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Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BACTERIOPHAGE MS2 COVALENT COAT PROTEIN DIMER

Authors :   P. Plevka, K. Tars, L. Liljas

Date :   15 May 08 (Deposition) - 12 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

Chains :   Asym. Unit : J,L  (2x)
Biol. Unit 1: J,L  (24x)

Keywords :   Ms2, Virus, Dimer, Virion, Octahedron, Rna-Binding, Coat Protein, Capsid Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Plevka, K. Tars, L. Liljas
Crystal Packing Of A Bacteriophage Ms2 Coat Protein Mutant Corresponds To Octahedral Particles.
Protein Sci. V. 17 1731 2008
PubMed-ID: 18662904 | Reference-DOI: 10.1110/PS.036905.108

Molecule 1 - MS2 COAT PROTEIN
	Chains	:	J, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 2-130,2 AND 4-130
	Organism Scientific	:	ENTEROBACTERIO PHAGE MS2
	Organism Taxid	:	12022
	Other Details	:	EACH CHAIN COMPRISES A REPEAT UNIT CONTAINING RESIDUES 2-130 (PDB RESIDUES 1-129), RESIDUE 2 (PDB RESIDUE 130) AND 4-130 (PDB RESIDUES 131-257)

		1	2
Asymmetric Unit (2x)	:	J	L
Biological Unit 1 (24x)	:	J	L

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2VTU)

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

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

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

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

(no "Exon" information available for 2VTU)

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
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Chain J from PDB  Type:PROTEIN  Length:257
 aligned with CAPSD_BPMS2 | P03612 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:257
                                                                                                                                                          130                                                                                                                                
                                    11        21        31        41        51        61        71        81        91       101       111       121        |-         -         -         -         -         -         -         -         -         -         -         -         -       
          CAPSD_BPMS2     2 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY--------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------d2vtuj1 J:130-257 MS2 virus coat protein                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..........eee...........ee................................eee........eee.......ee........hhhhhhhhhhhhhh.....hhhhhhh...................................ee...........ee..ee.....eeee............................ee...ee....hhhhhhhhhhhhhh.....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vtu J   1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIYANFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain L from PDB  Type:PROTEIN  Length:257
 aligned with CAPSD_BPMS2 | P03612 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:257
                                                                                                                                                          130                                                                                                                                
                                    11        21        31        41        51        61        71        81        91       101       111       121        |-         -         -         -         -         -         -         -         -         -         -         -         -       
          CAPSD_BPMS2     2 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY--------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------d2vtul1 L:130-257 MS2 virus coat protein                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeee.....eeee.........eeeeeee............ee......ee....ee........eee.........hhhhhhhhhhhhhhh....hhhhhh..........................eeee.....eeee.........eeeeeee............ee......ee....ee........eee.........hhhhhhhhhhhhhhh....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vtu L   1 ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIYANFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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(

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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: 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: MS2 virus coat protein (28)

Bacteriophage MS2 [TaxId: 12022] (28)

1a	d2vtuj1	J:130-257
1b	d2vtul1	L:130-257

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

(no "Pfam Domain" information available for 2VTU)

Asymmetric Unit(hide GO term definitions)

Chain J,L (CAPSD_BPMS2 | P03612)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
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.

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	2vtu
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1aq3	STRUCTURE OF A MS2 COAT PROTEIN MUTANT IN COMPLEX WITH ANRNA OPERATOR
1aq4	STRUCTURE OF A MS2 COAT PROTEIN MUTANT IN COMPLEX WITH ANRNA OPERATOR
1bms	MOL_ID: 1; MOLECULE: BACTERIOPHAGE MS2 CAPSID ; CHAIN: A, B, C; ENGINEERED: YES; MUTATION : P78N
1msc
1mst	MOL_ID: 1; MOLECULE: BACTERIOPHAGE MS2 CAPSID ; CHAIN: A, B, C; ENGINEERED: YES; MUTATION : E76D
1mva	STRUCTURE OF A PROTEIN CAPSID OF THE T45A MUTANT OF PHAGEMS2
1mvb	STRUCTURE OF A PROTEIN CAPSID OF THE T59S MUTANT OF PHAGEMS2
1u1y	CRYSTAL STRUCTURE OF A COMPLEX BETWEEN WT BACTERIOPHAGE MS2COAT PROTEIN AND AN F5 APTAMER RNA STEMLOOP WITH2AMINOPURINE SUBSTITUTED AT THE-10 POSITION
1zdh	STRUCTURE OF BACTERIOPHAGE COAT PROTEIN- OPERATOR COMPLEX
1zdi	STRUCTURE OF MS2 PROTEIN CAPSID
1zdj	STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
1zdk	STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX
1zse	RNA STEMLOOP FROM BACTERIOPHAGE QBETA COMPLEXED WITH ANN87S MUTANT MS2 CAPSID
2b2d	RNA STEMLOOP OPERATOR FROM BACTERIOPHAGE QBETA COMPLEXEDWITH AN N87S,E89K MUTANT MS2 CAPSID
2b2e	RNA STEMLOOP FROM BACTERIOPHAGE MS2 COMPLEXED WITH AN N87S,E89K MUTANT MS2 CAPSID
2b2g	MS2 WILD-TYPE RNA STEMLOOP COMPLEXED WITH AN N87S MUTANTMS2 CAPSID
2bny	MS2 (N87A MUTANT) - RNA HAIRPIN COMPLEX
2bq5	MS2 (N87AE89K MUTANT) - RNA HAIRPIN COMPLEX
2bs0	MS2 (N87AE89K MUTANT) - VARIANT QBETA RNA HAIRPIN COMPLEX
2bs1	MS2 (N87AE89K MUTANT) - QBETA RNA HAIRPIN COMPLEX
2bu1	MS2-RNA HAIRPIN (5BRU -5) COMPLEX
2c4q	MS2-RNA HAIRPIN (2ONE -5) COMPLEX
2c4y	MS2-RNA HAIRPIN (2THIOURACIL-5) COMPLEX
2c4z	MS2-RNA HAIRPIN (2SU -5-6) COMPLEX
2c50	MS2-RNA HAIRPIN (A -5) COMPLEX
2c51	MS2-RNA HAIRPIN (G -5) COMPLEX
2iz8	MS2-RNA HAIRPIN (C-7) COMPLEX
2iz9	MS2-RNA HAIRPIN (4ONE -5) COMPLEX
2izm	MS2-RNA HAIRPIN (C-10) COMPLEX
2izn	MS2-RNA HAIRPIN (G-10) COMPLEX
2ms2	MS2 VIRUS (BACTERIOPHAGE)
5msf	F5 APTAMER MS2 COAT PROTEIN COMPLEX
6msf	F6 APTAMER MS2 COAT PROTEIN COMPLEX
7msf	F7 APTAMER MS2 COAT PROTEIN COMPLEX

Description

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Ligands, Modified Residues, Ions (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (5, 5)

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