7XHR | pdb_00007xhr

Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis

• PDB DOI: https://doi.org/10.2210/pdb7XHR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bombyx mori cypovirus 1
• Expression System: Triticum aestivum
• Mutation(s): No 


• Deposited: 2022-04-10 Released: 2023-02-01 
• Deposition Author(s): Abe, S., Tanaka, J., Kojima, M., Hirata, K., Yamashita, K., Ueno, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.184 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.161 (DCC) 

Starting Model: experimental

Literature

Cell-free protein crystallization for nanocrystal structure determination.

Abe, S., Tanaka, J., Kojima, M., Kanamaru, S., Hirata, K., Yamashita, K., Kobayashi, A., Ueno, T.

(2022) Sci Rep 12: 16031-16031

• PubMed: 36192567 
• DOI: https://doi.org/10.1038/s41598-022-19681-9
• Primary Citation Related Structures: 
  7XHR, 7XHS, 7XWS


• PubMed Abstract: 
  

  In-cell protein crystallization (ICPC) has been investigated as a technique to support the advancement of structural biology because it does not require protein purification and a complicated crystallization process. However, only a few protein structures have been reported because these crystals formed incidentally in living cells and are insufficient in size and quality for structure analysis. Here, we have developed a cell-free protein crystallization (CFPC) method, which involves direct protein crystallization using cell-free protein synthesis. We have succeeded in crystallization and structure determination of nano-sized polyhedra crystal (PhC) at a high resolution of 1.80 Å. Furthermore, nanocrystals were synthesized at a reaction scale of only 20 μL using the dialysis method, enabling structural analysis at a resolution of 1.95 Å. To further demonstrate the potential of CFPC, we attempted to determine the structure of crystalline inclusion protein A (CipA), whose structure had not yet been determined. We added chemical reagents as a twinning inhibitor to the CFPC solution, which enabled us to determine the structure of CipA at 2.11 Å resolution. This technology greatly expands the high-throughput structure determination method of unstable, low-yield, fusion, and substrate-biding proteins that have been difficult to analyze with conventional methods.

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Organizational Affiliation: 
• School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan. [e-mail].
School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan.
SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan. [e-mail].
International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 28.44 kDa 
• Atom Count: 2,152 
• Modeled Residue Count: 247 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhedrin	A	247	Bombyx mori cypovirus 1	Mutation(s): 0
UniProt
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus) Explore P11041  Go to UniProtKB:  P11041

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACE	B [auth A]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.184 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.161 (DCC) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.61	α = 90
b = 103.61	β = 90
c = 103.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrystFEL	data scaling
Coot	model building
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Abe, S., Tanaka, J., Kojima, M., Hirata, K., Yamashita, K., Ueno, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05421
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H02830
Japan Science and Technology	Japan	JPMJTR20U1

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description