[English] 日本語
- PDB-5nbz: Wzz dodecamer fitted by MDFF to the Wzz experimental map from cryo-EM -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 5nbz
TitleWzz dodecamer fitted by MDFF to the Wzz experimental map from cryo-EM
KeywordsMEMBRANE PROTEIN / Wzz Polysaccharide Chain Length membrane protein Cryo-electron microscopy Single particle analysis / Membrane protein
Specimen sourceStaphylococcus aureus / bacteria /
MethodElectron microscopy (9 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsFord, R.C. / Kargas, V. / Collins, R.F. / Whitfield, C. / Clarke, B.R. / Siebert, A. / Bond, P.J. / Clare, D.K.
CitationStructure, 2017, 25, 806-815.e3

Structure, 2017, 25, 806-815.e3 Yorodumi Papers
Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States.
Richard F Collins / Vasileios Kargas / Brad R Clarke / C Alistair Siebert / Daniel K Clare / Peter J Bond / Chris Whitfield / Robert C Ford

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2017 / Release: Apr 5, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 5, 2017Structure modelrepositoryInitial release
1.1Jun 28, 2017Structure modelDatabase referencescitation_citation.title

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3611
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links


Deposited unit
A: WzzB
B: WzzB
C: WzzB
D: WzzB
E: WzzB
F: WzzB
G: WzzB
H: WzzB
I: WzzB
J: WzzB
K: WzzB
L: WzzB

Theoretical massNumber of molelcules
Total (without water)321,12212

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)41770
ΔGint (kcal/M)-125
Surface area (Å2)142600


#1: Protein/peptide

Mass: 26760.129 Da / Num. of mol.: 12 / Source: (gene. exp.) Staphylococcus aureus / bacteria / / Production host: Escherichia coli

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Dodecameric complex / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.36 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: 20mM Tris pH 7.5, 150mM NaCl, 0.025% dodecyl maltoside.
pH: 7.5
SpecimenConc.: 0.3 mg/ml
Details: Dodecamers with C12 symmetry with a small fraction of head-to-head D12 complexes.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 kelvins / Details: 1 x 4sec blot

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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


3D reconstructionResolution: 9 Å / Resolution method: OTHER / Number of particles: 22000 / Details: ResMap / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4E29 / Pdb chain ID: A / Pdb chain residue range: 55-291

About Yorodumi


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


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