[English] 日本語
Yorodumi
- PDB-6b43: CryoEM structure and atomic model of the Kaposi's sarcoma-associa... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6b43
TitleCryoEM structure and atomic model of the Kaposi's sarcoma-associated herpesvirus capsid
DescriptorMajor capsid protein
Small capsomere-interacting protein
(Triplex capsid protein ...) x 2
KeywordsVIRUS / human herpesvirus 8 / human tumor virus / dsDNA virus capsid assembly / HK97-like fold
Specimen sourceHuman herpesvirus 8 / virus / HHV-8 / ヒトヘルペスウイルス 8
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle)
AuthorsDai, X.H. / Gong, D.Y. / Sun, R. / Zhou, Z.H.
CitationTo Be Published

To Be Published Search PubMed
Structure and mutagenesis reveal capsid protein interactions essential to KSHV replication.
Dai, X.H. / Gong, D.Y. / Lim, H.Y. / Jih, J. / Wu, T.T. / Sun, R. / Zhou, Z.H.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 25, 2017 / Release: Nov 8, 2017

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-7047
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
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

-
Components

#1: Polypeptide(L)
Major capsid protein / MCP


Mass: 153574.188 Da / Num. of mol.: 16 / Details: Coded by gene ORF25.
Source: (natural) Human herpesvirus 8 / virus / ヒトヘルペスウイルス 8
References: UniProt: D0UZN7
#2: Polypeptide(L)
Small capsomere-interacting protein


Mass: 18597.824 Da / Num. of mol.: 15 / Details: Coded by gene ORF65.
Source: (natural) Human herpesvirus 8 / virus / ヒトヘルペスウイルス 8
References: UniProt: Q76RF4
#3: Polypeptide(L)
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 / virus / ヒトヘルペスウイルス 8
References: UniProt: Q76RF6
#4: Polypeptide(L)
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 / virus / ヒトヘルペスウイルス 8
References: UniProt: C7E5A9

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: Human herpesvirus 8 / 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 deg. / Units: MEGADALTONS / 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 Å / 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.

-
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 FIELD / 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 / Dimension width: 7676 / Dimension height: 7420 / Movie frames/image: 26 / Used frames/image: 1-26

-
Processing

SoftwareName: PHENIX / Version: dev_2875: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1ETHANPARTICLE SELECTION1
2LeginonIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
9IMIRSINITIAL EULER ASSIGNMENT1
10IMIRSFINAL EULER ASSIGNMENT1
13PHENIXMODEL REFINEMENT1
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

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more