[English] 日本語
Yorodumi
- EMDB-15868: Cryo-EM structure of cytochrome bc1 complex (complex-III) from re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15868
TitleCryo-EM structure of cytochrome bc1 complex (complex-III) from respiratory supercomplex of Tetrahymena thermophila
Map dataSharpened mask refined map
Sample
  • Complex: Dimeric cytochrome bc1 complex (complex-III2)
    • Protein or peptide: x 12 types
  • Ligand: x 7 types
Function / homology
Function and homology information


quinol-cytochrome-c reductase / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity ...quinol-cytochrome-c reductase / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane
Similarity search - Function
Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily ...Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / 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 / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Transmembrane protein, putative / Transmembrane protein, putative / Peptidase M16 inactive domain protein / Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit / M16 family peptidase, putative / Transmembrane protein, putative / Uncharacterized protein / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome protein c1 / Apocytochrome b
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote) / Tetrahymena thermophila SB210 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMuhleip A / Kock Flygaard R / Amunts A
Funding support Sweden, European Union, 4 items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
Cancerfonden2017/1041 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Citation
Journal: Nature / Year: 2023
Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts /
Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex
Authors: Muhleip A / Flygaard RK / Haapanen O / Baradaran R / Gruhl T / Tobiasson V / Marechal A / Sharma V / Amunts A
History
DepositionSep 27, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15868.png

Downloads & links

-
Map

FileDownload / File: emd_15868.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened mask refined map
Voxel sizeX=Y=Z: 1.25 Å
Density
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-2.920636 - 5.0904384
Average (Standard dev.)-0.0024742913 (±0.14935043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 600.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15868_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened mask refined map

Fileemd_15868_additional_1.map
AnnotationUnsharpened mask refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Rieske B-state map from focused classification

Fileemd_15868_additional_2.map
AnnotationRieske B-state map from focused classification
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Rieske C-state map from focused classification

Fileemd_15868_additional_3.map
AnnotationRieske C-state map from focused classification
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A

Fileemd_15868_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B

Fileemd_15868_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Dimeric cytochrome bc1 complex (complex-III2)

EntireName: Dimeric cytochrome bc1 complex (complex-III2)
Components
  • Complex: Dimeric cytochrome bc1 complex (complex-III2)
    • Protein or peptide: Peptidase M16 inactive domain protein
    • Protein or peptide: M16 family peptidase, putative
    • Protein or peptide: Apocytochrome b
    • Protein or peptide: Cytochrome protein c1
    • Protein or peptide: Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit
    • Protein or peptide: Ubiquinol-cytochrome C reductase hinge protein
    • Protein or peptide: UQCRTT1
    • Protein or peptide: Transmembrane protein, putativeTransmembrane protein
    • Protein or peptide: Transmembrane protein, putativeTransmembrane protein
    • Protein or peptide: UQCRTT3/UP1
    • Protein or peptide: Transmembrane protein, putativeTransmembrane protein
    • Protein or peptide: UQCRTT2
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARDIOLIPIN
  • Ligand: Ubiquinone-8Coenzyme Q10
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

+
Supramolecule #1: Dimeric cytochrome bc1 complex (complex-III2)

SupramoleculeName: Dimeric cytochrome bc1 complex (complex-III2) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Organelle: Mitochondrion
Molecular weightTheoretical: 640 KDa

+
Macromolecule #1: Peptidase M16 inactive domain protein

MacromoleculeName: Peptidase M16 inactive domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 58.023914 KDa
SequenceString: MFGRISQRIS KLARLQRAFS TLQKQAQSNV VKSERLQFSK ARLTDFGELP QGEIPTALQY DRPCRVETLA NGVRLAVEPS SVSPLAAVS VVVRAGTRQE TLETSGVAQF VQRLVLRGTS KRNREQIEKE LALLGGNLKV QVGRETTTYT LSVLPENVEK A VDFLGDIL ...String:
MFGRISQRIS KLARLQRAFS TLQKQAQSNV VKSERLQFSK ARLTDFGELP QGEIPTALQY DRPCRVETLA NGVRLAVEPS SVSPLAAVS VVVRAGTRQE TLETSGVAQF VQRLVLRGTS KRNREQIEKE LALLGGNLKV QVGRETTTYT LSVLPENVEK A VDFLGDIL QNSVFNKQQV EAEKEAVYNN ALSAQNDQQG LLLENIHFTA YRDHYFGQPT HGIRENLHNI TDEVVKNFVK TN YVGSNFV VAAAGNVNSQ AFLQAAEKAF GTVAQKDATT FVPNTEKPYF TPSYMTIRDD EMHNLNVGVF FEAPSWTDPD FFT INFFQR ILGEYQADKY TGQHLNTSDR QYSLIHKELG NLPDVTIHKT HYLPYSDTGL FGSYFYGNEI FGNQMLFLSQ MILS EYASY INQAEIYRAR AKYFNELLAE QNSADIASSI ATQVTYLNRR VPRSEVAKRI SSLDSGLINR AATRWFWDKE LAIVT WGPS HGLIAGSHYN RSIKRSTLGW YGNTHYYIV

+
Macromolecule #2: M16 family peptidase, putative

MacromoleculeName: M16 family peptidase, putative / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 53.030543 KDa
SequenceString: MLSKITQNTL KSLSGQCKQA FSVRKAFYDF IYKDDKSAET YKVTTADPRT PVQGFRGQTA EDVAAKYEVT KLANGVTIIT ESQTFPSQV DMGILLDVGT RDETNETSGS LLSIKNTYLK TVLNTNETIN YGVVQQSGGS FEMEYDQETA YFKANCLAHD A TDVFSMVA ...String:
MLSKITQNTL KSLSGQCKQA FSVRKAFYDF IYKDDKSAET YKVTTADPRT PVQGFRGQTA EDVAAKYEVT KLANGVTIIT ESQTFPSQV DMGILLDVGT RDETNETSGS LLSIKNTYLK TVLNTNETIN YGVVQQSGGS FEMEYDQETA YFKANCLAHD A TDVFSMVA DCALEPRSTV AASVGVEKNQ NTHKLESYLK TGELFNESVF KTAYGLKGLG LPLKGLRGNV KNLSSYTLQK FQ LENITPN RIFVCAAGVE SHQEFVDLVQ TKLAQIPSAE GQKTHQREKS EYLGGEVRNL TEESNVTLAL LFQSVPWSSA DIV AFNVAA ALLNNLRLKK NLLQKYAYFD QAEALNFHFT DSGLFGLRTS GSADRAKDIL NHSIAELKAI ASGVNADELL TAKA ALKNS VLSALERQTD RLEETVKNVR TFNKIQHTDY VKQIDSVTAD QVAKAVAKVL TSNPTFVAQG SQVNALPTYD AIRNL LK

+
Macromolecule #3: Apocytochrome b

MacromoleculeName: Apocytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 50.635547 KDa
SequenceString: MEWNKGTYMS TSIKKIVQYF SVMTVSFHDI NSLFGFFTFL TIASQLVSGT MLAFSLVPEP MLIPMVREEE DVEDLYTDDF FWLHERGVD MLFIFSYFHL FRKIYLNNFE YEQEAAWKSG VFTFLLFQVV VFLGLVLCCT HLSDITLAIA ANLYDTFFAG K GKFYWWIF ...String:
MEWNKGTYMS TSIKKIVQYF SVMTVSFHDI NSLFGFFTFL TIASQLVSGT MLAFSLVPEP MLIPMVREEE DVEDLYTDDF FWLHERGVD MLFIFSYFHL FRKIYLNNFE YEQEAAWKSG VFTFLLFQVV VFLGLVLCCT HLSDITLAIA ANLYDTFFAG K GKFYWWIF TSKELNTDTI IRLAYLHYVL AFFLAYLGLI HGVDMHYDWK NESSMDGLET EMIWFDEALS NELGAMIEII LI VMIVCFF MYPEPEALSY EFFMWGDIGF INDVRFLSVA PHWYFRPFMA WLTVCPFHKI GLFGLIYYFF ILFYQPVIHG TNE QNNYTK RNVAFVSFFI NRSDIMTPKY HSVEDNLLHQ ITFWLFLCSA LYVTSYLPYG RFYNRINGNY GTLWSFMYIF FYLG NSFLR RPLITELYLF NAFVKSKFLK K

+
Macromolecule #4: Cytochrome protein c1

MacromoleculeName: Cytochrome protein c1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 37.616629 KDa
SequenceString: MKSFVAAGII GLSLANSQNK EVQNFIYRDD IGAFWGIKGY EELVTEVGTH KGHNYWPQFS FLGTYDSGSV RRGFQVFARN CGNCHGMIY KKYDYLLDKA YRQLELAQMV SDFTIHPAHQ HFKQYYYQEW DERDRVICDH IYPPYFSQDQ AKNANGGVWP T DFSKIKLR ...String:
MKSFVAAGII GLSLANSQNK EVQNFIYRDD IGAFWGIKGY EELVTEVGTH KGHNYWPQFS FLGTYDSGSV RRGFQVFARN CGNCHGMIY KKYDYLLDKA YRQLELAQMV SDFTIHPAHQ HFKQYYYQEW DERDRVICDH IYPPYFSQDQ AKNANGGVWP T DFSKIKLR PGGINYIYNI STGYHFTPPF GMDVPKGKYF NPYFDHMIIG MPRQLVDGLV DYDDGTPAST PQMAYDVSNF IN FMQRRVG YKRPDKMVRY YMVFTGGLLI LPFKYFKTKA YYRNLLSLRW EMYAVRDGVY YNHFKYGGYN SRAYQFRGYF WA

+
Macromolecule #5: Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron...

MacromoleculeName: Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 30.696961 KDa
SequenceString: MFSKTLAHVT RSCNKLNQVQ AYNFGVLSEY NQRLSKKLHK GHLVEDKPTF FVTSSRPGNF GDHIDFKVNI DNWFDENRVH NEHETDIRR TQIYTLNAIY YGGLLSFARL YAMGVIGRLN GWKRYERDTY SEVDIGALPP GEVMQMVWNG TPIFIRRLTS N EVKEENEL ...String:
MFSKTLAHVT RSCNKLNQVQ AYNFGVLSEY NQRLSKKLHK GHLVEDKPTF FVTSSRPGNF GDHIDFKVNI DNWFDENRVH NEHETDIRR TQIYTLNAIY YGGLLSFARL YAMGVIGRLN GWKRYERDTY SEVDIGALPP GEVMQMVWNG TPIFIRRLTS N EVKEENEL PSNTLLDKDK EVILSDAGNT KVIVVSAVCT HLGCIPIPYL GAYKGYVCIC HGSVYDKFAR VRQGPALLNL PA INNSIHD EGTLVCMEQL KFPHEPSQRF WA

+
Macromolecule #6: Ubiquinol-cytochrome C reductase hinge protein

MacromoleculeName: Ubiquinol-cytochrome C reductase hinge protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 9.885511 KDa
SequenceString:
MSNVSDAQIQ EWIKRGEDPK EFLLKECAPQ CTAWKEKLGR CEAKLKSLVN ADPEMSCMYP LRDWVTCIEA CVQPAITRNL FGSKYM

+
Macromolecule #7: UQCRTT1

MacromoleculeName: UQCRTT1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 39.193523 KDa
SequenceString: MVRLEKILWE QLVNVKAFSR QRVIGAPSKW YNENRTEWFK VAQHNAFNTG FSGVILRALE PLLAKFIYRW RLDIAHQRGL TLEDSLLFM DRELRRCYFF ETVARQNLHP YTVLFMKKRR ARYYKVERGL RGFYVPDWVR KEAEERQLSE TVDNIFNWEN F VYREYMSD ...String:
MVRLEKILWE QLVNVKAFSR QRVIGAPSKW YNENRTEWFK VAQHNAFNTG FSGVILRALE PLLAKFIYRW RLDIAHQRGL TLEDSLLFM DRELRRCYFF ETVARQNLHP YTVLFMKKRR ARYYKVERGL RGFYVPDWVR KEAEERQLSE TVDNIFNWEN F VYREYMSD MTPIGRWTSL SKITPLDMFQ YYGLFRNEAW DRFFYNEAFY ESYSEKEKQE ANGNPFGKFN LQTADGRAQF EK EVNTFIE RYPFAVTKPG QKFDFTRFYA LEDLANKRDT SKYDPALLES VKNELKQSAA LPADNGANKT KKSKPILPDW LQP KFGKAF QA

+
Macromolecule #8: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 15.677771 KDa
SequenceString:
MNVTGAGLTH VKDFHSDEMR VFRGGLRHIA DKQGNLIYGS VNSSVRYYHD KMSYERGFIQ HSRSPSNQFI NFHFMLGGFR TYVLERFFK QVWYRRNIRT FWFPVLISYT SGCITMRMYD NNCYDYFYFS D

+
Macromolecule #9: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 14.262554 KDa
SequenceString:
MVYGKLIFNN IKEYTPSWIK TIPYSQVTKP ILRKQPQIVG KINADPKVKK FWVFLRENVQ YYPFLWQFFI LGTSFVWFHV CYDPWLAIY QANNAHRSLE TALTKEKAHK KKLAEQEESE

+
Macromolecule #10: UQCRTT3/UP1

MacromoleculeName: UQCRTT3/UP1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 5.634938 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #11: Transmembrane protein, putative

MacromoleculeName: Transmembrane protein, putative / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
Molecular weightTheoretical: 7.455741 KDa
SequenceString:
MYLPTFYKLF HETNAFRLKR YVGYGPLLLT WSIWTLYPAL YNMIYSDFIP PERGVPKRIV DA

+
Macromolecule #12: UQCRTT2

MacromoleculeName: UQCRTT2 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Molecular weightTheoretical: 4.850612 KDa
SequenceString:
MAPVFLKALR YVIYSYPLYV CYLIKQAQIN AQGSEKEEEH H

+
Macromolecule #13: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 13 / Number of copies: 15 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

+
Macromolecule #14: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 14 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 15 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #16: Ubiquinone-8

MacromoleculeName: Ubiquinone-8 / type: ligand / ID: 16 / Number of copies: 3 / Formula: UQ8
Molecular weightTheoretical: 727.109 Da
Chemical component information

ChemComp-UQ8:
Ubiquinone-8

+
Macromolecule #17: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 17 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM / Discrete optimized protein energy

+
Macromolecule #18: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 18 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

+
Macromolecule #19: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 19 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 2.6 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 25.66 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138746
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more