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Protein

External scaffolding protein D

Gene

D

Organism
Enterobacteria phage phiX174 (Isolate Sanger) (Bacteriophage phi-X174)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Assembles the procapsid by joining twelve 12S pre-assembly complex into a T=1 icosahedral particle, called 108S procapsid. Ten proteins D bind each 12S complex, which are formed by three pentamers of F, G, B protein and a H protein. The scaffolding protein is released from the provirion after genome packaging to form the mature virion.2 Publications

GO - Biological processi

Keywordsi

Biological processViral capsid assembly, Viral release from host cell

Names & Taxonomyi

Protein namesi
Recommended name:
External scaffolding protein D
Alternative name(s):
Scaffolding protein D
Short name:
GPD
Gene namesi
Name:D
OrganismiEnterobacteria phage phiX174 (Isolate Sanger) (Bacteriophage phi-X174)
Taxonomic identifieri1217068 [NCBI]
Taxonomic lineageiVirusesssDNA virusesMicroviridaeBullavirinaePhix174microvirus
Virus hostiEscherichia coli C [TaxID: 498388]
Proteomesi
  • UP000005893 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Host cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi61G → D: Confers a lethal phenotype. 1 Publication1
Mutagenesisi61G → E: Confers a lethal phenotype. 1 Publication1
Mutagenesisi61G → V: Confers a lethal phenotype. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by host2 Publications
ChainiPRO_00001648802 – 152External scaffolding protein DAdd BLAST151

Proteomic databases

PRIDEiP69486.

Interactioni

Subunit structurei

Component of the procapsid particle composed of 60 copies of the internally located B, 240 copies of the external scaffolding protein D, 60 copies of each of the viral structural proteins F and G, and 12 copies of protein H.1 Publication

Structurei

Secondary structure

1152
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 23Combined sources19
Helixi31 – 38Combined sources8
Beta strandi39 – 41Combined sources3
Helixi45 – 47Combined sources3
Helixi48 – 59Combined sources12
Helixi61 – 65Combined sources5
Helixi75 – 85Combined sources11
Helixi88 – 97Combined sources10
Turni98 – 100Combined sources3
Helixi104 – 109Combined sources6
Helixi117 – 129Combined sources13
Helixi140 – 143Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AL0X-ray3.501/2/3/41-152[»]
1CD3X-ray3.501/2/3/41-152[»]
1M0Felectron microscopy16.001/2/3/41-152[»]
1TX9X-ray3.31A/B2-152[»]
ProteinModelPortaliP69486.
SMRiP69486.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69486.

Family & Domainsi

Sequence similaritiesi

Belongs to the microvirus D protein family.Curated

Phylogenomic databases

OrthoDBiVOG09000102.

Family and domain databases

Gene3Di1.10.1850.10. 1 hit.
InterProiView protein in InterPro
IPR004196. Scaffold_D.
IPR036632. Scaffold_D_sf.
PfamiView protein in Pfam
PF02925. gpD. 1 hit.
ProDomiView protein in ProDom or Entries sharing at least one domain
PD016331. Bact_scaffold_pD. 1 hit.
SUPFAMiSSF48045. SSF48045. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P69486-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQVTEQSVR FQTALASIKL IQASAVLDLT EDDFDFLTSN KVWIATDRSR
60 70 80 90 100
ARRCVEACVY GTLDFVGYPR FPAPVEFIAA VIAYYVHPVN IQTACLIMEG
110 120 130 140 150
AEFTENIING VERPVKAAEL FAFTLRVRAG NTDVLTDAEE NVRQKLRAEG

VM
Length:152
Mass (Da):16,937
Last modified:January 23, 2007 - v2
Checksum:iE8C912DCBA48D5E4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02482 Genomic DNA. Translation: AAA32575.1.
X07809 Genomic DNA. Translation: CAA30667.1.
PIRiA04245. ZDBPF4.

Similar proteinsi

Entry informationi

Entry nameiSCAFD_BPPHS
AccessioniPrimary (citable) accession number: P69486
Secondary accession number(s): P03637
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 22, 2017
This is version 76 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families