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- EMDB-29978: McrD binds asymmetrically to methyl-coenzyme M reductase improvin... -

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Basic information

Entry
Database: EMDB / ID: EMD-29978
TitleMcrD binds asymmetrically to methyl-coenzyme M reductase improving active site accessibility during assembly
Map data
Sample
  • Complex: Assembly intermediate of the MCR complex bound to mcrD
    • Protein or peptide: Methyl-coenzyme M reductase subunit alphaCoenzyme-B sulfoethylthiotransferase
    • Protein or peptide: Methyl-coenzyme M reductase subunit betaCoenzyme-B sulfoethylthiotransferase
    • Protein or peptide: Methyl-coenzyme M reductase subunit gammaCoenzyme-B sulfoethylthiotransferase
    • Protein or peptide: Methyl coenzyme M reductase, subunit DCoenzyme-B sulfoethylthiotransferase
  • Ligand: 1-THIOETHANESULFONIC ACID
  • Ligand: FACTOR 430
  • Ligand: Coenzyme B
Keywordsmethanogenesis / MCR complex / TRANSFERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsJoiner AMN / Chadwick GL / Nayak DD
Funding support United States, 7 items
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, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29978.png

Downloads & links

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Map

FileDownload / File: emd_29978.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.115 Å
Density
Contour LevelBy AUTHOR: 0.42
Minimum - Maximum-0.78186905 - 1.6960241
Average (Standard dev.)-0.0010141894 (±0.08940483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 249.76001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29978_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29978_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Assembly intermediate of the MCR complex bound to mcrD

EntireName: Assembly intermediate of the MCR complex bound to mcrD
Components
  • Complex: Assembly intermediate of the MCR complex bound to mcrD
    • Protein or peptide: Methyl-coenzyme M reductase subunit alphaCoenzyme-B sulfoethylthiotransferase
    • Protein or peptide: Methyl-coenzyme M reductase subunit betaCoenzyme-B sulfoethylthiotransferase
    • Protein or peptide: Methyl-coenzyme M reductase subunit gammaCoenzyme-B sulfoethylthiotransferase
    • Protein or peptide: Methyl coenzyme M reductase, subunit DCoenzyme-B sulfoethylthiotransferase
  • Ligand: 1-THIOETHANESULFONIC ACID
  • Ligand: FACTOR 430
  • Ligand: Coenzyme B

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Supramolecule #1: Assembly intermediate of the MCR complex bound to mcrD

SupramoleculeName: Assembly intermediate of the MCR complex bound to mcrD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Methanosarcina acetivorans C2A (archaea)

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Macromolecule #1: Methyl-coenzyme M reductase subunit alpha

MacromoleculeName: Methyl-coenzyme M reductase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: coenzyme-B sulfoethylthiotransferase
Source (natural)Organism: Methanosarcina acetivorans C2A (archaea)
Molecular weightTheoretical: 62.180078 KDa
SequenceString: MAADIFAKFK KSMEVKFTQE YGSNKQAGGD ITGKTEKFLR LGPEQDARKQ EMIKAGKEIA EKRGIAFYNP MMHMGAPLGQ RAITPYTIS GTDIVAEPDD LHYVNNAAMQ QMWDDIRRTC IVGLDMAHET LEKRLGKEVT PETINHYLET LNHAMPGAAV V QEMMVETH ...String:
MAADIFAKFK KSMEVKFTQE YGSNKQAGGD ITGKTEKFLR LGPEQDARKQ EMIKAGKEIA EKRGIAFYNP MMHMGAPLGQ RAITPYTIS GTDIVAEPDD LHYVNNAAMQ QMWDDIRRTC IVGLDMAHET LEKRLGKEVT PETINHYLET LNHAMPGAAV V QEMMVETH PALVDDCYVK IFTGDDELAD EIDKQYVINV NKMFSEEQAA QIKASIGKTT WQAIHIPTIV SRTTDGAQTS RW AAMQIGM SFISAYAMCA GEAAVADLSF AAK(MHS)AALVSM GEMLPAR(AGM)AR GPNEPGGLSF GHLSDIVQTS RVSKD PAKI ALEVVGAGCM LYDQIWLGSY MSGGVGFTQY ATAAYTDDIL DNNTYYDVDY INDKYNGAAN LGTDNKVKAT LDVVKD IAT ESTLYGIETY EKFPTALEDH FGGSQRATVL AAASGVACAL ATGNANAGLS GWYLSMYVHK EAWGRLGFFG FDLQDQ (SMC)GA TNVLSYQGDE GLPDELRGPN YPNYAMNVGH QGGYAGIAQA AHSGRGDAFT VNPLLKVCFA DELMPFNFAE PRR EFGRGA IREFMPAGER SLVIPAK

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Macromolecule #2: Methyl-coenzyme M reductase subunit beta

MacromoleculeName: Methyl-coenzyme M reductase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans C2A (archaea)
Molecular weightTheoretical: 45.17407 KDa
SequenceString: MSDTVDIYDD RGKLLESNVD IMSLAPTRNA AIKKIILDTK RSVAVSLAGI QGALASGKMG GKGRQILGRG LNYDLVGNAD AIAENVKNL VQVDEGDDTS VKVIKGGKSL LIQAPSSRIA AGADYMSATT VGAAAVTQTI IDMFGTDMYD APIAKSAVWG S YPQTMDLM ...String:
MSDTVDIYDD RGKLLESNVD IMSLAPTRNA AIKKIILDTK RSVAVSLAGI QGALASGKMG GKGRQILGRG LNYDLVGNAD AIAENVKNL VQVDEGDDTS VKVIKGGKSL LIQAPSSRIA AGADYMSATT VGAAAVTQTI IDMFGTDMYD APIAKSAVWG S YPQTMDLM GGNVQGVLSI PQNNEGLGFS LRNIMANHIA AITSRGAMNA AALSSIYEQS GIFEMGGAVG MFERHQLLGL AC QGLNANN VVYDIVKENG KDGTIGTVIE SIVGRAVEDG VISVDKTAPS GYKFYKANDV PMWNAYAAAG TLAATFVNCG AGR AAQNVS STLLYFNDIL EKETGLPGCD YGKVQGVAVG FSFFSHSIYG GGGPGVFNGN HVVTRHSRGF AIPCVCAAVA LDAG TQMFT IESTSGLIGD VFGSIEEFRQ PIKAVAGAL

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Macromolecule #3: Methyl-coenzyme M reductase subunit gamma

MacromoleculeName: Methyl-coenzyme M reductase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans C2A (archaea)
Molecular weightTheoretical: 27.630184 KDa
SequenceString: MAYEAQYYPG ATSVGANRRK HMSGKLEKLR EISDEDLTAV LGHRAPGSDY PSTHPPLAEM GEPACSIREA VAATPGAAAG DRVRYVQFA DSMYNAPATP YFRSYFAAIN FRGVDPGTLS GRQIVEARER DMEQCAKVQM ETEMTDPALA GMRGATVHGH S VRLQEDGV ...String:
MAYEAQYYPG ATSVGANRRK HMSGKLEKLR EISDEDLTAV LGHRAPGSDY PSTHPPLAEM GEPACSIREA VAATPGAAAG DRVRYVQFA DSMYNAPATP YFRSYFAAIN FRGVDPGTLS GRQIVEARER DMEQCAKVQM ETEMTDPALA GMRGATVHGH S VRLQEDGV MFDMLDRRRL EGGVIIMDKD QVAIPLDRKV NLGKPMSSEE AAKRTTIYRV DNVAFRDDAE VIEWVHRVFD QR TSYGFQP K

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Macromolecule #4: Methyl coenzyme M reductase, subunit D

MacromoleculeName: Methyl coenzyme M reductase, subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans C2A (archaea)
Molecular weightTheoretical: 21.842742 KDa
Recombinant expressionOrganism: Methanosarcina acetivorans C2A (archaea)
SequenceString: MDYKDDDDKG GGWSHPQFEK GGGMSDSASN TEDSIQIEIF PSRILSPETA QKLISELYQV DGIIRVMVQG PRLPERVSAG PGTGEKVEH PLRKPIQIGD QVIELKISVG RIRLEIENAE TKEKVRSVCD KMLPFSFEFR EGHFLRRKPT VTDYAKLGPE T DPRLLGMV ...String:
MDYKDDDDKG GGWSHPQFEK GGGMSDSASN TEDSIQIEIF PSRILSPETA QKLISELYQV DGIIRVMVQG PRLPERVSAG PGTGEKVEH PLRKPIQIGD QVIELKISVG RIRLEIENAE TKEKVRSVCD KMLPFSFEFR EGHFLRRKPT VTDYAKLGPE T DPRLLGMV DPKAKVNQLV FIEKREKEDD TDKDE

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Macromolecule #5: 1-THIOETHANESULFONIC ACID

MacromoleculeName: 1-THIOETHANESULFONIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: COM
Molecular weightTheoretical: 142.197 Da
Chemical component information

ChemComp-COM:
1-THIOETHANESULFONIC ACID

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Macromolecule #6: FACTOR 430

MacromoleculeName: FACTOR 430 / type: ligand / ID: 6 / Number of copies: 1 / Formula: F43
Molecular weightTheoretical: 906.58 Da
Chemical component information

ChemComp-F43:
FACTOR 430 / Cofactor F430

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Macromolecule #7: Coenzyme B

MacromoleculeName: Coenzyme B / type: ligand / ID: 7 / Number of copies: 1 / Formula: TP7
Molecular weightTheoretical: 343.334 Da
Chemical component information

ChemComp-TP7:
Coenzyme B / Coenzyme B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.55 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
25.0 mMNH2C(CH2OH)3Tris base
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification occurred under aerobic conditions.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65000
FSC plot (resolution estimation)

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