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- EMDB-16008: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-16008
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
Map data
Sample
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
    • Protein or peptide: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
    • Protein or peptide: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7-2, mitochondrial
  • Ligand: ZINC ION
  • Ligand: water
Function / homology
Function and homology information


mitochondrial processing peptidase / plant-type cell wall / plant-type vacuole / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / plastid / chloroplast / mitochondrial membrane ...mitochondrial processing peptidase / plant-type cell wall / plant-type vacuole / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / plastid / chloroplast / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial outer membrane / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / nucleolus / mitochondrion / proteolysis / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein ...Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 7-2, mitochondrial / Probable mitochondrial-processing peptidase subunit beta, mitochondrial / Cytochrome b-c1 complex subunit Rieske-1, mitochondrial / Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / thale cress (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsKlusch N / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
History
DepositionOct 21, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16008.png

Downloads & links

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Map

FileDownload / File: emd_16008.map.gz / Format: CCP4 / Size: 66.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.57 Å/pix.
x 300 pix.
= 171.9 Å		0.57 Å/pix.
x 237 pix.
= 135.801 Å		0.57 Å/pix.
x 246 pix.
= 140.958 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.1475964 - 6.072588
Average (Standard dev.)1.8749071e-12 (±0.27869537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin360275161
Dimensions237246300
Spacing300237246
CellA: 171.90001 Å / B: 135.80101 Å / C: 140.95801 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16008_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16008_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_16008_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Sample components

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Entire : Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP ...

EntireName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
Components
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
    • Protein or peptide: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
    • Protein or peptide: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7-2, mitochondrial
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP ...

SupramoleculeName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Probable mitochondrial-processing peptidase subunit alpha-1, mito...

MacromoleculeName: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 54.459766 KDa
SequenceString: MYRTAASRAR ALKGVLTRSL RPARYASSSA VAETSSSTPA YLSWLSGGSR AALTSLDMPL QGVSLPPPLA DKVEPSKLQI TTLPNGLKI ASETTPNPAA SIGLYVDCGS IYEAPYFHGA THLLERMAFK STLNRTHFRL VREIEAIGGN TSASASREQM S YTIDALKT ...String:
MYRTAASRAR ALKGVLTRSL RPARYASSSA VAETSSSTPA YLSWLSGGSR AALTSLDMPL QGVSLPPPLA DKVEPSKLQI TTLPNGLKI ASETTPNPAA SIGLYVDCGS IYEAPYFHGA THLLERMAFK STLNRTHFRL VREIEAIGGN TSASASREQM S YTIDALKT YVPEMVEVLI DSVRNPAFLD WEVNEELRKM KVEIAELAKN PMGFLLEAIH SAGYSGPLAS PLYAPESALD RL NGELLEE FMTENFTAAR MVLAASGVEH EELLKVAEPL TSDLPNVPPQ LAPKSQYVGG DFRQHTGGEA THFAVAFEVP GWN NEKEAV TATVLQMLMG GGGSFSAGGP GKGMHSWLYR RVLNEYQEVQ SCTAFTSIFN DTGLFGIYGC SSPQFAAKAI ELAA KELKD VAGGKVNQAH LDRAKAATKS AVLMNLESRM IAAEDIGRQI LTYGERKPVD QFLKSVDQLT LKDIADFTSK VISKP LTMG SFGDVLAVPS YDTISSKFR

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Macromolecule #2: Probable mitochondrial-processing peptidase subunit beta, mitocho...

MacromoleculeName: Probable mitochondrial-processing peptidase subunit beta, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: mitochondrial processing peptidase
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 59.23475 KDa
SequenceString: MAMKNLLSLA RRSQRRLFLT QATRSSSSFS AIDSVPASAS PTALSPPPPH LMPYDHAAEI IKNKIKKLEN PDKRFLKYAS PHPILASHN HILSAPETRV TTLPNGLRVA TESNLSAKTA TVGVWIDAGS RFESDETNGT AHFLEHMIFK GTDRRTVRAL E EEIEDIGG ...String:
MAMKNLLSLA RRSQRRLFLT QATRSSSSFS AIDSVPASAS PTALSPPPPH LMPYDHAAEI IKNKIKKLEN PDKRFLKYAS PHPILASHN HILSAPETRV TTLPNGLRVA TESNLSAKTA TVGVWIDAGS RFESDETNGT AHFLEHMIFK GTDRRTVRAL E EEIEDIGG HLNAYTSREQ TTYYAKVLDS NVNQALDVLA DILQNSKFEE QRINRERDVI LREMQEVEGQ TDEVVLDHLH AT AFQYTPL GRTILGPAQN VKSITREDLQ NYIKTHYTAS RMVIAAAGAV KHEEVVEQVK KLFTKLSSDP TTTSQLVANE PAS FTGSEV RMIDDDLPLA QFAVAFEGAS WTDPDSVALM VMQTMLGSWN KNVGGGKHVG SDLTQRVAIN EIAESIMAFN TNYK DTGLF GVYAVAKADC LDDLSYAIMY EVTKLAYRVS DADVTRARNQ LKSSLLLHMD GTSPIAEDIG RQLLTYGRRI PTAEL FARI DAVDASTVKR VANKYIYDKD IAISAIGPIQ DLPDYNKFRR RTYWNRY

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Macromolecule #3: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 29.645584 KDa
SequenceString: MLRVAGRRLF SVSQRSSTAT SFVVSRDHTL SDGGGDSSSA PRSLPSADLS SYHRSLIRGF SSQVLAQGNE IGFGSEVPAT VEAVKTPNS KIVYDDHNHE RYPPGDPSKR AFAYFVLSGG RFVYASVLRL LVLKLIVSMS ASKDVLALAS LEVDLGSIEP G TTVTVKWR ...String:
MLRVAGRRLF SVSQRSSTAT SFVVSRDHTL SDGGGDSSSA PRSLPSADLS SYHRSLIRGF SSQVLAQGNE IGFGSEVPAT VEAVKTPNS KIVYDDHNHE RYPPGDPSKR AFAYFVLSGG RFVYASVLRL LVLKLIVSMS ASKDVLALAS LEVDLGSIEP G TTVTVKWR GKPVFIRRRT EDDIKLANSV DVGSLRDPQE DSVRVKNPEW LVVVGVCTHL GCIPLPNAGD YGGWFCPCHG SH YDISGRI RKGPAPYNLE VPTYSFLEEN KLLIG

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Macromolecule #4: Cytochrome b-c1 complex subunit 7-2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 7-2, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 14.620021 KDa
SequenceString:
MASFLQRLVD PRKNFLARMH MKSVSNRLRR YGLRYDDLYD PLYDLDIKEA LNRLPREIVD ARNQRLMRAM DLSMKHEYLP DNLQAVQTP FRSYLQDMLA LVKRERAERE ALGALPLYQR TIP

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 894 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration0.18 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1215138
Startup modelType of model: EMDB MAP
EMDB ID:

11878

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 213993
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot (ver. 0.9.5)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8bep:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)

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