[English] 日本語
Yorodumi
- PDB-4v8w: Structure and conformational variability of the Mycobacterium tub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v8w
TitleStructure and conformational variability of the Mycobacterium tuberculosis fatty acid synthase multienzyme complex
ComponentsTYPE-I FATTY ACID SYNTHASE
KeywordsHYDROLASE / FATTY ACID SYNTHESIS / SAMPLE HETEROGENEITY / PROTEIN FLEXIBILITY / CODIMENSIONAL PRINCIPAL COMPONENT ANALYSIS
Function / homologyFLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsCiccarelli, L. / Connell, S.R. / Enderle, M. / Mills, D.J. / Vonck, J. / Grininger, M.
CitationJournal: Structure / Year: 2013
Title: Structure and conformational variability of the mycobacterium tuberculosis fatty acid synthase multienzyme complex.
Authors: Luciano Ciccarelli / Sean R Connell / Mathias Enderle / Deryck J Mills / Janet Vonck / Martin Grininger /
Abstract: Antibiotic therapy in response to Mycobacterium tuberculosis infections targets de novo fatty acid biosynthesis, which is orchestrated by a 1.9 MDa type I fatty acid synthase (FAS). Here, we ...Antibiotic therapy in response to Mycobacterium tuberculosis infections targets de novo fatty acid biosynthesis, which is orchestrated by a 1.9 MDa type I fatty acid synthase (FAS). Here, we characterize M. tuberculosis FAS by single-particle cryo-electron microscopy and interpret the data by docking the molecular models of yeast and Mycobacterium smegmatis FAS. Our analysis reveals a porous barrel-like structure of considerable conformational variability that is illustrated by the identification of several conformational states with altered topology in the multienzymatic assembly. This demonstrates that the barrel-like structure of M. tuberculosis FAS is not just a static scaffold for the catalytic domains, but may play an active role in coordinating fatty acid synthesis. The conception of M. tuberculosis FAS as a highly dynamic assembly of domains revises the view on bacterial type I fatty acid synthesis and might inspire new strategies for inhibition of de novo fatty acid synthesis in M. tuberculosis.
History
DepositionApr 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4BJF, 4BJG
Revision 1.1Dec 10, 2014Group: Other
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model / Data collection
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.image_processing_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1Dec 11, 2019Group: Other / Category: atom_sites / pdbx_database_status
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] / _pdbx_database_status.process_site
Revision 2.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "ED" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2357
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: TYPE-I FATTY ACID SYNTHASE
E: TYPE-I FATTY ACID SYNTHASE
F: TYPE-I FATTY ACID SYNTHASE
A: TYPE-I FATTY ACID SYNTHASE
B: TYPE-I FATTY ACID SYNTHASE
C: TYPE-I FATTY ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,982,06612
Polymers1,979,3286
Non-polymers2,7386
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
TYPE-I FATTY ACID SYNTHASE


Mass: 329887.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM TUBERCULOSIS (bacteria)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
Sequence detailsUNP ACCESSION A0R1H7 (M. SMEGMATIS) IS MODELLED TO FIT THE M. TUBERCULOSIS EM MAP

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mycobacterium tuberculosis fatty acid synthase multienzyme complex
Type: COMPLEX
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 16, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1800 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1EMAN23D reconstruction
2SPARX3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 17.5 Å / Num. of particles: 9136
Details: THE MODEL IS DERIVED FROM PDB ENTRY 3ZEN BOEHRINGER ET AL., 2013 AND REPRESENTS A RIGID BODY DOCKING OF THE MODEL INTO A CRYO-EM MAP. IN CHAIN F THE MAT AND DH DOMAINS WHERE FIT ...Details: THE MODEL IS DERIVED FROM PDB ENTRY 3ZEN BOEHRINGER ET AL., 2013 AND REPRESENTS A RIGID BODY DOCKING OF THE MODEL INTO A CRYO-EM MAP. IN CHAIN F THE MAT AND DH DOMAINS WHERE FIT INDEPENDENTLY OF THE REST OF THE MODEL. IN CHAIN D, RESIDUES 1- 400 (AT DOMAIN) WERE DELETED AS THE DENSITY OF THE EM MAP IN THAT REGION IS FRAGMENTED DUE TO FLEXIBILITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2357. (DEPOSITION ID: 11618).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY
Atomic model buildingPDB-ID: 3ZEN

3zen
PDB Unreleased entry


Accession code: 3ZEN / Source name: PDB / Type: experimental model
RefinementHighest resolution: 17.5 Å
Refinement stepCycle: LAST / Highest resolution: 17.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60061 0 93 0 60154

+
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