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- PDB-8gf6: Apo-apo MCR assembly intermediate -

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Basic information

Entry
Database: PDB / ID: 8gf6
TitleApo-apo MCR assembly intermediate
Components
  • Methyl coenzyme M reductase, subunit D
  • Methyl-coenzyme M reductase subunit alpha
  • Methyl-coenzyme M reductase subunit beta
  • Methyl-coenzyme M reductase subunit gamma
KeywordsTRANSFERASE / methanogenesis / MCR complex
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm
Similarity search - Function
Methyl-coenzyme M reductase, protein D / Methyl-coenzyme M reductase operon protein D / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit ...Methyl-coenzyme M reductase, protein D / Methyl-coenzyme M reductase operon protein D / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain
Similarity search - Domain/homology
Methyl-coenzyme M reductase subunit beta / Methyl coenzyme M reductase, subunit D / Methyl-coenzyme M reductase subunit gamma / Methyl-coenzyme M reductase subunit alpha
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJoiner, A.M.N. / Chadwick, G.L. / Nayak, D.D.
Funding support United States, 7items
OrganizationGrant numberCountry
Other privateArnold and Mabel Beckman Foundation
David and Lucile Packard Foundation United States
Simons Foundation822981 United States
Other privateRose Hills Innovator Program
Other privateSearle Scholars Program
Chan Zuckerberg Initiative United States
Other privateMiller Institute for Basic Research in Science
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.
Authors: Grayson L Chadwick / Aaron M N Joiner / Sangeetha Ramesh / Douglas A Mitchell / Dipti D Nayak /
Abstract: Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane, and its activity accounts for nearly all biologically produced methane released into the atmosphere. The assembly of MCR is an ...Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane, and its activity accounts for nearly all biologically produced methane released into the atmosphere. The assembly of MCR is an intricate process involving the installation of a complex set of posttranslational modifications and the unique Ni-containing tetrapyrrole called coenzyme F. Despite decades of research, details of MCR assembly remain largely unresolved. Here, we report the structural characterization of MCR in two intermediate states of assembly. These intermediate states lack one or both F cofactors and form complexes with the previously uncharacterized McrD protein. McrD is found to bind asymmetrically to MCR, displacing large regions of the alpha subunit and increasing active-site accessibility for the installation of F-shedding light on the assembly of MCR and the role of McrD therein. This work offers crucial information for the expression of MCR in a heterologous host and provides targets for the design of MCR inhibitors.
History
DepositionMar 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase subunit alpha
C: Methyl-coenzyme M reductase subunit beta
D: Methyl-coenzyme M reductase subunit beta
E: Methyl-coenzyme M reductase subunit gamma
F: Methyl-coenzyme M reductase subunit gamma
X: Methyl coenzyme M reductase, subunit D


Theoretical massNumber of molelcules
Total (without water)291,8117
Polymers291,8117
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, electron microscopy, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Methyl-coenzyme M reductase subunit alpha / Coenzyme-B sulfoethylthiotransferase alpha


Mass: 62180.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea)
References: UniProt: Q8THH1, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase subunit beta


Mass: 45174.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8THG7
#3: Protein Methyl-coenzyme M reductase subunit gamma


Mass: 27630.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8THH0
#4: Protein Methyl coenzyme M reductase, subunit D


Mass: 21842.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Gene: mcrD / Production host: Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8THG8
Has ligand of interestN

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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: Assembly intermediate of the MCR complex bound to mcrD
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Methanosarcina acetivorans C2A (archaea)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
225 mMTris baseNH2C(CH2OH)31
SpecimenConc.: 0.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Vitrification occurred under aerobic conditions

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00918692
ELECTRON MICROSCOPYf_angle_d1.08325320
ELECTRON MICROSCOPYf_dihedral_angle_d26.8612632
ELECTRON MICROSCOPYf_chiral_restr0.0652801
ELECTRON MICROSCOPYf_plane_restr0.0083357

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