1M0F - JenaLib

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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURAL STUDIES OF BACTERIOPHAGE ALPHA3 ASSEMBLY, CRYO-ELECTRON MICROSCOPY

Authors :   R. A. Bernal, S. Hafenstein, N. H. Olson, V. D. Bowman, P. R. Chipman, T. S. Baker, B. A. Fane, M. G. Rossmann

Date :   12 Jun 02 (Deposition) - 25 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   16.00

Chains :   Asym. Unit : B,F,G,1,2,3,4
Biol. Unit 1: B,F,G,1,2,3,4  (60x)

Keywords :   Bacteriophage, Cryo Electron Microscopy, Procapsid, Morphogenesis, Microviridae, Assembly, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Bernal, S. Hafenstein, N. H. Olson, V. D. Bowman, P. R. Chipman, T. S. Baker, B. A. Fane, M. G. Rossmann
Structural Studies Of Bacteriophage Alpha3 Assembly
J. Mol. Biol. V. 325 11 2003
PubMed-ID: 12473449 | Reference-DOI: 10.1016/S0022-2836(02)01201-9
(for further references see the PDB file header)

Molecule 1 - SCAFFOLDING PROTEIN D
	Chains	:	1, 2, 3, 4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ENTEROBACTERIA PHAGE ALPHA3
	Organism Taxid	:	10849
	Synonym	:	GPD

Molecule 2 - CAPSID PROTEIN F
	Chains	:	F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ENTEROBACTERIA PHAGE ALPHA3
	Organism Taxid	:	10849
	Synonym	:	F PROTEIN, GPF

Molecule 3 - MAJOR SPIKE PROTEIN G
	Chains	:	G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ENTEROBACTERIA PHAGE ALPHA3
	Organism Taxid	:	10849
	Synonym	:	G PROTEIN, GPG

Molecule 4 - SCAFFOLDING PROTEIN B
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ENTEROBACTERIA PHAGE ALPHA3
	Organism Taxid	:	10849
	Synonym	:	GPB

		1	2	3	4	5	6	7
Asymmetric Unit	:	B	F	G	1	2	3	4
Biological Unit 1 (60x)	:	B	F	G	1	2	3	4

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1M0F)

(no "Site" information available for 1M0F)

(no "SS Bond" information available for 1M0F)

(no "Cis Peptide Bond" information available for 1M0F)

(no "SAP(SNP)/Variant" information available for 1M0F)

(no "PROSITE Motif" information available for 1M0F)

(no "Exon" information available for 1M0F)

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 1 from PDB  Type:PROTEIN  Length:143
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:143
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   
          SCAFD_BPPHS     6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRA 148
               SCOP domains d1m0f1_ 1: Bacteriophage alpha3 assembly                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0f 1   6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRA 148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145

Chain 2 from PDB  Type:PROTEIN  Length:135
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:135
                                    15        25        35        45        55        65        75        85        95       105       115       125       135     
          SCAFD_BPPHS     6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEE 140
               SCOP domains d1m0f2_ 2: Bacteriophage alpha3 assembly                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0f 2   6 EQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEE 140
                                    15        25        35        45        55        65        75        85        95       105       115       125       135

Chain 3 from PDB  Type:PROTEIN  Length:140
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:140
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
          SCAFD_BPPHS     5 TEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
               SCOP domains d1m0f3_ 3: Bacteriophage alpha3 assembly                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0f 3   5 TEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQ 144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain 4 from PDB  Type:PROTEIN  Length:146
 aligned with SCAFD_BPPHS | P69486 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:146
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146      
          SCAFD_BPPHS     7 QSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM 152
               SCOP domains d1m0f4_ 4: Bacteriophage alpha3 assembly                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0f 4   7 QSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM 152
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146

Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains d1m0fb_ B: Bacteriophage alpha3 assembly                             SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1m0f B   1 MEQLTKNQRKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF 120
                                   |62        72        82        92       102       112        
                                   8|                                                           
                                   61

Chain F from PDB  Type:PROTEIN  Length:360
 aligned with VGF_BPAL3 | P08767 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:422
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429  
            VGF_BPAL3    10 REIVDLSHLAFDCGMLGRLKTVSWTPVIAGDSFELDAVGALRLSPLRRGLAIDSKVDFFTFYIPHRHVYGDQWIQFMRDGVNAQPLPSVTCNRYPDHAGYVGTIVPANNRIPKFLHQSYLNIYNNYFRAPWMPERTEANPSNLNEDDARYRFRCCHLKNIWSAPLPPETKLAEEMGIESNSIDIMGLQAAYAQLHTEQERTYFMQRYRDVISSFGGSTSYDADNRPLLVMHTDFWASGYDVDGTDQSSLGQFSGRVQQTFKHSVPRFFVPEHGVMMTLALIRFPPISPLEHHYLAGKSQLTYTDLAGDPALIGNLPPREISYRDLFRDGRSGIKIKVAESIWYRTHPDYVNFKYHDLHGFPFLDDAPGTSTGDNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVSVYRHMPTVRDSIMTS 431
               SCOP domains d1m0ff_ F: Bacteriophage alpha3 assembly                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................................................................................................................--------------------------------------------------------------....................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0f F  10 REIVDLSHLAFDCGMLGRLKTVSWTPVIAGDSFELDAVGALRLSPLRRGLAIDSKVDFFTFYIPHRHVYGDQWIQFMRDGVNAQPLPSVTCNRYPDHAGYVGTIVPANNRIPKFLHQSYLNIYNNYFRAPWMPERTEANPSNLNEDDARYGFRCCHLKNIW--------------------------------------------------------------NRPLLVMHTDFWASGYDVDGTDQSSLGQFSGRVQQTFKHSVPRFFVPEHGVMMTLALIRFPPISPLEHHYLAGKSQLTYTDLAGDPALIGNLPPREISYRDLFRDGRSGIKIKVAESIWYRTHPDYVNFKYHDLHGFPFLDDAPGTSTGDNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVSVYRHMPTVRDSIMTS 431
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169|        -         -         -         -         -         -   |   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429  
                                                                                                                                                                                          170                                                            233

Chain G from PDB  Type:PROTEIN  Length:187
 aligned with G_BPAL3 | P31281 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
              G_BPAL3     1 MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIVRFESASEQPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEYQVLQPLK 187
               SCOP domains d1m0fg_ G: Bacteriophage alpha3 assembly                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0f G   1 MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIVRFESASEQPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEYQVLQPLK 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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: Low resolution protein structures (283)

Fold: Viruses and virus-receptor complexes (17)

Superfamily: Viruses and virus-receptor complexes (17)

Family: Viruses and virus-receptor complexes (17)

Protein domain: Bacteriophage alpha3 assembly (1)

Bacteriophage alpha3 [TaxId: 10849] (1)

1a	d1m0f1_	1:
1b	d1m0f2_	2:
1c	d1m0f3_	3:
1d	d1m0f4_	4:
1e	d1m0fb_	B:
1f	d1m0ff_	F:
1g	d1m0fg_	G:

(no "CATH Domain" information available for 1M0F)

(no "Pfam Domain" information available for 1M0F)

Asymmetric Unit(hide GO term definitions)

Chain 1,2,3,4 (SCAFD_BPPHS | P69486)

biological process
	GO:0046797	viral procapsid maturation	The refolding and structural rearrangements of individual capsid subunits to transition from the intermediate procapsid, to the more stable capsid structure.
	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.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.

Chain F (VGF_BPAL3 | P08767)

molecular function
	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: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 G (G_BPAL3 | P31281)

biological process
	GO:0019048	modulation by virus of host morphology or physiology	The process in which a virus effects a change in the structure or processes of its host organism.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	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: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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1m0f)

	Sites
(no "Sites" information available for 1m0f)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1m0f)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1m0f
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	SCAFD_BPPHS \| P69486
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	VGF_BPAL3 \| P08767
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
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UniProtKB/Swiss-Prot
	G_BPAL3 \| P31281	:	1m06 1rb8
	SCAFD_BPPHS \| P69486	:	1al0 1cd3 1tx9
	VGF_BPAL3 \| P08767	:	1m06 1rb8

1cd3	PROCAPSID OF THE BACTERIOPHAGE PHIX174
1gff	STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF BACTERIOPHAGE G4
1phx	DNA PACKAGING INTERMEDIATES OF THE BACTERIOPHAGE PHIX174

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 7)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 12)

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