[English] 日本語
Yorodumi
- PDB-5yys: Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yys
TitleCryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (FKP)in Bacteroides fragilis
ComponentsL-fucokinase, L-fucose-1-P guanylyltransferase
KeywordsTRANSFERASE / bifunctional / kinase / ATP / GTP
Function / homology
Function and homology information


fucokinase / fucose-1-phosphate guanylyltransferase / fucokinase activity / GDP-L-fucose salvage / nucleotidyltransferase activity / ATP binding
Similarity search - Function
L-fucokinase / Fucose pyrophosphorylase domain / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
L-fucokinase/L-fucose-1-P guanylyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, J. / Hu, H. / Liu, Y. / Zhou, Q. / Wu, P. / Yan, N. / Wang, H.W. / Wu, J.W. / Sun, L.
CitationJournal: Protein Cell / Year: 2019
Title: Cryo-EM structure of L-fucokinase/GDP-fucose pyrophosphorylase (FKP) in Bacteroides fragilis.
Authors: Ying Liu / Huifang Hu / Jia Wang / Qiang Zhou / Peng Wu / Nieng Yan / Hong-Wei Wang / Jia-Wei Wu / Linfeng Sun /
History
DepositionDec 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 12, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6859
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-fucokinase, L-fucose-1-P guanylyltransferase
B: L-fucokinase, L-fucose-1-P guanylyltransferase
C: L-fucokinase, L-fucose-1-P guanylyltransferase
D: L-fucokinase, L-fucose-1-P guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)423,1314
Polymers423,1314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6440 Å2
ΔGint-20 kcal/mol
Surface area149300 Å2

-
Components

#1: Protein
L-fucokinase, L-fucose-1-P guanylyltransferase


Mass: 105782.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacteroides fragilis (bacteria) / References: UniProt: Q58T34
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: FKP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacteroides fragilis (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96749 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01624592
ELECTRON MICROSCOPYf_angle_d2.24733488
ELECTRON MICROSCOPYf_dihedral_angle_d12.20214724
ELECTRON MICROSCOPYf_chiral_restr0.13832
ELECTRON MICROSCOPYf_plane_restr0.0144340

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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