[English] 日本語
Yorodumi
- PDB-5vrf: CryoEM Structure of the Zinc Transporter YiiP from helical crystals -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5vrf
TitleCryoEM Structure of the Zinc Transporter YiiP from helical crystals
ComponentsCadmium and zinc efflux pump FieF
KeywordsMEMBRANE PROTEIN / zinc antiporter / membrane protein / cation diffusion facilitator / metal transport / helical crystals / Structural Genomics / PSI-Biology / Transcontinental EM Initiative for Membrane Protein Structure / TEMIMPS
Function / homologyCation efflux transmembrane domain superfamily / Cation efflux protein / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux family / Dimerisation domain of Zinc Transporter / zinc efflux active transmembrane transporter activity / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / integral component of membrane ...Cation efflux transmembrane domain superfamily / Cation efflux protein / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux family / Dimerisation domain of Zinc Transporter / zinc efflux active transmembrane transporter activity / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / integral component of membrane / plasma membrane / Cadmium and zinc efflux pump FieF
Function and homology information
Specimen sourceShewanella oneidensis MR-1 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4.1 Å resolution
AuthorsCoudray, N. / Lopez-Redondo, M. / Zhang, Z. / Alexopoulos, J. / Stokes, D.L. / Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS)
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP.
Authors: Maria Luisa Lopez-Redondo / Nicolas Coudray / Zhening Zhang / John Alexopoulos / David L Stokes
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 10, 2017 / Release: Mar 14, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 14, 2018Structure modelrepositoryInitial release
1.1Mar 28, 2018Structure modelData collection / Database references / Othercell / citation_cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8728
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Cadmium and zinc efflux pump FieF
A: Cadmium and zinc efflux pump FieF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,49410
Polyers64,9702
Non-polymers5238
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5350
ΔGint (kcal/M)-249
Surface area (Å2)31850
MethodPISA

-
Components

#1: Protein/peptide Cadmium and zinc efflux pump FieF


Mass: 32485.211 Da / Num. of mol.: 2 / Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: fieF, SO_4475 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8E919
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: YiiP dimer in an inward-facing conformation / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.06 MDa / Experimental value: YES
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21 (DE3)
Buffer solutionDetails: Buffer was changed twice per day. / pH: 7
Buffer component
IDConc.NameFormulaBuffer ID
1100 mMsodium chlorideNaCl1
25 mMmagnesium chlorideMgCl21
35 mMsodium azideNaN31
SpecimenConc.: 0.6 mg/ml
Details: The protein was purified in 0.2% n-dodecyl beta-D-maltoside
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: EMS
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 5400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 3 / Number of real images: 2743
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 2-16

-
Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1SPARX/EMAN2EMAN2.1particle selectionsxhelixboxer.py
2RELION2.0particle selection2D Classissification
3Leginonimage acquisition
6CTFFIND4.1CTF correction
7Gctf0.50CTF correction
10Coot0.8.6model fitting
12RELION2.0initial Euler assignment
13RELION2.0final Euler assignment
14RELION2.0classification
15RELION2.03D reconstruction
16PHENIX1.11model refinementreal_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -17 deg. / Axial rise/subunit: 28.2 Å / Axial symmetry: D5
Particle selectionDetails: 2293 filaments selected with SPARX/EMAN2, then windowed into 141,904 segments (450x450 pixel overlapping segments)
Number of particles selected: 141904
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 72333
Details: Reconstruction was achieved using the IHRSR method implemented in RELION 2.0.
Symmetry type: HELICAL
Atomic model buildingDetails: The residues were manually adjusted in COOT relying on the large side-chain residues, and the whole system was further optimized using the real_space_refine algorithm in Phenix to ensure proper fit. The conformation was subjected to 13 rounds of COOT/Phenix refinements.
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 3J1Z
Pdb chain ID: A,B / Pdb chain residue range: 7-288
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0114458
ELECTRON MICROSCOPYf_angle_d1.2746074
ELECTRON MICROSCOPYf_dihedral_angle_d3.7652622
ELECTRON MICROSCOPYf_chiral_restr0.056730
ELECTRON MICROSCOPYf_plane_restr0.008760

+
About Yorodumi

-
News

-
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

+
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more