P22535 (CAPSD_BPPRD) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Major capsid protein P3

Alternative name(s):
Protein P3

Gene names

Name:

III

Organism

Enterobacteria phage PRD1 (Bacteriophage PRD1)

Taxonomic identifier

10658 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Tectiviridae › Tectivirus

Virus host

Pseudomonas aeruginosa [TaxID: 287]
Pseudomonas fluorescens [TaxID: 294]
Pseudomonas putida (Arthrobacter siderocapsulatus) [TaxID: 303]
Acinetobacter calcoaceticus [TaxID: 471]
Escherichia coli [TaxID: 562]
Proteus mirabilis [TaxID: 584]
Vibrio cholerae [TaxID: 666]
Salmonella typhimurium [TaxID: 90371]

Protein attributes

Sequence length	395 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.
Subunit structure	Homotrimer.
Subcellular location	Virion.

Ontologies

Keywords
Cellular component	Virion
Molecular function	Capsid protein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular component	viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed; by host Ref.1

Chain

2 – 395

394

Major capsid protein P3

PRO_0000165345

Regions

Compositional bias

3 – 45

43

Gln-rich

Secondary structure

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395

Helix Strand Turn

Details...

Helix

17 – 34

18

Beta strand

35 – 47

13

Turn

49 – 51

3

Beta strand

54 – 57

4

Beta strand

63 – 78

16

Beta strand

85 – 87

3

Helix

91 – 94

4

Beta strand

95 – 102

8

Beta strand

108 – 113

6

Helix

114 – 125

12

Beta strand

142 – 145

4

Beta strand

147 – 149

3

Beta strand

152 – 154

3

Beta strand

159 – 175

17

Beta strand

191 – 196

6

Turn

199 – 201

3

Beta strand

202 – 204

3

Beta strand

214 – 217

4

Helix

220 – 222

3

Beta strand

223 – 239

17

Helix

251 – 254

4

Beta strand

256 – 265

10

Beta strand

274 – 277

4

Beta strand

283 – 293

11

Beta strand

303 – 313

11

Helix

321 – 332

12

Beta strand

333 – 335

3

Beta strand

340 – 344

5

Beta strand

346 – 348

3

Helix

352 – 355

4

Beta strand

358 – 365

8

Beta strand

371 – 382

12

Sequences

	Sequence		Length	Mass (Da)
	P22535 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 44731365E74C4375	FASTA	395	43,448
	10 20 30 40 50 60 MAQVQQLTPA QQAALRNQQA MAANLQARQI VLQQSYPVIQ QVETQTFDPA NRSVFDVTPA 70 80 90 100 110 120 NVGIVKGFLV KVTAAITNNH ATEAVALTDF GPANLVQRVI YYDPDNQRHT ETSGWHLHFV 130 140 150 160 170 180 NTAKQGAPFL SSMVTDSPIK YGDVMNVIDA PATIAAGATG ELTMYYWVPL AYSETDLTGA 190 200 210 220 230 240 VLANVPQSKQ RLKLEFANNN TAFAAVGANP LEAIYQGAGA ADCEFEEISY TVYQSYLDQL 250 260 270 280 290 300 PVGQNGYILP LIDLSTLYNL ENSAQAGLTP NVDFVVQYAN LYRYLSTIAV FDNGGSFNAG 310 320 330 340 350 360 TDINYLSQRT ANFSDTRKLD PKTWAAQTRR RIATDFPKGV YYCDNRDKPI YTLQYGNVGF 370 380 390 VVNPKTVNQN ARLLMGYEYF TSRTELVNAG TISTT

References

[1]	"Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane." Bamford J.K.H., Bamford D.H. Virology 177:445-451(1990) [PubMed: 2196741] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11.
[2]	"A snapshot of viral evolution from genome analysis of the tectiviridae family." Saren A.M., Ravantti J.J., Benson S.D., Burnett R.M., Paulin L., Bamford D.H., Bamford J.K.H. J. Mol. Biol. 350:427-440(2005) [PubMed: 15946683] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Crystallization of the major coat protein of PRD1, a bacteriophage with an internal membrane." Stewart P.L., Ghosh S., Bamford D.H., Burnett R.M. J. Mol. Biol. 230:349-352(1993) [PubMed: 8450547] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
[4]	"The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution." Benson S.D., Bamford J.K.H., Bamford D.H., Burnett R.M. Acta Crystallogr. D 58:39-59(2002) [PubMed: 11752778] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (1.65 ANGSTROMS).
[5]	"Insights into assembly from structural analysis of bacteriophage PRD1." Abrescia N.G.A., Cockburn J.J.B., Grimes J.M., Sutton G.C., Diprose J.M., Butcher S.J., Fuller S.D., San Martin C., Burnett R.M., Stuart D.I., Bamford D.H., Bamford J.K.H. Nature 432:68-74(2004) [PubMed: 15525981] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS).
[6]	"Membrane structure and interactions with protein and DNA in bacteriophage PRD1." Cockburn J.J., Abrescia N.G., Grimes J.M., Sutton G.C., Diprose J.M., Benevides J.M., Thomas G.J. Jr., Bamford J.K.H., Bamford D.H., Stuart D.I. Nature 432:122-125(2004) [PubMed: 15525993] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS).
+	Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Virus Particle ExploreR db

Icosahedral capsid structure

Virus Particle ExploreR db

Icosahedral capsid structure of SUS607 mutant

Virus Particle ExploreR db

Icosahedral virus capsid P3-shell structure

Virus Particle ExploreR db

Icosahedral capsid structure of SUS1 mutant

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY848689 Genomic DNA. Translation: AAX45916.1.
M55567 Genomic DNA. Translation: AAA32445.1.

PIR

A46345.

RefSeq

NP_040692.1. NC_001421.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CJD	X-ray	1.85	A/B/C	2-394	[»]
1GW7	electron microscopy	13.50	A/B/C/D/E/F/G/H/I/J/K/L	2-395	[»]
1GW8	electron microscopy	13.30	A/B/C/D/E/F/G/H/I/J/K/L	2-395	[»]
1HB5	electron microscopy	12.00	A/B/C/D/E/F/G/H/I	2-395	[»]
1HB7	electron microscopy	14.00	A/B/C/D/E/F/G/H/I/J/K/L	2-395	[»]
1HB9	electron microscopy	25.00	A/B/C/D/E/F/G/H/I/J/K/L	2-395	[»]
1HQN	X-ray	2.20	A/B/C	2-395	[»]
1HX6	X-ray	1.65	A/B/C	2-395	[»]
1W8X	X-ray	4.20	A/B/C/D/E/F/G/H/I/J/K/L	1-395	[»]

ProteinModelPortal

P22535.

SMR

P22535. Positions 4-395.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1260932.

GenomeReviews

Gene locus III in contig AY848689_GR.

Family and domain databases

InterPro

IPR015108. Phage_PRD1_P3.
IPR016115. Phage_PRD1_P3_N.
IPR016112. Virus_hexon.
[Graphical view]

Gene3D

G3DSA:2.70.9.30. Coat_p3_sub1_phage. 1 hit.

Pfam

PF09018. Phage_Capsid_P3. 1 hit.
[Graphical view]

SUPFAM

SSF49749. Coat_hexon/vp54/p3_dsDNA-vir. 2 hits.

ProtoNet

Search...

Entry information

Entry name

CAPSD_BPPRD

Accession

Primary (citable) accession number: P22535
Secondary accession number(s): Q3T4N2

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1991
Last sequence update:	January 23, 2007
Last modified:	October 19, 2011
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program