d2qudb_ B: automated matches                                                                                                    SCOP domains
               CATH domains 2qudB00 B:1-127 MS2 Viral Coat Protein                                                                                          CATH domains
           Pfam domains (1) Phage_coat-2qudB01 B:1-127                                                                                                      Pfam domains (1)
           Pfam domains (2) Phage_coat-2qudB02 B:1-127                                                                                                      Pfam domains (2)
         Sec.struct. author ..eeeeee..eeeeeeeeee...eeeee..........eeeeeeee.....eeeeeeeeeeeee.----------..eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qud B   1 SKTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVV----------PKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR 127
                                    10        20        30        40        50        60    |    -     |  80        90       100       110       120       
                                                                                           65         76

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: RNA bacteriophage capsid protein (40)

Superfamily: RNA bacteriophage capsid protein (40)

Family: RNA bacteriophage capsid protein (40)

Protein domain: automated matches (6)

Pseudomonas phage [TaxId: 12023] (2)

1a	d2quda_	A:
1b	d2qudb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: MS2 Viral Coat Protein (42)

Homologous Superfamily: MS2 Viral Coat Protein (42)

Pseudomonas phage pp7. Organism_taxid: 12023. (2)

1a	2qudA00	A:-3-127
1b	2qudB00	B:1-127

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Phage_coat] (2)

Family: Phage_coat (2)

Pseudomonas phage PP7 (Bacteriophage PP7) (2)

1a	Phage_coat-2qudB01	B:1-127
1b	Phage_coat-2qudB02	B:1-127

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (COAT_BPPP7 | P03630)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
	GO:0039617	T=3 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Chain A,B (Q38062_BPPP7 | Q38062)

cellular component
	GO:0019028		viral capsid		The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

Asymmetric/Biological Unit
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	2qud
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	COAT_BPPP7 \| P03630
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		Protein-protein Interaction	:	DIP
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	Q38062_BPPP7 \| Q38062
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	Q38062_BPPP7 \| Q38062
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UniProtKB/Swiss-Prot
	COAT_BPPP7 \| P03630	:	2qux
	Q38062_BPPP7 \| Q38062	:	2qux
UniProtKB/TrEMBL
	Q38062_BPPP7 \| Q38062	:	1dwn

1dwn	PP7 CAPSID
2qux

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (4, 5)

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