[English] 日本語
Yorodumi
- PDB-1pdi: Fitting of the C-terminal part of the short tail fibers into the ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1pdi
TitleFitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate
DescriptorShort tail fiber protein
KeywordsSTRUCTURAL PROTEIN
Specimen sourceEnterobacteria phage T4 / virus
MethodElectron microscopy (12 Å resolution / Particle / Single particle)
AuthorsKostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationNat. Struct. Biol., 2003, 10, 688-693

primary. Nat. Struct. Biol., 2003, 10, 688-693 Yorodumi Papers
Three-dimensional structure of bacteriophage T4 baseplate.
Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann

#1. J.Mol.Biol., 2001, 314, 1137-1146
Crystal Structure of a Heat-and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.

#2. To be published Search PubMed
Structure of the receptor-binding domain of the bacteriophage T4 short tail fibre
Thomassen, E. / Gielen, G. / Schuetz, M. / Miller, S. / van Raaij, M.J.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 19, 2003 / Release: Sep 9, 2003
RevisionDateData content typeGroupProviderType
1.0Sep 9, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE The differences between the database reference sequence and the deposited sequence arise because the source of the fitted model is bacteriophage T4alc7, whereas the protein used in the structural solution is from bacteriophage T4D. The sequence of the protein from T4D has not yet been deposited. Only coordinates for CA atoms were submitted.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY COMPONENTS COM_ID: 1 NAME:GP12 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1048
  • Imaged by Jmol
  • Download
  • With
  • 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: Short tail fiber protein
B: Short tail fiber protein
C: Short tail fiber protein
D: Short tail fiber protein
E: Short tail fiber protein
F: Short tail fiber protein
G: Short tail fiber protein
H: Short tail fiber protein
I: Short tail fiber protein
J: Short tail fiber protein
K: Short tail fiber protein
L: Short tail fiber protein
M: Short tail fiber protein
N: Short tail fiber protein
O: Short tail fiber protein
P: Short tail fiber protein
Q: Short tail fiber protein
R: Short tail fiber protein


Theoretical massNumber of molelcules
Total (without water)537,40818
Polyers537,40818
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Polypeptide(L)
Short tail fiber protein / Protein Gp12 / p12 / Coordinate model: Cα atoms only


Mass: 29856.020 Da / Num. of mol.: 18 / Source: (natural) Enterobacteria phage T4 / virus / References: UniProt: P10930

Cellular component

Molecular function

Biological process

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsParent ID
1T4 baseplate-tail tube complexVIRUST4 double mutant, 18-,23-, produces baseplate-tail tube assemblies0
2gp12trimer1
Buffer solutionName: water / Details: water / pH: 7
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon
VitrificationCryogen name: ETHANE / Details: ethane vitrification
Crystal grow
*PLUS
Temp unit: K / Method: electron microscopy

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 47000 / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 70 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

EM software
IDNameVersionCategory
1SITUS COLORES2MODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: CTF correction of individual particles with Wiener filtering
SymmetryPoint symmetry: C6
3D reconstructionMethod: model-based projection matching / Resolution: 12 Å / Number of particles: 945 / Nominal pixel size: 3.11 / Actual pixel size: 2.98 / Magnification calibration: TMV particles images
Details: modifed version of program SPIDER was used for the reconstruction
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--Laplacian transform real space
Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation Coefficient maximization
Atomic model buildingPDB-ID: 1OCY
Number of atoms included #LASTProtein: 5004 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 5004

+
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