[English] 日本語
Yorodumi
- PDB-6b1t: Improved cryoEM structure of human adenovirus type 5 with atomic ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6b1t
TitleImproved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII
DescriptorHexon protein
Penton protein
Hexon-interlacing protein
Pre-protein VI
Pre-histone-like nucleoprotein
(Pre-hexon-linking protein ...) x 2
KeywordsVIRUS / human adenovirus / cement protein / dsDNA genome packaging / genome-capsid co-assembly
Specimen sourceHuman adenovirus C serotype 5 / virus / HAdV-5
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsDai, X.H. / Wu, L. / Sun, R. / Zhou, Z.H.
CitationJ. Virol., 2017

J. Virol., 2017 Yorodumi Papers
Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.
Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 18, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Oct 4, 2017Structure modelAdvisorypdbx_database_PDB_obs_spr_pdbx_database_PDB_obs_spr.replace_pdb_id
1.2Oct 18, 2017Structure modelAuthor supporting evidence / Database referencescitation / citation_author / pdbx_audit_support_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 / _pdbx_audit_support.funding_organization

-
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-7034
  • 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: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI


Theoretical massNumber of molelcules
Total (without water)1,568,67825
Polyers1,568,67825
Non-polymers00
Water0
#1
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI
x 60


Theoretical massNumber of molelcules
Total (without water)94,120,7031500
Polyers94,120,7031500
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: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI
x 5


  • icosahedral pentamer
  • 7.84 MDa, 125 polymers
Theoretical massNumber of molelcules
Total (without water)7,843,392125
Polyers7,843,392125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
U: Pre-protein VI
V: Pre-protein VI
W: Pre-histone-like nucleoprotein
X: Pre-protein VI
Y: Pre-protein VI
x 6


  • icosahedral 23 hexamer
  • 9.41 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)9,412,070150
Polyers9,412,070150
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

-
Polypeptide(L) , 4 types, 18 molecules ABCDEFGHIJ...

#1: Polypeptide(L)
Hexon protein / CP-H / Protein II


Mass: 108107.617 Da / Num. of mol.: 12 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P04133

Cellular component

Molecular function

Biological process

  • microtubule-dependent intracellular transport of viral material towards nucleus (GO: 0075521)
  • viral entry into host cell (GO: 0046718)
#2: Polypeptide(L)Penton protein / CP-P / Penton base protein / Protein III


Mass: 63356.602 Da / Num. of mol.: 1 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P12538

Cellular component

Molecular function

Biological process

  • clathrin-dependent endocytosis of virus by host cell (GO: 0075512)
  • virion attachment to host cell (GO: 0019062)
#5: Polypeptide(L)
Hexon-interlacing protein / Protein IX


Mass: 14468.134 Da / Num. of mol.: 4 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P03281

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)Pre-histone-like nucleoprotein / Pre-core protein VII / pVII / pVIIn2


Mass: 1198.438 Da / Num. of mol.: 1 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P68951

Cellular component

Molecular function

Biological process

-
Pre-hexon-linking protein ... , 2 types, 3 molecules NOP

#3: Polypeptide(L)Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 65322.805 Da / Num. of mol.: 1 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P12537

Cellular component

#4: Polypeptide(L)Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24710.590 Da / Num. of mol.: 2 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P24936

Cellular component

Molecular function

-
Pre-protein ... , 2 types, 4 molecules UVYX

#6: Polypeptide(L)Pre-protein VI / pVI / pVIn


Mass: 3584.953 Da / Num. of mol.: 3 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P24937
#8: Polypeptide(L)Pre-protein VI / pVI


Mass: 23460.559 Da / Num. of mol.: 1 / Source: (natural) Human adenovirus C serotype 5 / References: UniProt: P24937

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Human adenovirus 5 / Type: VIRUS / Details: Cultured in HEK293T cells and purified from media
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
Source: NATURAL
Molecular weightValue: 150 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Human adenovirus C serotype 5
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 900 Å / Triangulation number (T number): 25
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMTris-HClC4H11NO31
2150mMsodium chlorideNaCl1
31mMmagnesium chlorideMgCl21
SpecimenDetails: Purified virion / Embedding 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: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins

-
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: 81000 / 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): 80 kelvins
Image recordingAverage exposure time: 9 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 5608
EM imaging opticsEnergyfilter name: Gatan Image Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 2.5 microns / Dimension width: 7676 / Dimension height: 7420 / Movie frames/image: 32 / Used frames/image: 2-32

-
Processing

SoftwareName: PHENIX / Version: dev_2875: / Classification: refinement
EM software
IDNameCategoryImaging IDImage processing IDFitting ID
2LeginonIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7ChimeraMODEL FITTING1
9IMIRSINITIAL EULER ASSIGNMENT1
10IMIRSFINAL EULER ASSIGNMENT1
12eLite3DRECONSTRUCTION1
13PHENIXMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 96375
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53000 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008102532
ELECTRON MICROSCOPYf_angle_d0.846139427
ELECTRON MICROSCOPYf_dihedral_angle_d7.39861040
ELECTRON MICROSCOPYf_chiral_restr0.05714905
ELECTRON MICROSCOPYf_plane_restr0.00718313

+
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