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- PDB-2x31: Modelling of the complex between subunits BchI and BchD of magnes... -

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Entry
Database: PDB / ID: 2x31
TitleModelling of the complex between subunits BchI and BchD of magnesium chelatase based on single-particle cryo-EM reconstruction at 7.5 ang
Components
  • MAGNESIUM-CHELATASE 38 KDA SUBUNIT
  • MAGNESIUM-CHELATASE 60 KDA SUBUNIT
KeywordsLIGASE / BACTERIOCHLOROPHYLL BIOSYNTHESIS / PHOTOSYNTHESIS
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, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium-chelatase subunit ChlI-like / 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, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium-chelatase subunit ChlI-like / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsLunqvist, J. / Elmlund, H. / Peterson Wulff, R. / Berglund, L. / Elmlund, D. / Emanuelsson, C. / Hebert, H. / Willows, R.D. / 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 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other / Version format compliance
Revision 1.2Mar 20, 2013Group: Derived calculations / Refinement description
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / em_imaging
Item: _cell.Z_PDB / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
Revision 1.5May 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

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Assembly

Deposited unit
A: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
B: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
C: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
D: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
E: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
F: MAGNESIUM-CHELATASE 60 KDA SUBUNIT
G: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
H: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
I: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
J: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
K: MAGNESIUM-CHELATASE 38 KDA SUBUNIT
L: MAGNESIUM-CHELATASE 38 KDA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)345,67912
Polymers345,67912
Non-polymers00
Water00
1


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

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Components

#1: Protein
MAGNESIUM-CHELATASE 60 KDA SUBUNIT / MG-PROTOPORPHYRIN IX CHELATASE / MG-CHELATASE SUBUNIT D


Mass: 19666.758 Da / Num. of mol.: 6 / Fragment: RESIDUES 373-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P26175, magnesium chelatase
#2: Protein
MAGNESIUM-CHELATASE 38 KDA SUBUNIT / MG-PROTOPORPHYRIN IX CHELATASE


Mass: 37946.340 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P26239, magnesium chelatase
Sequence detailsHOMOLOGY MODEL OF INTEGRIN I DOMAINS OF SUBUBUNIT BCHD A,B,C,D,E,F SUBUNITS BCHI G,H,I,J,K,L BASED ...HOMOLOGY MODEL OF INTEGRIN I DOMAINS OF SUBUBUNIT BCHD A,B,C,D,E,F SUBUNITS BCHI G,H,I,J,K,L BASED ON PDB ENTRY 1G8P

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: BCHID COMPLEX OF RHODOBACTER CAPSULATUS MG CHELATASE / Type: COMPLEX
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 5500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Image scansNum. digital images: 18
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 7.5 Å / Num. of particles: 29400 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1G8P

1g8p


Accession code: 1G8P / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7.5 Å
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22890 0 0 0 22890

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