[English] 日本語
Yorodumi
- PDB-5m6s: folding intermediate of spectrin R16 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5m6s
Titlefolding intermediate of spectrin R16
Descriptorspectrin
KeywordsSTRUCTURAL PROTEIN / spectrin / r16
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (4.8 Å resolution / Particle / Single particle)
AuthorsNilsson, O.B. / Nickson, A.A. / Clarke, J.
CitationNat. Struct. Mol. Biol., 2017, 24, 221-225

Nat. Struct. Mol. Biol., 2017, 24, 221-225 Yorodumi Papers
Cotranslational folding of spectrin domains via partially structured states.
Ola B Nilsson / Adrian A Nickson / Jeffrey J Hollins / Stephan Wickles / Annette Steward / Roland Beckmann / Gunnar von Heijne / Jane Clarke

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 25, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Jan 25, 2017Structure modelDatabase references
1.2Feb 1, 2017Structure modelDatabase references
1.3Mar 15, 2017Structure modelDatabase references
1.4Aug 2, 2017Structure modelData collectionem_image_scans / em_software_em_software.name / _em_software.version

-
Structure visualization

Movie
  • Deposited structure unit
  • 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: spectrin


Theoretical massNumber of molelcules
Total (without water)19,3711
Polyers19,3711
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)6420
MethodPISA

-
Components

#1: Polypeptide(L)spectrin


Mass: 19370.596 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Biological process

Cellular component

Molecular function

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: spectrin folding intermediate bound to 70s ribosome / Type: RIBOSOME / Entity ID: 1 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategoryImaging IDImage processing ID
2EM-ToolsIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
9SPIDERINITIAL EULER ASSIGNMENT1
10SPIDERFINAL EULER ASSIGNMENT1
11SPIDERCLASSIFICATION1
12SPIDERRECONSTRUCTION1
CTF correctionType: NONE
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 46067
Details: To exclude potential overfitting, the data were processed using a frequency limited refinement protocol by truncating high frequencies (low-pass filter at 8 A)
Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

+
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