[English] 日本語
Yorodumi
- EMDB-13261: Providencia stuartii Arginine decarboxylase (Adc), decamer structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13261
TitleProvidencia stuartii Arginine decarboxylase (Adc), decamer structure
Map dataSharpened map
Sample
  • Complex: Decameric form of P. stuartii Adc
    • Protein or peptide: Biodegradative arginine decarboxylase
Function / homology
Function and homology information


arginine decarboxylase / arginine decarboxylase activity / amino acid metabolic process / cytoplasm
Similarity search - Function
Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain ...Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biodegradative arginine decarboxylase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsDesfosses A / Jessop M / Bacia-Verloop M / Gutsche I
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)647784European Union
Agence Nationale de la Recherche (ANR)ANR-2018-CE11-0005-02 France
CitationJournal: Commun Biol / Year: 2022
Title: Structural and biochemical characterisation of the Providencia stuartii arginine decarboxylase shows distinct polymerisation and regulation.
Authors: Matthew Jessop / Karine Huard / Ambroise Desfosses / Guillaume Tetreau / Diego Carriel / Maria Bacia-Verloop / Caroline Mas / Philippe Mas / Angélique Fraudeau / Jacques-Philippe Colletier / Irina Gutsche /
Abstract: Bacterial homologous lysine and arginine decarboxylases play major roles in the acid stress response, physiology, antibiotic resistance and virulence. The Escherichia coli enzymes are considered as ...Bacterial homologous lysine and arginine decarboxylases play major roles in the acid stress response, physiology, antibiotic resistance and virulence. The Escherichia coli enzymes are considered as their archetypes. Whereas acid stress triggers polymerisation of the E. coli lysine decarboxylase LdcI, such behaviour has not been observed for the arginine decarboxylase Adc. Here we show that the Adc from a multidrug-resistant human pathogen Providencia stuartii massively polymerises into filaments whose cryo-EM structure reveals pronounced differences between Adc and LdcI assembly mechanisms. While the structural determinants of Adc polymerisation are conserved only in certain Providencia and Burkholderia species, acid stress-induced polymerisation of LdcI appears general for enterobacteria. Analysis of the expression, activity and oligomerisation of the P. stuartii Adc further highlights the distinct properties of this unusual protein and lays a platform for future investigation of the role of supramolecular assembly in the superfamily or arginine and lysine decarboxylases.
History
DepositionJul 26, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13261.png

Downloads & links

-
Map

FileDownload / File: emd_13261.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.44619864 - 1.1016498
Average (Standard dev.)0.0014815305 (±0.040176228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_13261_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_13261_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_13261_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Decameric form of P. stuartii Adc

EntireName: Decameric form of P. stuartii Adc
Components
  • Complex: Decameric form of P. stuartii Adc
    • Protein or peptide: Biodegradative arginine decarboxylase

-
Supramolecule #1: Decameric form of P. stuartii Adc

SupramoleculeName: Decameric form of P. stuartii Adc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Providencia stuartii (bacteria) / Strain: ATCC 29914
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightExperimental: 858 KDa

-
Macromolecule #1: Biodegradative arginine decarboxylase

MacromoleculeName: Biodegradative arginine decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: arginine decarboxylase
Source (natural)Organism: Providencia stuartii (bacteria)
Molecular weightTheoretical: 86.15025 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRALIVYTEL TDKDSVISHA VARLASELND EHVETVIIRD FEDGLAYIRS NTSIDCLLYG RDMSDRDEQI QAHRLITQLH RRQEDVPVF LLSDREEALV AFDRNMMEQV DEFAWILEDS ADFIAGRVLA AIQRYRSQLL PPLMKSLIKY SDVHEYSWAA P GHQGGVGF ...String:
MRALIVYTEL TDKDSVISHA VARLASELND EHVETVIIRD FEDGLAYIRS NTSIDCLLYG RDMSDRDEQI QAHRLITQLH RRQEDVPVF LLSDREEALV AFDRNMMEQV DEFAWILEDS ADFIAGRVLA AIQRYRSQLL PPLMKSLIKY SDVHEYSWAA P GHQGGVGF TKTPAGRIYH DFFGENLFRT DIGIERVAVG SLLDHTGAFG ECEKNAARIF GADQSYSVVV GTSGSNRTIM QA CMTDDDV VVIDRNCHKS IEQGLILTGA KPVYMIPSRN RYGIIGPIYP KEMTPDAIKF KIAANPLTKG KVKQKPAYSV VTN CTYDGV CYNARKVQDL LDGSLDRIHF DEAWYGYARF NPLYRNHFAM RDEERTENEP TIFATHSTH(LLP) LLNALSQASF IHVRNGRNA IDFNRFNQAY LMHSTTSPLY AICASNDIAA DMMDGNSGRS LTDEVIRESI DFRQSLAYLY KEFLNDDEWF F KPWNQEMV KDPATGKRYA FEDAPVELLM REQSCWVMHP EDKWHGFNDI PDNWAMLDPI KVSILAPGMG DDGKLLDTGV PA ALVTAWL NHYGIVPTRT TDFQIMFLFS MGITKGKWGT LVNTLLSFKR HYDNNTALKK VLPEVVASAP EIYGEMGLRD LGD KMFAYL QKNNPGARLN QAYSQLPQVM MTPRDAYQQI VANRVEAVPV DQLMGRVAAN SIIPYPPGIP MLLSGENFGD ENSP HIHYL RSLQAWDSEF PGFEHETEGT EIIDGQYYVM CVKTCDE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 6.5
Details: 25 mM MES, 150 mM NaCl, 1 mM DTT, 0.1 mM PLP, pH 6.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 10023 / Average exposure time: 3.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 303475
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 46854
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7p9b:
Providencia stuartii Arginine decarboxylase (Adc), decamer structure

+
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