[English] 日本語
Yorodumi
- EMDB-17762: Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17762
TitleCryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) complex with prFMN bound
Map dataPCD holo-complex with prFMN co-factor bound
Sample
  • Complex: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
    • Protein or peptide: Phthaloyl-CoA decarboxylase
  • Ligand: hydroxylated prenyl-FMN
  • Ligand: FE (III) ION
  • Ligand: POTASSIUM ION
KeywordsprFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase / FLAVOPROTEIN
Function / homology
Function and homology information


3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / cytosol
Similarity search - Function
: / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
Phthaloyl-CoA decarboxylase
Similarity search - Component
Biological speciesThauera chlorobenzoica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsKayastha K / Ermler U
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Active Pcd complex with prFMN bound
Authors: Kayastha K / Ermler U
History
DepositionJun 28, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17762.png

Downloads & links

-
Map

FileDownload / File: emd_17762.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPCD holo-complex with prFMN co-factor bound
Voxel sizeX=Y=Z: 1.116 Å
Density
Contour LevelBy AUTHOR: 0.0105
Minimum - Maximum-0.020756237 - 0.066668086
Average (Standard dev.)0.000096289994 (±0.002448544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 267.84003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_17762_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17762_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound

EntireName: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
Components
  • Complex: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
    • Protein or peptide: Phthaloyl-CoA decarboxylase
  • Ligand: hydroxylated prenyl-FMN
  • Ligand: FE (III) ION
  • Ligand: POTASSIUM ION

-
Supramolecule #1: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound

SupramoleculeName: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thauera chlorobenzoica (bacteria)
Molecular weightTheoretical: 360 KDa

-
Macromolecule #1: Phthaloyl-CoA decarboxylase

MacromoleculeName: Phthaloyl-CoA decarboxylase / type: protein_or_peptide / ID: 1 / Details: prFMN / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thauera chlorobenzoica (bacteria)
Molecular weightTheoretical: 58.985941 KDa
Recombinant expressionOrganism: Thauera chlorobenzoica (bacteria)
SequenceString: MNDLATKGIS EAAERVGEKD LRAALEWFRS KGYLVETNKE VNPDLEITGL QKIFDGSLPM LFNNVKDMPH ARAITNLFGD IRVVEELFG WENSLDRVKK VARAIDHPLK PVIIGQDEAP VQEEVLTTDL DVNKWLTAIR HTPLETEMTI GSGISCVVGP Y FDGGSHIG ...String:
MNDLATKGIS EAAERVGEKD LRAALEWFRS KGYLVETNKE VNPDLEITGL QKIFDGSLPM LFNNVKDMPH ARAITNLFGD IRVVEELFG WENSLDRVKK VARAIDHPLK PVIIGQDEAP VQEEVLTTDL DVNKWLTAIR HTPLETEMTI GSGISCVVGP Y FDGGSHIG YNRMNFRWGN VGTFQISPGS HMWQVMTEHY KDDEPIPLTM CFGVPPSCTY VAGAGFDYAI LPKGCDEIGI AG AIQGSPV RLVKCRTIDA YTLADAEYVL EGYLHPRDKR YETAESEAAD IQGRFHFHPE WAGYMGKAYK APTFHVTAIT MRR RESKPI IFPLGVHTAD DANIDTSVRE SAIFALCERL QPGIVQNVHI PYCMTDWGGC IIQVKKRNQI EEGWQRNFLA AILA CSQGM RLAIAVSEDV DIYSMDDIMW CLTTRVNPQT DILNPLPGGR GQTFMPAERM TSGDKQWTAS NTQFEGGMGI DATVP YGYE SDFHRPVYGV DLVKPENFFD AKDIDKMKSR MAGWVLSLAR TGR

UniProtKB: Phthaloyl-CoA decarboxylase

-
Macromolecule #2: hydroxylated prenyl-FMN

MacromoleculeName: hydroxylated prenyl-FMN / type: ligand / ID: 2 / Number of copies: 6 / Formula: BYN
Molecular weightTheoretical: 542.476 Da
Chemical component information

ChemComp-BYN:
hydroxylated prenyl-FMN

-
Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 18 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 135 sec. / Pretreatment - Pressure: 38.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9974 / Average exposure time: 2.82 sec. / Average electron dose: 50.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2206933
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 743306
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8pmk:
Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) complex with prFMN bound

+
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://pdbjlvh1.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