[English] 日本語
Yorodumi
- EMDB-35343: Respiratory complex CIII2, focus-refined of type II, Wild type mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35343
TitleRespiratory complex CIII2, focus-refined of type II, Wild type mouse under cold temperature
Map dataFocus-refined map, CIII2, Cold Acclimated, Type II of Respiratory Supercomplex
Sample
  • Complex: Respiratory Supercomplex CI:CIII2
    • Protein or peptide: x 10 types
  • Ligand: x 7 types
KeywordsRespiratory complex / Respiratory supercomplex / ELECTRON TRANSPORT
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / Respiratory electron transport / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex III ...Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / Respiratory electron transport / response to mercury ion / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex III / Mitochondrial protein degradation / : / : / response to alkaloid / quinol-cytochrome-c reductase / response to copper ion / ubiquinol-cytochrome-c reductase activity / response to glucagon / cellular respiration / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / electron transport coupled proton transport / response to hyperoxia / animal organ regeneration / response to cadmium ion / response to hormone / respiratory electron transport chain / hippocampus development / response to activity / mitochondrial membrane / metalloendopeptidase activity / response to toxic substance / 2 iron, 2 sulfur cluster binding / response to calcium ion / myelin sheath / response to ethanol / mitochondrial inner membrane / response to hypoxia / oxidoreductase activity / response to xenobiotic stimulus / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome b / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShin Y-C / Liao M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1 DK081418 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1 DK089883 United States
CitationJournal: Cell / Year: 2024
Title: Structural basis of respiratory complex adaptation to cold temperatures.
Authors: Young-Cheul Shin / Pedro Latorre-Muro / Amina Djurabekova / Oleksii Zdorevskyi / Christopher F Bennett / Nils Burger / Kangkang Song / Chen Xu / Joao A Paulo / Steven P Gygi / Vivek Sharma / ...Authors: Young-Cheul Shin / Pedro Latorre-Muro / Amina Djurabekova / Oleksii Zdorevskyi / Christopher F Bennett / Nils Burger / Kangkang Song / Chen Xu / Joao A Paulo / Steven P Gygi / Vivek Sharma / Maofu Liao / Pere Puigserver /
Abstract: In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation upon cold ...In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation upon cold exposure remains elusive. Herein, we combined thermoregulatory physiology and cryoelectron microscopy (cryo-EM) to study endogenous respiratory supercomplexes from mice exposed to different temperatures. A cold-induced conformation of CI:III (termed type 2) supercomplex was identified with a ∼25° rotation of CIII around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting catalytic states that favor electron transfer. Large-scale supercomplex simulations in mitochondrial membranes reveal how lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations, and biochemical analyses unveil the thermoregulatory mechanisms and dynamics of increased respiratory capacity in brown fat at the structural and energetic level.
History
DepositionFeb 10, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35343.png

Downloads & links

-
Map

FileDownload / File: emd_35343.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus-refined map, CIII2, Cold Acclimated, Type II of Respiratory Supercomplex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.3744335 - 2.2925763
Average (Standard dev.)0.0009275471 (±0.053126425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_35343_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focus-refined map, CIII2, Cold Acclimated, Type II of...

Fileemd_35343_half_map_1.map
AnnotationFocus-refined map, CIII2, Cold Acclimated, Type II of Respiratory Supercomplex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focus-refined map, CIII2, Cold Acclimated, Type II of...

Fileemd_35343_half_map_2.map
AnnotationFocus-refined map, CIII2, Cold Acclimated, Type II of Respiratory Supercomplex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Respiratory Supercomplex CI:CIII2

EntireName: Respiratory Supercomplex CI:CIII2
Components
  • Complex: Respiratory Supercomplex CI:CIII2
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
  • Ligand: HEME C
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: UBIQUINONE-10
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CARDIOLIPIN

+
Supramolecule #1: Respiratory Supercomplex CI:CIII2

SupramoleculeName: Respiratory Supercomplex CI:CIII2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.32 MDa

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

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.910594 KDa
SequenceString: MAASAVCRAA CSGTQVLLRT RRSPALLRLP ALRGTATFAQ ALQSVPETQV SILDNGLRVA SEQSSHATCT VGVWIDAGSR YETEKNNGA GYFLEHLAFK GTKNRPGNAL EKEVESIGAH LNAYSTREHT AYLIKALSKD LPKVVELLAD IVQNSSLEDS Q IEKERDVI ...String:
MAASAVCRAA CSGTQVLLRT RRSPALLRLP ALRGTATFAQ ALQSVPETQV SILDNGLRVA SEQSSHATCT VGVWIDAGSR YETEKNNGA GYFLEHLAFK GTKNRPGNAL EKEVESIGAH LNAYSTREHT AYLIKALSKD LPKVVELLAD IVQNSSLEDS Q IEKERDVI LREMQENDAS MQNVVFDYLH ATAFQGTPLA QAVEGPSENV RRLSRTDLTD YLNRHYKAPR MVLAAAGGVE HQ QLLDLAQ KHLSSVSRVY EEDAVPGLTP CRFTGSEIRH RDDALPLAHV AIAVEGPGWA NPDNVTLQVA NAIIGHYDCT YGG GVHLSS PLASVAVANK LCQSFQTFNI SYSDTGLLGA HFVCDAMSID DMVFFLQGQW MRLCTSATES EVTRGKNILR NALV SHLDG TTPVCEDIGR SLLTYGRRIP LAEWESRIQE VDAQMLRDIC SKYFYDQCPA VAGYGPIEQL PDYNRIRSGM FWLRF

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

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

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.28973 KDa
SequenceString: MKLLSRAGSF SRFYSLKVAP KVKTSAAPGG VPLQPQDLEF TKLPNGLVIA SLENYAPLSR IGLFVKAGSR YEDSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTATRENM AYTVEGIRSD IEILMEFLLN VTTAPEFRRW EVAALRSQLK I DKAVAFQN ...String:
MKLLSRAGSF SRFYSLKVAP KVKTSAAPGG VPLQPQDLEF TKLPNGLVIA SLENYAPLSR IGLFVKAGSR YEDSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTATRENM AYTVEGIRSD IEILMEFLLN VTTAPEFRRW EVAALRSQLK I DKAVAFQN SQTRIIENLH DVAYKNALAN PLYCPDYRMG KITSEELHYF VQNHFTSARM ALVGLGVSHS VLKQVAEQFL NM RGGLGLA GAKAKYRGGE IREQNGDNLV HAAIVAESAA IGNAEANAFS VLQHLLGAGP HIKRGNNTTS LLSQSVAKGS HQP FDVSAF NASYSDSGLF GIYTISQAAA AGEVINAAYN QVKAVAQGNL SSADVQAAKN KLKAGYLMSV ETSEGFLSEI GSQA LAAGS YMPPSTVLQQ IDSVADADVV KAAKKFVSGK KSMAASGNLG HTPFLDEL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

+
Macromolecule #3: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.240305 KDa
SequenceString: MTNMRKTHPL FKIINHSFID LPAPSNISSW WNFGSLLGVC LMVQIITGLF LAMHYTSDTM TAFSSVTHIC RDVNYGWLIR YMHANGASM FFICLFLHVG RGLYYGSYTF METWNIGVLL LFAVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTT L VEWIWGGF ...String:
MTNMRKTHPL FKIINHSFID LPAPSNISSW WNFGSLLGVC LMVQIITGLF LAMHYTSDTM TAFSSVTHIC RDVNYGWLIR YMHANGASM FFICLFLHVG RGLYYGSYTF METWNIGVLL LFAVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTT L VEWIWGGF SVDKATLTRF FAFHFILPFI IAALAIVHLL FLHETGSNNP TGLNSDADKI PFHPYYTIKD ILGILIMFLI LM TLVLFFP DMLGDPDNYM PANPLNTPPH IKPEWYFLFA YAILRSIPNK LGGVLALILS ILILALMPFL HTSKQRSLMF RPI TQILYW ILVANLLILT WIGGQPVEHP FIIIGQLASI SYFSIILILM PISGIIEDKM LKLYP

UniProtKB: Cytochrome b

+
Macromolecule #4: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 35.374652 KDa
SequenceString: MAAAAASLRR TVLGPRGVGL PGASAPGLLG GARSRQLPLR TPQAVSLSSK SGPSRGRKVM LSALGMLAAG GAGLAVALHS AVSASDLEL HPPSYPWSHR GLLSSLDHTS IRRGFQVYKQ VCSSCHSMDY VAYRHLVGVC YTEEEAKALA EEVEVQDGPN D DGEMFMRP ...String:
MAAAAASLRR TVLGPRGVGL PGASAPGLLG GARSRQLPLR TPQAVSLSSK SGPSRGRKVM LSALGMLAAG GAGLAVALHS AVSASDLEL HPPSYPWSHR GLLSSLDHTS IRRGFQVYKQ VCSSCHSMDY VAYRHLVGVC YTEEEAKALA EEVEVQDGPN D DGEMFMRP GKLSDYFPKP YPNPEAARAA NNGALPPDLS YIVRARHGGE DYVFSLLTGY CEPPTGVSLR EGLYFNPYFP GQ AIGMAPP IYTEVLEYDD GTPATMSQVA KDVATFLRWA SEPEHDHRKR MGLKMLLMMG LLLPLTYAMK RHKWSVLKSR KLA YRPPK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

+
Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.406635 KDa
SequenceString: MLSVAARSGP FAPVLSATSR GVAGALRPLL QGAVPAASEP PVLDVKRPFL CRESLSGQAA ARPLVATVGL NVPASVRFSH TDVKVPDFS DYRRAEVLDS TKSSKESSEA RKGFSYLVTA TTTVGVAYAA KNVVSQFVSS MSASADVLAM SKIEIKLSDI P EGKNMAFK ...String:
MLSVAARSGP FAPVLSATSR GVAGALRPLL QGAVPAASEP PVLDVKRPFL CRESLSGQAA ARPLVATVGL NVPASVRFSH TDVKVPDFS DYRRAEVLDS TKSSKESSEA RKGFSYLVTA TTTVGVAYAA KNVVSQFVSS MSASADVLAM SKIEIKLSDI P EGKNMAFK WRGKPLFVRH RTKKEIDQEA AVEVSQLRDP QHDLDRVKKP EWVILIGVCT HLGCVPIANA GDFGGYYCPC HG SHYDASG RIRKGPAPLN LEVPAYEFTS DDVVVVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

+
Macromolecule #6: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.587532 KDa
SequenceString:
MAGRSAVSAS SKWLDGFRKW YYNAAGFNKL GLMRDDTLHE TEDVKEAIRR LPEDLYNDRM FRIKRALDLT MRHQILPKDQ WTKYEEDKF YLEPYLKEVI RERKEREEWA KK

UniProtKB: Cytochrome b-c1 complex subunit 7

+
Macromolecule #7: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.783245 KDa
SequenceString:
MGREFGNLAR IRHVISYSLS PFEQRAFPSY FSKGIPNVLR RTRERILRVA PPFVVVYLIY TWGNQEFEQS KRKNPAMYEN DK

UniProtKB: Cytochrome b-c1 complex subunit 8

+
Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.452694 KDa
SequenceString:
MGLEDERKML TGSGDPKEEE EEELVDPLTT VREHCEQLEK CVKARERLEL CDNRVSSRSQ TEEDCTEELF DFLHARDHCV AHKLFKNLK

UniProtKB: Cytochrome b-c1 complex subunit 6, mitochondrial

+
Macromolecule #9: Cytochrome b-c1 complex subunit 9

MacromoleculeName: Cytochrome b-c1 complex subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 7.457526 KDa
SequenceString:
MSSPTIPSRL YSLLFRRTST FALTIAVGAL FFERAFDQGA DAIYEHINEG KLWKHIKHKY ENKE

UniProtKB: Cytochrome b-c1 complex subunit 9

+
Macromolecule #10: Cytochrome b-c1 complex subunit 10

MacromoleculeName: Cytochrome b-c1 complex subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 6.546627 KDa
SequenceString:
MLSRFLGPRY RELARNWIPT AGMWGTVGAV GLVWATDWRL ILDWVPYING KFKKDD

UniProtKB: Cytochrome b-c1 complex subunit 10

+
Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 11 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #12: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...

MacromoleculeName: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
type: ligand / ID: 12 / Number of copies: 2 / Formula: UQ6
Molecular weightTheoretical: 592.891 Da
Chemical component information

ChemComp-UQ6:
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL

+
Macromolecule #13: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 13 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #14: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 14 / Number of copies: 3 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

+
Macromolecule #15: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 15 / Number of copies: 1 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

+
Macromolecule #16: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 16 / Number of copies: 1 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

+
Macromolecule #17: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 17 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.33 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 46.1 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 45.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7o3h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177076
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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