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- PDB-6b43: CryoEM structure and atomic model of the Kaposi's sarcoma-associa... -

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Basic information

Entry
Database: PDB / ID: 6b43
TitleCryoEM structure and atomic model of the Kaposi's sarcoma-associated herpesvirus capsid
Components
  • Major capsid protein
  • Small capsomere-interacting protein
  • Triplex capsid protein 1
  • Triplex capsid protein 2
KeywordsVIRUS / human herpesvirus 8 / human tumor virus / dsDNA virus capsid assembly / HK97-like fold
Function / homologyGammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus major capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus VP23 like capsid protein / Herpes virus major capsid protein / Herpesvirus capsid shell protein VP19C / T=16 icosahedral viral capsid ...Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus major capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus VP23 like capsid protein / Herpes virus major capsid protein / Herpesvirus capsid shell protein VP19C / T=16 icosahedral viral capsid / viral capsid assembly / viral capsid / host cell nucleus / viral process / structural molecule activity / DNA binding / Triplex capsid protein 2 / Major capsid protein / Small capsomere-interacting protein / Triplex capsid protein 1
Function and homology information
Specimen sourceHuman herpesvirus 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsDai, X.H. / Gong, D.Y. / Sun, R. / Zhou, Z.H.
CitationJournal: Nature / Year: 2018
Title: Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication.
Authors: Xinghong Dai / Danyang Gong / Hanyoung Lim / Jonathan Jih / Ting-Ting Wu / Ren Sun / Z Hong Zhou
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 25, 2017 / Release: Nov 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelAuthor supporting evidence / Othercell / pdbx_audit_support_cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _pdbx_audit_support.funding_organization
1.2Jan 31, 2018Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.3Feb 7, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.4Apr 11, 2018Structure modelAdvisory / Data collectionpdbx_database_PDB_obs_spr

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-7047
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  • Superimposition on EM map
  • EMDB-7047
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2


Theoretical massNumber of molelcules
Total (without water)3,260,81346
Polyers3,260,81346
Non-polymers00
Water0
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
x 60


Theoretical massNumber of molelcules
Total (without water)195,648,7982760
Polyers195,648,7982760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
x 5


  • icosahedral pentamer
  • 16.3 MDa, 230 polymers
Theoretical massNumber of molelcules
Total (without water)16,304,066230
Polyers16,304,066230
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
x 6


  • icosahedral 23 hexamer
  • 19.6 MDa, 276 polymers
Theoretical massNumber of molelcules
Total (without water)19,564,880276
Polyers19,564,880276
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide
Major capsid protein / MCP


Mass: 153574.188 Da / Num. of mol.: 16 / Details: Coded by gene ORF25. / Source: (natural) Human herpesvirus 8 / Variant: clone BAC16 / References: UniProt: D0UZN7
#2: Protein/peptide
Small capsomere-interacting protein


Mass: 18597.824 Da / Num. of mol.: 15 / Details: Coded by gene ORF65. / Source: (natural) Human herpesvirus 8 / Variant: clone BAC16 / References: UniProt: Q76RF4
#3: Protein/peptide
Triplex capsid protein 1


Mass: 36374.840 Da / Num. of mol.: 5
Details: Coded by gene ORF62. It is the monomer in the heterotrimeric triplex structure.
Source: (natural) Human herpesvirus 8 / Variant: clone BAC16 / References: UniProt: Q76RF6
#4: Protein/peptide
Triplex capsid protein 2


Mass: 34278.473 Da / Num. of mol.: 10
Details: Coded by gene ORF26. Forms the dimer in the heterotrimeric triplex structure.
Source: (natural) Human herpesvirus 8 / Variant: clone BAC16 / References: UniProt: C7E5A9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human herpesvirus 8Herpesviridae / Type: VIRUS
Details: KSHV lytic replication was induced in an iSLK-puro cell line harboring the KSHV-BAC16 plasmid.
Entity ID: 1, 2, 3, 4 / Source: NATURAL
Molecular weightValue: 200 MDa / Experimental value: NO
Source (natural)Organism: Human herpesvirus 8 / Strain: JSC-1
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 1300 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.4
Buffer componentName: phosphate buffered saline / Formula: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 298 kelvins
Details: The sample was manually blotted and frozen with a homemade plunger.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 14000 / Calibrated magnification: 24271 / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 79 kelvins
Image recordingAverage exposure time: 13 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 3 / Number of real images: 8007
Image scansSampling size: 2.5 microns / Width: 7676 / Height: 7420 / Movie frames/image: 26 / Used frames/image: 1-26

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Processing

SoftwareName: PHENIX / Version: dev_2875: / Classification: refinement
EM software
IDNameVersionCategory
1ETHANparticle selection
2Leginonimage acquisition
4CTFFIND3CTF correction
9IMIRSinitial Euler assignment
10IMIRSfinal Euler assignment
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Particles were boxed with ETHAN, and then manually examined.
Number of particles selected: 44343
SymmetryPoint symmetry: I
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25315 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008219357
ELECTRON MICROSCOPYf_angle_d1.119298106
ELECTRON MICROSCOPYf_dihedral_angle_d6.325132195
ELECTRON MICROSCOPYf_chiral_restr0.05933590
ELECTRON MICROSCOPYf_plane_restr0.00838789

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