Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 1,455.55 kDa 
• Atom Count: 101,490 
• Modelled Residue Count: 12,990 
• Deposited Residue Count: 13,140 
• Unique protein chains: 1

 6YFN

Virus-like particle of bacteriophage ESE058

• PDB DOI: 10.2210/pdb6YFN/pdb

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Leviviridae sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-26 Released: 2020-09-02 
• Deposition Author(s): Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.
• Funding Organization(s): European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.234 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.

Rumnieks, J., Lieknina, I., Kalnins, G., Sisovs, M., Akopjana, I., Bogans, J., Tars, K.

(2020) Sci Adv 6

• PubMed: 32917600 
• DOI: 10.1126/sciadv.abc0023
• Primary Citation of Related Structures:  
  6YF7, 6YF9, 6YFA, 6YFB, 6YFC, 6YFD, 6YFE, 6YFF, 6YFG, 6YFH, 6YFI, 6YFJ, 6YFK, 6YFL, 6YFM, 6YFN, 6YFO, 6YFP, 6YFQ, 6YFR, 6YFS, 6YFT, 6YFU


• PubMed Abstract: 
  

The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.

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Organizational Affiliation: 

Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
coat protein	A [auth AA], B [auth AB], C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], H [auth AH], I [auth AI], J [auth AJ], K [auth AK], L [auth AL], M [auth AM], N [auth AN], O [auth AO], P [auth AP], Q [auth AQ], R [auth AR], S [auth AS], T [auth AT], U [auth AU], V [auth AV], W [auth AW], X [auth AX], Y [auth AY], Z [auth AZ], AA [auth BA], BA [auth BB], CA [auth BC], DA [auth BD], EA [auth BE], FA [auth BF], GA [auth BG], HA [auth BH], IA [auth BI], JA [auth BJ], KA [auth BK], LA [auth BL], MA [auth BM], NA [auth BN], OA [auth BO], PA [auth BP], QA [auth BQ], RA [auth BR], SA [auth BS], TA [auth BT], UA [auth BU], VA [auth BV], WA [auth BW], XA [auth BX], YA [auth BY], ZA [auth BZ], AB [auth CA], BB [auth CB], CB [auth CC], DB [auth CD], EB [auth CE], FB [auth CF], GB [auth CG], HB [auth CH], IB [auth CI], JB [auth CJ], KB [auth CK], LB [auth CL], MB [auth CM], NB [auth CN], OB [auth CO], PB [auth CP], QB [auth CQ], RB [auth CR], SB [auth CS], TB [auth CT], UB [auth CU], VB [auth CV], WB [auth CW], XB [auth CX], YB [auth CY], ZB [auth CZ], AC [auth DA], BC [auth DB], CC [auth DC], DC [auth DD], EC [auth DE], FC [auth DF], GC [auth DG], HC [auth DH], IC [auth DI], JC [auth DJ], KC [auth DK], LC [auth DL]	146	Leviviridae sp.	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	AD [auth BD], BD, CD [auth BG], DD [auth BG], ED [auth BJ], FD [auth BM], GD [auth BM], HD [auth BP], ID [auth BP], JD [auth BS], KD [auth BS], LD [auth BV], MC [auth AC], MD [auth BV], NC [auth AC], ND [auth BY], OC [auth AF], OD [auth BY], PC [auth AF], PD [auth CE], QC [auth AI], RC [auth AL], SC [auth AO], TC [auth AO], UC [auth AR], VC [auth AU], WC [auth AU], XC [auth AX], YC [auth BA], ZC [auth BA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.234 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 500.893	α = 90
b = 500.893	β = 90
c = 287.055	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
FFT	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-02 
Deposition Author(s): Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.

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Funding Organization	Location	Grant Number
European Regional Development Fund	Latvia	1.1.1.1/16/A/104

Revision History  

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2020-12-16
  Changes: Database references