5OSN | pdb_00005osn

Crystal Structure of Bovine Enterovirus 2 determined with Serial Femtosecond X-ray Crystallography

• PDB DOI: https://doi.org/10.2210/pdb5OSN/pdb
• Entry: 5OSN supersedes: 5MQU

• Classification: VIRUS
• Organism(s): Enterovirus E
• Mutation(s): No 


• Deposited: 2017-08-17 Released: 2017-08-30 
• Deposition Author(s): Roedig, P., Ginn, H.M., Pakendorf, T., Sutton, G., Harlos, K., Walter, T.S., Meyer, J., Fischer, P., Duman, R., Vartiainen, I., Reime, B., Warmer, M., Brewster, A.S., Young, I.D., Michels-Clark, T., Sauter, N.K., Kotecha, A., Kelly, J., Rowlands, D.J., Sikorsky, M., Nelson, S., Damiani, D.S., Alonso-Mori, R., Ren, J., Fry, E.E., David, C., Stuart, D.I., Wagner, A., Meents, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

High-speed fixed-target serial virus crystallography.

Roedig, P., Ginn, H.M., Pakendorf, T., Sutton, G., Harlos, K., Walter, T.S., Meyer, J., Fischer, P., Duman, R., Vartiainen, I., Reime, B., Warmer, M., Brewster, A.S., Young, I.D., Michels-Clark, T., Sauter, N.K., Kotecha, A., Kelly, J., Rowlands, D.J., Sikorsky, M., Nelson, S., Damiani, D.S., Alonso-Mori, R., Ren, J., Fry, E.E., David, C., Stuart, D.I., Wagner, A., Meents, A.

(2017) Nat Methods 14: 805-810

• PubMed: 28628129 
• DOI: https://doi.org/10.1038/nmeth.4335
• Primary Citation Related Structures: 
  5MQW, 5OSN


• PubMed Abstract: 
  

  We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.

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Organizational Affiliation: 
• Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Diamond Light Source Limited, Didcot, UK.
Institute of Photonics, University of Eastern Finland, Joensuu, Finland.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
Pirbright Institute, Pirbright, UK.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
Paul Scherrer Institut, Villigen-PSI, Switzerland.
Center for Free Electron Laser Science (CFEL), Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 92.7 kDa 
• Atom Count: 6,590 
• Modeled Residue Count: 793 
• Deposited Residue Count: 833 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	275	Enterovirus E	Mutation(s): 0
UniProt
Find proteins for Q65480 (Enterovirus E) Explore Q65480  Go to UniProtKB:  Q65480

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	B	244	Enterovirus E	Mutation(s): 0
UniProt
Find proteins for Q65480 (Enterovirus E) Explore Q65480  Go to UniProtKB:  Q65480

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	C	243	Enterovirus E	Mutation(s): 0
UniProt
Find proteins for Q65480 (Enterovirus E) Explore Q65480  Go to UniProtKB:  Q65480

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	D	71	Enterovirus E	Mutation(s): 0
UniProt
Find proteins for Q65480 (Enterovirus E) Explore Q65480  Go to UniProtKB:  Q65480

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPH	E [auth A]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N
OSF	J [auth C]	octyl sulfate C8 H17 O4 S UZZYXUGECOQHPU-UHFFFAOYSA-M
GLU	H [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	F [auth A], G [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 436.6	α = 90
b = 436.6	β = 90
c = 436.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Roedig, P., Ginn, H.M., Pakendorf, T., Sutton, G., Harlos, K., Walter, T.S., Meyer, J., Fischer, P., Duman, R., Vartiainen, I., Reime, B., Warmer, M., Brewster, A.S., Young, I.D., Michels-Clark, T., Sauter, N.K., Kotecha, A., Kelly, J., Rowlands, D.J., Sikorsky, M., Nelson, S., Damiani, D.S., Alonso-Mori, R., Ren, J., Fry, E.E., David, C., Stuart, D.I., Wagner, A., Meents, A.
• This entry supersedes: 5MQU

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Data collection, Database references
• Version 2.0: 2018-10-03
  Changes: Atomic model, Data collection, Derived calculations, Refinement description
• Version 2.1: 2018-10-10
  Changes: Data collection, Structure summary
• Version 2.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 2.3: 2019-07-31
  Changes: Data collection, Refinement description
• Version 2.4: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description