[English] 日本語
Yorodumi
- EMDB-1678: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1678
TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
Map dataCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
Sample
  • Sample: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
  • Protein or peptide: Biosynthetic enzyme
KeywordsAAA+ atpase / metallation / tetrapyrroles
Function / homology
Function and homology information


bacteriochlorophyll biosynthetic process / magnesium chelatase / magnesium chelatase activity / photosynthesis / ATP hydrolysis activity / ATP binding
Similarity search - Function
Magnesium chelatase, ATPase subunit D / Magnesium-chelatase BchD/ChlD, VWA domain / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain ...Magnesium chelatase, ATPase subunit D / Magnesium-chelatase BchD/ChlD, VWA domain / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Magnesium-chelatase 60 kDa subunit / Magnesium-chelatase 38 kDa subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsLundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S
CitationJournal: Structure / Year: 2010
Title: ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
Authors: Joakim Lundqvist / Hans Elmlund / Ragna Peterson Wulff / Lisa Berglund / Dominika Elmlund / Cecilia Emanuelsson / Hans Hebert / Robert D Willows / Mats Hansson / Martin Lindahl / Salam Al-Karadaghi /
Abstract: Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg(2+) into protoporphyrin IX (PPIX). Here we report the reconstruction using ...Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg(2+) into protoporphyrin IX (PPIX). Here we report the reconstruction using single-particle cryo-electron microscopy of the complex between subunits BchD and BchI of Rhodobacter capsulatus Mg-chelatase in the presence of ADP, the nonhydrolyzable ATP analog AMPPNP, and ATP at 7.5 A, 14 A, and 13 A resolution, respectively. We show that the two AAA+ modules of the subunits form a unique complex of 3 dimers related by a three-fold axis. The reconstructions demonstrate substantial differences between the conformations of the complex in the presence of ATP and ADP, and suggest that the C-terminal integrin-I domains of the BchD subunits play a central role in transmitting conformational changes of BchI to BchD. Based on these data a model for the function of magnesium chelatase is proposed.
History
DepositionJan 8, 2010-
Header (metadata) releaseJan 18, 2010-
Map releaseJan 21, 2010-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1678.jpg

Downloads & links

-
Map

FileDownload / File: emd_1678.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
Voxel sizeX=Y=Z: 2.33 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.0280966 - 0.0773895
Average (Standard dev.)0.000822421 (±0.00452024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 186.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z186.400186.400186.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.0280.0770.001

-
Supplemental data

-
Sample components

-
Entire : Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP

EntireName: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
Components
  • Sample: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
  • Protein or peptide: Biosynthetic enzyme

-
Supramolecule #1000: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP

SupramoleculeName: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 660 KDa

-
Macromolecule #1: Biosynthetic enzyme

MacromoleculeName: Biosynthetic enzyme / type: protein_or_peptide / ID: 1 / Name.synonym: Mg chelatase / Recombinant expression: Yes
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 660 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL
Image recordingDigitization - Scanner: ZEISS SCAI / Number real images: 6

-
Image processing

Final two d classificationNumber classes: 526
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 17623

-
Atomic model buiding 1

Initial modelPDB ID:

1g8p

RefinementSpace: REAL
Output model

PDB-2x31:
Modelling of the complex between subunits BchI and BchD of magnesium chelatase based on single-particle cryo-EM reconstruction at 7.5 ang

+
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