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Yorodumi- EMDB-16008: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16008 | |||||||||
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Title | Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information mitochondrial processing peptidase / plant-type cell wall / protein processing involved in protein targeting to mitochondrion / plant-type vacuole / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast ...mitochondrial processing peptidase / plant-type cell wall / protein processing involved in protein targeting to mitochondrion / plant-type vacuole / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / plastid / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / nucleolus / mitochondrion / proteolysis / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / thale cress (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.29 Å | |||||||||
Authors | Klusch N / Kuehlbrandt W | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16008.map.gz | 62.2 MB | EMDB map data format | |
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Header (meta data) | emd-16008-v30.xml emd-16008.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16008_fsc.xml | 26.5 KB | Display | FSC data file |
Images | emd_16008.png | 167.9 KB | ||
Others | emd_16008_additional_1.map.gz emd_16008_half_map_1.map.gz emd_16008_half_map_2.map.gz | 87.3 MB 1 GB 1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16008 | HTTPS FTP |
-Validation report
Summary document | emd_16008_validation.pdf.gz | 820.3 KB | Display | EMDB validaton report |
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Full document | emd_16008_full_validation.pdf.gz | 819.9 KB | Display | |
Data in XML | emd_16008_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | emd_16008_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16008 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16008 | HTTPS FTP |
-Related structure data
Related structure data | 8bepMC 8bedC 8beeC 8befC 8behC 8belC 8bpxC 8bq5C 8bq6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16008.map.gz / Format: CCP4 / Size: 66.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.573 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_16008_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16008_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16008_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP ...
Entire | Name: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain) |
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Components |
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-Supramolecule #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP ...
Supramolecule | Name: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain) type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Probable mitochondrial-processing peptidase subunit alpha-1, mito...
Macromolecule | Name: Probable mitochondrial-processing peptidase subunit alpha-1, mitochondrial type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: thale cress (thale cress) |
Molecular weight | Theoretical: 54.459766 KDa |
Sequence | String: 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 |
-Macromolecule #2: Probable mitochondrial-processing peptidase subunit beta, mitocho...
Macromolecule | Name: Probable mitochondrial-processing peptidase subunit beta, mitochondrial type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: mitochondrial processing peptidase |
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Source (natural) | Organism: thale cress (thale cress) |
Molecular weight | Theoretical: 59.23475 KDa |
Sequence | String: 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 |
-Macromolecule #3: Cytochrome b-c1 complex subunit Rieske-1, mitochondrial
Macromolecule | Name: 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 |
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Source (natural) | Organism: thale cress (thale cress) |
Molecular weight | Theoretical: 29.645584 KDa |
Sequence | String: 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 |
-Macromolecule #4: Cytochrome b-c1 complex subunit 7-2, mitochondrial
Macromolecule | Name: Cytochrome b-c1 complex subunit 7-2, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: thale cress (thale cress) |
Molecular weight | Theoretical: 14.620021 KDa |
Sequence | String: MASFLQRLVD PRKNFLARMH MKSVSNRLRR YGLRYDDLYD PLYDLDIKEA LNRLPREIVD ARNQRLMRAM DLSMKHEYLP DNLQAVQTP FRSYLQDMLA LVKRERAERE ALGALPLYQR TIP |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 894 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.18 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: 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. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Software | Name: Coot (ver. 0.9.5) |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-8bep: |