PDB-3iyo: Cryo-EM model of virion-sized HEV virion-sized capsid

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3iyo
Title	Cryo-EM model of virion-sized HEV virion-sized capsid
Descriptor	Capsid protein
Keywords	VIRUS, Amino Acid Sequence, Capsid, Capsid Proteins, Cryoelectron Microscopy, Dimerization, Image Processing, Computer-Assisted, Molecular Sequence Data, hepatitis E virus, Protein Conformation, Protein Folding, Protein Structure, Recombinant viral capsid, Virus Assembly, icosahedral virus
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-5173, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5173, Made by UCSF CHIMERA #7: Superimposing with EM 3D map: EMDB-5173, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-5173 Fit Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3zue PDB-2y7h PDB-3zx9 PDB-2y7c List of similar structure data about Omokage system

Article
Citation - primary
Article	J.Biol.Chem., Vol. , Page: - , Year: 2010,
Title	Structural basis for the RNA-dependent assembly pathway of hepatitis E virion-sized particles
Authors	Xing, L., Mayazaki, N., Li, T.C., Simons, M.N., Wall, J.S., Moore, M., Wang, C.Y., Takeda, N., Wakita, T., Miyamura, T., Cheng, R.H.

Components
ID 1 : Capsid protein
Image
Description	Capsid protein
Type	polypeptide(L)
Formula weight	71032.531 Da
Number of molecules	3
ID	1
Source	Method: Isolated from a natural source Common name: HEV NCBI taxonomy: ID:12461 Organism scientific: Hepatitis E virus
Links	UniProt: Q1AHV0, Sequence view

Electron Microscopy
Imaging
Microscope	Model: OTHER
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	200 kV
Electron dose	10 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	Nominal: 50000 X
Cs	Nominal: 2.0 mm
Detector distance	0.0
Specimen holder
Specimen holder	Model: GATAN LIQUID NITROGEN, Type: single-tilt
Tilt angle	Min: 0.0 degrees, Max: 0.0 degrees
Detector
Type	TVIPS TemCam-F415

Processing
2D projection selection
Software name	Situs
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
CTF correction method	each micrograph
Method	Polar Fourier Transform (PFT)
Number of particles	4348
Resolution	10.5 A
Resolution method	FSC at 0.5 cut-off
Software	P3DR
3D fitting
Details	Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs
Refinement Protocol	Rigid Body
Refinement Space	REAL
Software name	Situs
Target criteria	cross-correlation
3D fitting list
3D fitting id	1
Pdb chain id	A
PDB entry ID	2ZZQ PDB-2zzq
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	1397
Protein atoms	1397

PDB format

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Header only

mmCIF format

mmCIF

XML format

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No-atom

Ext-atom

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.8 MB .webm (WebM/VP8 format), 5.4 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.2 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 2.9 MB .webm (WebM/VP8 format), 3.8 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 2.8 MB .webm (WebM/VP8 format), 3.7 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.8 MB .webm (WebM/VP8 format), 5.6 MB

movie #6

	.mp4 (H.264/MPEG-4 AVC format), 3.8 MB .webm (WebM/VP8 format), 5.8 MB

movie #7

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.1 MB