[English] 日本語
Yorodumi
- EMDB-51125: Respiratory supercomplex CI1-CIII2-CIV2-(cbb3)1 from alphaproteob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51125
TitleRespiratory supercomplex CI1-CIII2-CIV2-(cbb3)1 from alphaproteobacterium
Map dataThis postprocessed .mrc file has been trimmed to a smaller box size of 375 pixels. This differs from that of the half-maps which has an untrimmed box size of 600 pixels and rescaled to 1.048 A/pix.
Sample
  • Complex: Respiratory supercomplex CI1-CIII2-CIV2 -(cbb3)1 from alphaproteobacterium
    • Complex: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)
      • Protein or peptide: x 19 types
    • Complex: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)
      • Protein or peptide: x 4 types
    • Complex: Transmembrane-anchored cytochrome c (c552)
      • Protein or peptide: x 1 types
    • Complex: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)
      • Protein or peptide: x 3 types
    • Complex: Alphaproteobacterial respiratory complex cbb3-oxidase
      • Protein or peptide: x 3 types
    • Complex: Interfacial transmembrane helices between CIII and cbb3-oxidase
      • Protein or peptide: x 2 types
  • Ligand: x 15 types
KeywordsSupercomplex / multi-subunit membrane protein complex / electron transport chain / native purification / respiration / ELECTRON TRANSPORT
Function / homology
Function and homology information


active transmembrane transporter activity / organelle envelope / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / NADH:ubiquinone reductase (H+-translocating) / : / membrane protein complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / aerobic electron transport chain ...active transmembrane transporter activity / organelle envelope / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / NADH:ubiquinone reductase (H+-translocating) / : / membrane protein complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / monoatomic cation transmembrane transporter activity / oxidative phosphorylation / quinol-cytochrome-c reductase / : / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / NADH dehydrogenase activity / organelle membrane / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / catalytic complex / quinone binding / ATP synthesis coupled electron transport / endomembrane system / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / methylation / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / heme binding / protein-containing complex binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome C oxidase, mono-heme subunit/FixO / Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV ...Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / N-terminal domain of cytochrome oxidase-cbb3, FixP / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome C oxidase, mono-heme subunit/FixO / Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Cytochrome c, class IC / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / : / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c, class IA/ IB / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome c / 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 / : / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / Rieske [2Fe-2S] domain / NADH-quinone oxidoreductase, chain 5-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile.
Similarity search - Domain/homology
Aa3 type cytochrome c oxidase subunit IV / NAD-dependent epimerase/dehydratase / NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Cytochrome c, class I / Cbb3-type cytochrome c oxidase subunit CcoP / Cytochrome c oxidase, cbb3-type, subunit II / cytochrome-c oxidase / Zinc finger CHCC-type domain-containing protein / Cytochrome c oxidase subunit 1 ...Aa3 type cytochrome c oxidase subunit IV / NAD-dependent epimerase/dehydratase / NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Cytochrome c, class I / Cbb3-type cytochrome c oxidase subunit CcoP / Cytochrome c oxidase, cbb3-type, subunit II / cytochrome-c oxidase / Zinc finger CHCC-type domain-containing protein / Cytochrome c oxidase subunit 1 / NADH-quinone oxidoreductase subunit N / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH dehydrogenase subunit E / NADH-quinone oxidoreductase subunit D / NADH-quinone oxidoreductase subunit C / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit A / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1 / Protein-L-isoaspartate O-methyltransferase / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.98 Å
AuthorsYaikhomba M / Hirst J / Croll TI / Spikes TE / Agip ANA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 and MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Minimal supercomplexes in alphaproteobacteria reveal conserved structural mechanisms for efficient respiration
Authors: Yaikhomba M / Hirst J / Croll TI / Spikes TE
History
DepositionJul 22, 2024-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51125.png

Downloads & links

-
Map

FileDownload / File: emd_51125.map.gz / Format: CCP4 / Size: 201.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis postprocessed .mrc file has been trimmed to a smaller box size of 375 pixels. This differs from that of the half-maps which has an untrimmed box size of 600 pixels and rescaled to 1.048 A/pix.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 375 pix.
= 393. Å		1.05 Å/pix.
x 375 pix.
= 393. Å		1.05 Å/pix.
x 375 pix.
= 393. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0112
Minimum - Maximum-0.011623317 - 0.067635596
Average (Standard dev.)0.0002114068 (±0.0032963555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions375375375
Spacing375375375
CellA=B=C: 393.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51125_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: One of the 2 half maps obtained from...

Fileemd_51125_half_map_1.map
AnnotationOne of the 2 half maps obtained from the 3D refinement procedure. The pixel size (1.07) here is the nominal one. The box size of this half map, 600 pixels, is not trimmed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: One of the 2 half maps obtained from...

Fileemd_51125_half_map_2.map
AnnotationOne of the 2 half maps obtained from the 3D refinement procedure. The pixel size (1.07) here is the nominal one. The box size of this half map, 600 pixels, is not trimmed.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Respiratory supercomplex CI1-CIII2-CIV2 -(cbb3)1 from alphaproteo...

EntireName: Respiratory supercomplex CI1-CIII2-CIV2 -(cbb3)1 from alphaproteobacterium
Components
  • Complex: Respiratory supercomplex CI1-CIII2-CIV2 -(cbb3)1 from alphaproteobacterium
    • Complex: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)
      • Protein or peptide: NADH-quinone oxidoreductase subunit A
      • Protein or peptide: NADH-quinone oxidoreductase subunit B
      • Protein or peptide: NADH-quinone oxidoreductase subunit C
      • Protein or peptide: NADH-quinone oxidoreductase subunit D
      • Protein or peptide: NADH dehydrogenase subunit E
      • Protein or peptide: NADH-quinone oxidoreductase subunit F
      • Protein or peptide: NADH-quinone oxidoreductase
      • Protein or peptide: NADH-quinone oxidoreductase subunit H
      • Protein or peptide: NADH-quinone oxidoreductase subunit I
      • Protein or peptide: NADH-quinone oxidoreductase subunit J
      • Protein or peptide: NADH-quinone oxidoreductase subunit K
      • Protein or peptide: NADH dehydrogenase subunit L
      • Protein or peptide: NADH dehydrogenase subunit M
      • Protein or peptide: NADH-quinone oxidoreductase subunit N
      • Protein or peptide: NAD-dependent epimerase/dehydratase
      • Protein or peptide: ETC complex I subunit conserved region
      • Protein or peptide: Zinc finger CHCC-type domain-containing protein
      • Protein or peptide: Protein-L-isoaspartate O-methyltransferase
      • Protein or peptide: NADH:ubiquinone oxidoreductase 17.2 kD subunit
    • Complex: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)
      • Protein or peptide: Cytochrome c oxidase subunit 1
      • Protein or peptide: Cytochrome c oxidase subunit 2
      • Protein or peptide: cytochrome-c oxidase
      • Protein or peptide: Aa3 type cytochrome c oxidase subunit IV
    • Complex: Transmembrane-anchored cytochrome c (c552)
      • Protein or peptide: Cytochrome c, class I
    • Complex: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)
      • Protein or peptide: Cytochrome b
      • Protein or peptide: Cytochrome c1
      • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
    • Complex: Alphaproteobacterial respiratory complex cbb3-oxidase
      • Protein or peptide: cytochrome-c oxidase
      • Protein or peptide: Cytochrome c oxidase, cbb3-type, subunit II
      • Protein or peptide: Cbb3-type cytochrome c oxidase subunit CcoP
    • Complex: Interfacial transmembrane helices between CIII and cbb3-oxidase
      • Protein or peptide: Transmembrane helix of unknown identity
      • Protein or peptide: Transmembrane helix of unknown identity
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: SODIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
  • Ligand: UBIQUINONE-10
  • Ligand: ZINC ION
  • Ligand: CARDIOLIPIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CALCIUM ION
  • Ligand: HEME C
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MANGANESE (II) ION
  • Ligand: DINUCLEAR COPPER ION

+
Supramolecule #1: Respiratory supercomplex CI1-CIII2-CIV2 -(cbb3)1 from alphaproteo...

SupramoleculeName: Respiratory supercomplex CI1-CIII2-CIV2 -(cbb3)1 from alphaproteobacterium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Supramolecule #2: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxido...

SupramoleculeName: Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#18, #27
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Supramolecule #3: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase...

SupramoleculeName: Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #22-#25
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Supramolecule #4: Transmembrane-anchored cytochrome c (c552)

SupramoleculeName: Transmembrane-anchored cytochrome c (c552) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #26
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Supramolecule #5: Alphaproteobacterial respiratory complex III (ubiquinone-cytochro...

SupramoleculeName: Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #19-#21
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Supramolecule #6: Alphaproteobacterial respiratory complex cbb3-oxidase

SupramoleculeName: Alphaproteobacterial respiratory complex cbb3-oxidase / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #30-#32
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Supramolecule #7: Interfacial transmembrane helices between CIII and cbb3-oxidase

SupramoleculeName: Interfacial transmembrane helices between CIII and cbb3-oxidase
type: complex / ID: 7 / Parent: 1 / Macromolecule list: #28-#29
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

+
Macromolecule #1: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 13.686093 KDa
SequenceString:
(FME)EYLLQEYLP ILVFLGMASA LAIVLILAAA VIAVRNPDPE KVSAYECGFN AFDDARMKFD VRFYLVSILF IIFDLE VAF LFPWAVSFAS LSDVAFWGMM VFLAVLTVGF AYEWKKGALE WA

UniProtKB: NADH-quinone oxidoreductase subunit A

+
Macromolecule #2: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 19.525543 KDa
SequenceString:
MMTGLNTAGA DRDLATAELN RELQDKGFLL TTTEDIINWA RNGSLHWMTF GLACCAVEMM QTSMPRYDLE RFGTAPRASP RQSDLMIVA GTLTNKMAPA LRKVYDQMPE PRYVISMGSC ANGGGYYHYS YSVVRGCDRI VPVDIYVPGC PPTAEALLYG I LQLQRRIR RTGTLVR

UniProtKB: NADH-quinone oxidoreductase subunit B

+
Macromolecule #3: NADH-quinone oxidoreductase subunit C

MacromoleculeName: NADH-quinone oxidoreductase subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 23.920102 KDa
SequenceString: MSEALSDEAL LELAEHIALR RENDVISTQV AFGELTVNAT LSGVIGLIEF LRNDPNCRFS TLIDITAVDN PARPARFDVV YHLLSMYQN QRIRVKVQVR EDELVPSLIG VFPGANWYER EVFDLFGILF SGHSDLRRIL TDYGFRGHPL RKDFPTTGYV E VRWSDIEK ...String:
MSEALSDEAL LELAEHIALR RENDVISTQV AFGELTVNAT LSGVIGLIEF LRNDPNCRFS TLIDITAVDN PARPARFDVV YHLLSMYQN QRIRVKVQVR EDELVPSLIG VFPGANWYER EVFDLFGILF SGHSDLRRIL TDYGFRGHPL RKDFPTTGYV E VRWSDIEK RVVYEPVNLV QEYRQFDFLS PWEGAKYVLP GDEKAPEAKK

UniProtKB: NADH-quinone oxidoreductase subunit C

+
Macromolecule #4: NADH-quinone oxidoreductase subunit D

MacromoleculeName: NADH-quinone oxidoreductase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 46.811484 KDa
SequenceString: MDGDIRKNSY DDGSMDALTG EQSIRNFNIN FGPQHPAAHG VLRMVLELDG EIVERADPHI GLLH(2MR)GTEKL MESRTY LQN LPYLDRLDYV APMNQEHAWC LAIERLTGTV IPRRASLIRV LYSEIGRILN HLMGVTTGAM DVGALTPPLW GFEAREE LM IFYERACGAR ...String:
MDGDIRKNSY DDGSMDALTG EQSIRNFNIN FGPQHPAAHG VLRMVLELDG EIVERADPHI GLLH(2MR)GTEKL MESRTY LQN LPYLDRLDYV APMNQEHAWC LAIERLTGTV IPRRASLIRV LYSEIGRILN HLMGVTTGAM DVGALTPPLW GFEAREE LM IFYERACGAR LHAAYFRPGG VHQDLPPDLL DDIEEWCERF PKLVDDLDTL LTENRIFKQR LVDIGIVTEA DALDWGYT G VMVRGSGLAW DLRRSQPYEC YDEFDFQIPV GRNGDCYDRY LCRMAEMRES CKIMQQAVQK LRAEPAGDVL ARGKLTPPR RAEMKRDMES LIHHFKLYTE GFKVPAGEVY AAVEAPKGEF GVYLVADGTN KPWRAKLRAP GFAHLQSIDW MSRGHMLADV PAIIATLDI VFGEVDR

UniProtKB: NADH-quinone oxidoreductase subunit D

+
Macromolecule #5: NADH dehydrogenase subunit E

MacromoleculeName: NADH dehydrogenase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 26.145865 KDa
SequenceString: MLRRLSPIQP DSFEFTPANL EWARAQMTKY PEGRQQSAII PVLWRAQEQE GWLSRPAIEY CADLLGMPYI RALEVATFYF MFQLQPVGS VAHIQICGTT TCMICGAEDL IRVCKEKIAP EPHALSADGR FSWEEVECLG ACTNAPMAQI GKDFYEDLTV E KLAALIDR ...String:
MLRRLSPIQP DSFEFTPANL EWARAQMTKY PEGRQQSAII PVLWRAQEQE GWLSRPAIEY CADLLGMPYI RALEVATFYF MFQLQPVGS VAHIQICGTT TCMICGAEDL IRVCKEKIAP EPHALSADGR FSWEEVECLG ACTNAPMAQI GKDFYEDLTV E KLAALIDR FAAGEVPVPG PQNGRFSAEA LGGPTALADL KGGEAHNASV ARALRLGDSI KRIDGTEVPI TTPWLATQNG V

UniProtKB: NADH dehydrogenase subunit E

+
Macromolecule #6: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 47.281141 KDa
SequenceString: MLNDQDRIFT NLYGMGDRSL AGAKKRGHWD GTAAIIQRGR DKIIDEMKAS GLRGRGGAGF PTGMKWSFMP KESDGRPSYL VINADESEP ATCKDREIMR HDPHTLIEGA LIASFAMGAH AAYIYIRGEF IREREALQAA IDECYDAGLL GRNAAGSGWD F DLYLHHGA ...String:
MLNDQDRIFT NLYGMGDRSL AGAKKRGHWD GTAAIIQRGR DKIIDEMKAS GLRGRGGAGF PTGMKWSFMP KESDGRPSYL VINADESEP ATCKDREIMR HDPHTLIEGA LIASFAMGAH AAYIYIRGEF IREREALQAA IDECYDAGLL GRNAAGSGWD F DLYLHHGA GAYICGEETA LLESLEGKKG MPRMKPPFPA GAGLYGCPTT VNNVESIAVV PTILRRGAEW FASFGRPNNA GV KLFGLTG HVNTPCVVEE AMSIPMRELI EKHGGGIRGG WKNLKAVIPG GASCPVLTAE QCENAIMDYD GMRELRSSFG TAC MIVMDQ STDVVKAIWR LSKFFKHESC GQCTPCREGT GWMMRVMERL VRGDAEVEEI DMLFDVTKQV EGHTICALGD AAAW PIQGL IRNFREEIED RIKAKRTGRM GAMAAE

UniProtKB: NADH-quinone oxidoreductase subunit F

+
Macromolecule #7: NADH-quinone oxidoreductase

MacromoleculeName: NADH-quinone oxidoreductase / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 73.289398 KDa
SequenceString: MADLRKIKID DTIIEVDPNM TLIQACEMAG IEVPRFCYHE RLSIAGNCRM CLVEVVGGPP KPAASCAMQV KDLRPGPEGA PSEIRTNSP MVKKAREGVM EFLLINHPLD CPICDQGGEC DLQDQAMAYG VDFSRYREPK RATEDLNLGP LVETHMTRCI S CTRCVRFT ...String:
MADLRKIKID DTIIEVDPNM TLIQACEMAG IEVPRFCYHE RLSIAGNCRM CLVEVVGGPP KPAASCAMQV KDLRPGPEGA PSEIRTNSP MVKKAREGVM EFLLINHPLD CPICDQGGEC DLQDQAMAYG VDFSRYREPK RATEDLNLGP LVETHMTRCI S CTRCVRFT TEVAGITQMG QTGRGEDSEI TSYLNQTLES NMQGNIIDLC PVGALVSKPY AFTARPWELT KTESIDVMDA LG SSIRIDT KGREVMRILP RNHDGVNEEW ISDKTRFVWD GLRRQRLDRP YIRENGRLRP ASWPEALEAA ARAMKGKKIA GLI GDLVPA EAAFSLKQLV EGLGGKVECR VDGARLPAGN RSAYVGTARI EDIDDAEMIQ LIGTNPRDEA PVLNARIRKA WSKG AKVGL VGEPVDLTYD YAHVGTDRAA LESLSSREIS DETKARPSIV IVGQGAIREA DGEAVLAHAM KLAENSNSGL LILHT AAGR VGAMDVGAVT EGGLLAAIDG AEVVYNLGAD EVDIDQGPFV IYQGSHGDRG AHRADIILPG ACYTEESGLF VNTEGR PQL AMRANFAPGE GKENWAILRA LSAELGATQP WDSLAGLRRK LVEAVPHLAQ IDQVPQNEWQ PLGRFDLGQA SFRYAIR DF YLTNPIARSS PLMGELSAMA AARKAPAPLA AE

UniProtKB: NADH-quinone oxidoreductase

+
Macromolecule #8: NADH-quinone oxidoreductase subunit H

MacromoleculeName: NADH-quinone oxidoreductase subunit H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 38.861152 KDa
SequenceString: MAEFWASPYG FALSMLLQGL AVIAFVMGSL IFMVYGDRKI WAAVQMRRGP NVVGPWGLLQ TFADALKYIV KEIVIPAGAD KFVYFLAPF LSMMLALFAF VVIPFDEGWV MANINVGILF IFAASSLEVY GVIMGGWASN SKYPFLASLR SAAQMISYEV S LGLIIIGI ...String:
MAEFWASPYG FALSMLLQGL AVIAFVMGSL IFMVYGDRKI WAAVQMRRGP NVVGPWGLLQ TFADALKYIV KEIVIPAGAD KFVYFLAPF LSMMLALFAF VVIPFDEGWV MANINVGILF IFAASSLEVY GVIMGGWASN SKYPFLASLR SAAQMISYEV S LGLIIIGI IISTGSMNLT AIVEAQRGDY GLLNWYWLPH LPMVVLFFVS ALAECNRPPF DLVEAESELV AGFMTEYSST PY LLFMAGE YIAMYLMCAL LSLLFFGGWL SPVPFIADGW WWMVIKMWFW FYMFAMVKAI VPRYRYDQLM RIGWKVFLPL SLG WVVLVA ILARYEILGG FWARFAVGG

UniProtKB: NADH-quinone oxidoreductase subunit H

+
Macromolecule #9: NADH-quinone oxidoreductase subunit I

MacromoleculeName: NADH-quinone oxidoreductase subunit I / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 18.925561 KDa
SequenceString:
MAFDFARATK YFLMWDFIKG FGLGMRYFVS PKPTLNYPHE KGPLSPRFRG EHALRRYPNG EERCIACKLC EAVCPAQAIT IDAEPREDG SRRTTRYDID MTKCIYCGFC QEACPVDAIV EGPNFEYATE TREELFYDKQ KLLANGERWE AEIARNLQLD A PYR

UniProtKB: NADH-quinone oxidoreductase subunit I

+
Macromolecule #10: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 21.73202 KDa
SequenceString: (FME)TFAFYLFAI SACVAGFMVV IGRNPVHSVL WLILAFLSAA GLFVLQGAEF VAMLLVVVYV GAVAVLFLFV VMMLDV DFA ELKGELARYL PLALVIGVVL LAQLGIAFSG WTPSDQAESL RAAPVDAAVE NTLGLGLVLY DRYVLMFQLA GLVLLVA MI GAIVLTMRHR ...String:
(FME)TFAFYLFAI SACVAGFMVV IGRNPVHSVL WLILAFLSAA GLFVLQGAEF VAMLLVVVYV GAVAVLFLFV VMMLDV DFA ELKGELARYL PLALVIGVVL LAQLGIAFSG WTPSDQAESL RAAPVDAAVE NTLGLGLVLY DRYVLMFQLA GLVLLVA MI GAIVLTMRHR KDVKRQNVLE QMWRDPAKTM ELKDVKPGQG L

UniProtKB: NADH-quinone oxidoreductase subunit J

+
Macromolecule #11: NADH-quinone oxidoreductase subunit K

MacromoleculeName: NADH-quinone oxidoreductase subunit K / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 10.863054 KDa
SequenceString:
MIGLTHYLVV GAILFVTGIF GIFVNRKNVI VILMSIELML LAVNINFVAF STHLGDLAGQ VFTMFVLTVA AAEAAIGLAI LVVFFRNRG TIAVEDVNVM KG

UniProtKB: NADH-quinone oxidoreductase subunit K

+
Macromolecule #12: NADH dehydrogenase subunit L

MacromoleculeName: NADH dehydrogenase subunit L / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 77.839367 KDa
SequenceString: (FME)EKFVLFAPL IASLIAGLGW RAIGEKAAQY LTTGVLFLSC LISWYLFLSF DGVPRHIPVL DWVVTGDFHA EWAIRL DRL TAIMLIVVTT VSALVHMYSL GYMAHDDNWT HDEHYKARFF AYLSFFTFAM LMLVTADNLL QMFFGWEGVG VASYLLI GF YYKKASANAA ...String:
(FME)EKFVLFAPL IASLIAGLGW RAIGEKAAQY LTTGVLFLSC LISWYLFLSF DGVPRHIPVL DWVVTGDFHA EWAIRL DRL TAIMLIVVTT VSALVHMYSL GYMAHDDNWT HDEHYKARFF AYLSFFTFAM LMLVTADNLL QMFFGWEGVG VASYLLI GF YYKKASANAA AMKAFIVNRV GDFGFLLGIF GIYWLTGSVQ FDEIFRQVPQ LAQTEMHFLW RDWNAANLLG FLLFVGAM G KSAQLLLHTW LPDAMEGPTP VSALIHAATM VTAGVFLVCR MSPLYEFAPD AKNFIVIIGA TTAFFAATVG LVQNDIKRV IAYSTCSQLG YMFVAAGVGV YSAAMFHLLT HAFFKAMLFL GAGSVIHAMH HEQDMRNYGG LRKKIPLTFW AMMIGTFAIT GVGIPLTHL GFAGFLSKDA IIESAYAGSG YAFWLLVIAA CFTSFYSWRL IFLTFYGKPR GDHHAHDHAH ESPPVMTIPL G VLAIGAVF AGMVWYGPFF GDHHKVTEYF HIAGAHHEAA EGEEAEHATA EAPVEHAVAD TATAEGEAAA EAEHAEIAAP VG GAIYMHP DNHIMDEAHH APAWVKVSPF VAMVLGLITA WTFYIANPSL PRRLAAQQPA LYRFLLNKWY FDEIYEFIFV RPA KWLGRV LWKGGDGAVI DGTINGVAMG LIPRLTRAAV RVQSGYLFHY AFAMVLGIVG LLIWVMMRGA H

UniProtKB: NADH dehydrogenase subunit L

+
Macromolecule #13: NADH dehydrogenase subunit M

MacromoleculeName: NADH dehydrogenase subunit M / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 56.547914 KDa
SequenceString: (FME)TNLLSIITF LPIVAAIIMA LFLRGQDEAA ARNAKWLALL TTTATFVISL FVLFRFDPAN TGFQFVEDHA WIMGLR YKM GVDGISVLFV LLTTFMMPLT ILSTWQVQDK VKEYMIAFLV LEGLMIGVFT ALDLVLFYLF FEAGLIPMFL IIGIWGG KD RIYASFKFFL ...String:
(FME)TNLLSIITF LPIVAAIIMA LFLRGQDEAA ARNAKWLALL TTTATFVISL FVLFRFDPAN TGFQFVEDHA WIMGLR YKM GVDGISVLFV LLTTFMMPLT ILSTWQVQDK VKEYMIAFLV LEGLMIGVFT ALDLVLFYLF FEAGLIPMFL IIGIWGG KD RIYASFKFFL YTFLGSVLML VAMIAMYRMA GTTDIPTLLT FDFPSENFRL LGMTVVGGMQ MLLFLAFFAS FAVKMPMW P VHTWLPDAHV QAPTAGSVLL AAVLLKMGGY GFLRFSLPMF PVASGVAQPY VFWLSAIAIV YTSLVALAQS DMKKVIAYS SVAHMGYVTM GVFAANQIGV DGAIFQMLSH GFISGALFLC VGVIYDRMHT REIDAYGGLV NRMPAYAAVF MFFTMANVGL PGTSGFVGE FLTLMGVFRV DTWVALVATS GVILSAAYAL WLYRRVTLGQ LIKESLKSIT DMTPRERWVF IPLIAMTLIL G VYPRLVTD VTGPAVAALV QDYNQSQPAA PVATAQASH

UniProtKB: NADH dehydrogenase subunit M

+
Macromolecule #14: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 52.56482 KDa
SequenceString: MTSLDFSTIL PEVVLAGYAL AALMAGAYLG KDRLARTLLW VTVAAFLVVA AMVGLGNHVD GAAFHGMFID DGFSRFAKVV TLVAAAGVL AMSADYMQRR NMLRFEFPII VALAVLGMMF MVSAGDLLTL YMGLELQSLA LYVVAAMRRD SVRSSEAGLK Y FVLGSLSS ...String:
MTSLDFSTIL PEVVLAGYAL AALMAGAYLG KDRLARTLLW VTVAAFLVVA AMVGLGNHVD GAAFHGMFID DGFSRFAKVV TLVAAAGVL AMSADYMQRR NMLRFEFPII VALAVLGMMF MVSAGDLLTL YMGLELQSLA LYVVAAMRRD SVRSSEAGLK Y FVLGSLSS GLLLYGASLV YGFAGTTGFE GIISTIEAGH LSLGVLFGLV FMLVGLSFKV SAVPFHMWTP DVYEGSPTPV TA FFATAPK VAAMALIARL VFDAFGHVIG DWSQIVAALA VMSMFLGSIA GIGQTNIKRL MAYSSIAHMG FALVGLAAGT AIG VQNMLL YMTIYAVMNI GTFAFILSME RDGVPVTDLA ALNRFAWTDP VKALAMLVLM FSLAGVPPTL GFFAKFGVLT AAVD AGMGW LAVLGVIASV IGAFYYLRIV YYMYFGGESE GMTSRMGAVQ YLALMVPALA MLVGAISMFG VDSAAGRAAE TLVGP VAAI EQPAEAAQAE PVQGE

UniProtKB: NADH-quinone oxidoreductase subunit N

+
Macromolecule #15: NAD-dependent epimerase/dehydratase

MacromoleculeName: NAD-dependent epimerase/dehydratase / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 35.386566 KDa
SequenceString: MSAAKLVTIY GGSGFLGRQI ARTMAAQGWR IRVAVRRPNE AGVVRTYGAP GQVEPVPCNV RDDLSVTACM ADADAVINCV GIMVREGKN TFDAIHEEAA GRIARIAAET GVKRFVHVSA IGADPDSASR YAASKGRGEA AVLAHRPDAM ILRPSVIFGP D DHFYNRIA ...String:
MSAAKLVTIY GGSGFLGRQI ARTMAAQGWR IRVAVRRPNE AGVVRTYGAP GQVEPVPCNV RDDLSVTACM ADADAVINCV GIMVREGKN TFDAIHEEAA GRIARIAAET GVKRFVHVSA IGADPDSASR YAASKGRGEA AVLAHRPDAM ILRPSVIFGP D DHFYNRIA SMTRLGPILF VPGANTLMQP VYVEDVARAA AMGAEGTAQP GIYELGGPDM LTMREVAQQV LVAIDRRRAI VG LPHWLAR VTGSALDLVQ AATGGLLTNR ILTRDQARLL RLPNRVSGEV KTFADLDIEP TAAPAVIADY LWRFRSSGQY EAI TASAKN LRNS

UniProtKB: NAD-dependent epimerase/dehydratase

+
Macromolecule #16: ETC complex I subunit conserved region

MacromoleculeName: ETC complex I subunit conserved region / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 12.048399 KDa
SequenceString:
MRVRIYKPAR NAMQSGTART RNWVLDFPPA DPRAIDPLMG WTSSDDTQSQ VRLRFETRKQ AEDYAREHGL DYEVIEPHTR AANIRPRGY GENFASDRRA PWTH

UniProtKB: ETC complex I subunit conserved region

+
Macromolecule #17: Zinc finger CHCC-type domain-containing protein

MacromoleculeName: Zinc finger CHCC-type domain-containing protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 7.069931 KDa
SequenceString:
MTIPAPEIQT VTSWKVACDG DEARGLGHPR VWLAIPRDTG WVECGYCDKR FVIDREHAHD DH

UniProtKB: Zinc finger CHCC-type domain-containing protein

+
Macromolecule #18: Protein-L-isoaspartate O-methyltransferase

MacromoleculeName: Protein-L-isoaspartate O-methyltransferase / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 23.528947 KDa
SequenceString: MTDFAQRRTM MVDTQVRPNE VTSYPVIEAM LNVPREQFVP ESRRDVAYVG NNIDLAPGRV LLEPRTLGKM MDILNLQNGD LVLDVGCGY GYSAAVMARI AEAVVAVEED AAMAAEAEGR LAAQDVFNVA VVQGALAEGC PGQAPYDAIL IEGAVEQVPE A LTEQLREG ...String:
MTDFAQRRTM MVDTQVRPNE VTSYPVIEAM LNVPREQFVP ESRRDVAYVG NNIDLAPGRV LLEPRTLGKM MDILNLQNGD LVLDVGCGY GYSAAVMARI AEAVVAVEED AAMAAEAEGR LAAQDVFNVA VVQGALAEGC PGQAPYDAIL IEGAVEQVPE A LTEQLREG GRIVALFREG NLGIVRLGHK LDGRVNWRFA FNAVAPLLPG FARPRGFVL

UniProtKB: Protein-L-isoaspartate O-methyltransferase

+
Macromolecule #19: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 50.154727 KDa
SequenceString: MAGIPHDHYE PKTGFERWLH RRLPIVSLVY DTLMIPTPKN LNWWWIWGIV LAFCLVLQIA TGIVLVMHYT PHVDLAFASV EHIMRDVNG GYMLRYLHAN GASLFFLAVY IHIFRGLYYG SYKAPREVTW IVGMLIYLMM MGTAFMGYVL PWGQMSFWGA T VITGLFGA ...String:
MAGIPHDHYE PKTGFERWLH RRLPIVSLVY DTLMIPTPKN LNWWWIWGIV LAFCLVLQIA TGIVLVMHYT PHVDLAFASV EHIMRDVNG GYMLRYLHAN GASLFFLAVY IHIFRGLYYG SYKAPREVTW IVGMLIYLMM MGTAFMGYVL PWGQMSFWGA T VITGLFGA IPGVGEAIQT WLLGGPAVDN PTLNRFFSLH YLLPFVIAAL VVVHIWAFHT TGNNNPTGVE VRRGSKEEAK KD TLPFWPY FVIKDLFALA VVLVVFFAIV GFMPNYLGHP DNYIEANPLV TPAHIVPEWY FLPFYAILRA FTADVWVVML VNW LSFGII DAKFFGVIAM FGAILVMALV PWLDTSRVRS GQYRPLFKWW FWLLAVDFVV LMWVGAMPAE GIYPYIALAG SAYW FAYFL IILPLLGIIE KPDAMPQTIE EDFNAHYGPE THPAE

UniProtKB: Cytochrome b

+
Macromolecule #20: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 46.904332 KDa
SequenceString: MTLRNASLTA VAALTVALAG GAVAQDASTA PGTTAPAGSS YHTNEAAPAA ADTAPAAEAA DEPAAEEAEA GEAEVTEEPA ATETPAEEP AADEPAATEE PDAEAEPAAE EAQATTEEAP AEEPAAEEPA AEEPAEEPAA DAPAEEAAAE EAPAEPEAAA E EPAAEEPE ...String:
MTLRNASLTA VAALTVALAG GAVAQDASTA PGTTAPAGSS YHTNEAAPAA ADTAPAAEAA DEPAAEEAEA GEAEVTEEPA ATETPAEEP AADEPAATEE PDAEAEPAAE EAQATTEEAP AEEPAAEEPA AEEPAEEPAA DAPAEEAAAE EAPAEPEAAA E EPAAEEPE ATEEEAPAEE AAAEEAPAEE VVEDEAAADH GDAAAQEAGD SHAAAHIEDI SFSFEGPFGK FDQHQLQRGL QV YTEVCSA CHGLRYVPLR TLADEGGPQL PEDQVRAYAA NFDITDPETE EDRPRVPTDH FPTVSGEGMG PDLSLMAKAR AGF HGPYGT GLSQLFNGIG GPEYIHAVLT GYDGEEKEEA GAVLYHNAAF AGNWIQMAAP LSDDQVTYED GTPATVDQMA TDVA AFLMW TAEPKMMDRK QVGFVSVIFL IVLAALLYLT NKKLWQPIKH PRKPE

UniProtKB: Cytochrome c1

+
Macromolecule #21: Ubiquinol-cytochrome c reductase iron-sulfur subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 20.889236 KDa
SequenceString: MEIKPVSHAD EHAGDHGATR RDFLYYATAG AGTVAAGAAA WTLVNQMNPS ADVQALASIQ VDVSGVETGT QLTVKWLGKP VFIRRRTED EIQAGREVDL GQLIDRSAQN SNKPDAPATD ENRTMDEAGE WLVMIGVCTH LGCVPIGDGA GDFGGWFCPC H GSHYDTSG ...String:
MEIKPVSHAD EHAGDHGATR RDFLYYATAG AGTVAAGAAA WTLVNQMNPS ADVQALASIQ VDVSGVETGT QLTVKWLGKP VFIRRRTED EIQAGREVDL GQLIDRSAQN SNKPDAPATD ENRTMDEAGE WLVMIGVCTH LGCVPIGDGA GDFGGWFCPC H GSHYDTSG RIRRGPAPQN LHIPVAEFLD DTTIKLG

UniProtKB: Ubiquinol-cytochrome c reductase iron-sulfur subunit

+
Macromolecule #22: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 62.486645 KDa
SequenceString: MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNV MITYHGVLMM FFVVIPALFG GFGNYFMPLH IGAPDMAFPR LNNLSYWMYV CGVALGVASL LAPGGNDQMG S GVGWVLYP ...String:
MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNV MITYHGVLMM FFVVIPALFG GFGNYFMPLH IGAPDMAFPR LNNLSYWMYV CGVALGVASL LAPGGNDQMG S GVGWVLYP PLSTTEAGYS MDLAIFAVHV SGASSILGAI NIITTFLNMR APGMTLFKVP LFAWSVFITA WLILLSLPVL AG AITMLLM DRNFGTQFFD PAGGGDPVLY QHILWFFGHP EVYIIILPGF GIISHVISTF AKKPIFGYLP MVLAMAAIGI LGF VVWAHH MYTAGMSLTQ QAYFMLATMT IAVPTGIKVF SWIATMWGGS IEFKTPMLWA FGFLFLFTVG GVTGVVLSQA PLDR VYHDT YYVVAHFHYV MSLGAVFGIF AGVYYWIGKM SGRQYPEWAG QLHFWMMFIG SNLIFFPQHF LGRQGMPRRY IDYPV EFAY WNNISSIGAY ISFASFLFFI GIVFYTLFAG KRVNVPNYWN EHADTLEWTL PSPPPEHTFE TLPKREDWDR AHAH

UniProtKB: Cytochrome c oxidase subunit 1

+
Macromolecule #23: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 32.563643 KDa
SequenceString: MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ QWLDHFVLYI ITAVTIFVCL LLLICIVRF NRRANPVPAR FTHNTPIEVI WTLVPVLILV AIGAFSLPIL FRSQEMPNDP DLVIKAIGHQ WYWSYEYPND G VAFDALML ...String:
MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ QWLDHFVLYI ITAVTIFVCL LLLICIVRF NRRANPVPAR FTHNTPIEVI WTLVPVLILV AIGAFSLPIL FRSQEMPNDP DLVIKAIGHQ WYWSYEYPND G VAFDALML EKEALADAGY SEDEYLLATD NPVVVPVGKK VLVQVTATDV IHAWTIPAFA VKQDAVPGRI AQLWFSVDQE GV YFGQCSE LCGINHAYMP IVVKAVSQEK YEAWLAGAKE EFAADASDYL PASPVKLASA E

UniProtKB: Cytochrome c oxidase subunit 2

+
Macromolecule #24: cytochrome-c oxidase

MacromoleculeName: cytochrome-c oxidase / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 30.833162 KDa
SequenceString: MAHVKNHDYQ ILPPSIWPFF GAIGAFVMLT GAVAWMKGIT FFGLPVEGPW MFLIGLVGVL YVMFGWWADV VNEGETGEHT PVVRIGLQY GFILFIMSEV MFFVAWFWAF IKNALYPMGP DSPIKDGVWP PEGIVTFDPW HLPLINTLIL LLSGVAVTWA H HAFVHEGD ...String:
MAHVKNHDYQ ILPPSIWPFF GAIGAFVMLT GAVAWMKGIT FFGLPVEGPW MFLIGLVGVL YVMFGWWADV VNEGETGEHT PVVRIGLQY GFILFIMSEV MFFVAWFWAF IKNALYPMGP DSPIKDGVWP PEGIVTFDPW HLPLINTLIL LLSGVAVTWA H HAFVHEGD RKTTINGLIV AVILGVCFTG LQAYEYSHAA FGLADTVYAG AFYMATGFHG AHVIIGTIFL FVCLIRLLKG QM TQKQHVG FEAAAWYWHF VDVVWLFLFV VIYIWGR

UniProtKB: Cytochrome c oxidase subunit 3

+
Macromolecule #25: Aa3 type cytochrome c oxidase subunit IV

MacromoleculeName: Aa3 type cytochrome c oxidase subunit IV / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 7.351497 KDa
SequenceString:
MGYPCARRIA SFTDRIMASH HEITDHKHGE MDIRHQQATF AGFIKGATWV SILSIAVLVF LALANS

UniProtKB: Aa3 type cytochrome c oxidase subunit IV

+
Macromolecule #26: Cytochrome c, class I

MacromoleculeName: Cytochrome c, class I / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 18.177406 KDa
SequenceString:
MFDTMTVTKA AGALIGSLLF LLLMSWAASG IFHVGTSGHG AEGEEHAQAY TIPVESAGGA EGEAVDEGPD FATVLASADP AAGEKVFGK CKACHKLDGN DGVGPHLNGV VGRTVAGVDG FNYSDPMKAH GGDWTPEALQ EFLTNPKAVV KGTKMAFAGL P KIEDRANL IAYLEGQQ

UniProtKB: Cytochrome c, class I

+
Macromolecule #27: NADH:ubiquinone oxidoreductase 17.2 kD subunit

MacromoleculeName: NADH:ubiquinone oxidoreductase 17.2 kD subunit / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 14.460885 KDa
SequenceString:
(FME)SFLLRFLTW WNSQTLNTQV WTKLYGEKVG EDDQGNVYYQ SGGGKRRWVI YNGESEASRI SPEWHGWLHH TYKEPP TAA PLAHKPWEKP HEPNLTGSSG AYHPAGSLYR AQPVERRDYD AWQPE

UniProtKB: NADH:ubiquinone oxidoreductase 17.2 kD subunit

+
Macromolecule #28: Transmembrane helix of unknown identity

MacromoleculeName: Transmembrane helix of unknown identity / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 2.996685 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)

+
Macromolecule #29: Transmembrane helix of unknown identity

MacromoleculeName: Transmembrane helix of unknown identity / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 2.571161 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)

+
Macromolecule #30: cytochrome-c oxidase

MacromoleculeName: cytochrome-c oxidase / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 60.042113 KDa
SequenceString: MLDTIKLIAL GTIAVLAAIA ANYARPDDLA YLVNALIIML AAGIMFLRVL RQMGNEQPAL EPHPETQYMD DVVRAGVIAT AFWGVVGFL VGVVIAFQLA FPALNLSDIT MGYTNFGKLR PLHTSAVIFA FGGNALIATS FYVVQRTSAA RLWGGNAAWF V FWGYQLFI ...String:
MLDTIKLIAL GTIAVLAAIA ANYARPDDLA YLVNALIIML AAGIMFLRVL RQMGNEQPAL EPHPETQYMD DVVRAGVIAT AFWGVVGFL VGVVIAFQLA FPALNLSDIT MGYTNFGKLR PLHTSAVIFA FGGNALIATS FYVVQRTSAA RLWGGNAAWF V FWGYQLFI VLAATGYILG ATQSKEYAEP EWYVDWWLTV VWVVYLAVFL GTILKRKEPH IYVANWFYLS FIVTIAMLHI VN NLAIPVS LFGSKSVQLF SGVQDAMTQW WYGHNAVGFF LTAGFLGMMY YFIPKQAERP VYSYKLSIIH FWALIFLYIW AGP HHLHYT ALPDWASTLG MVFSIILWMP SWGGMINGLM TLSGAWDKLR TDPIIRMMVV AVGFYGMATF EGPMMSIKAV NSLS HYTDW TIGHVHSGAL GWNGMITFGA LYYLVPRLWG RERLYSTGLV SWHFWLATIG LVLYAASMWV SGIMEGLMWR EVDAQ GFLV NAFADTVAAK FPMNVVRALG GVLYLGGALI MCYNLWATVA KQPKTQSTAA AVPAE

UniProtKB: cytochrome-c oxidase

+
Macromolecule #31: Cytochrome c oxidase, cbb3-type, subunit II

MacromoleculeName: Cytochrome c oxidase, cbb3-type, subunit II / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 27.362098 KDa
SequenceString: MAILEKHKVL EKNATLLLVF SFLVVTIGGI VEIAPLFYLQ NTIEKVQGMR PYTPLELKGR DIYVREGCYV CHSQMIRPMR DEVERYGHY SLAAESMYDH PFQWGSKRTG PDLARVGGRY SDEWHLDHLV DPQAVVPESI MPKYGFLLNR QVDASNMQQR L KTDALVGV ...String:
MAILEKHKVL EKNATLLLVF SFLVVTIGGI VEIAPLFYLQ NTIEKVQGMR PYTPLELKGR DIYVREGCYV CHSQMIRPMR DEVERYGHY SLAAESMYDH PFQWGSKRTG PDLARVGGRY SDEWHLDHLV DPQAVVPESI MPKYGFLLNR QVDASNMQQR L KTDALVGV PYDDAMIAAA VEDFRAQADP DADASGLEER YPGAQQRNFD RRPGVSEMDA LIAYLQVLGT MVDFSTFEPD PN R

UniProtKB: Cytochrome c oxidase, cbb3-type, subunit II

+
Macromolecule #32: Cbb3-type cytochrome c oxidase subunit CcoP

MacromoleculeName: Cbb3-type cytochrome c oxidase subunit CcoP / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 37.597531 KDa
SequenceString: MADTDDEHAS PQNPDNRIEL ERQAADEAHK AKILAHPPEG PGGDPLHPPV TPRPGATRVV RDRKGGRRVV EVPSTGHSWD GIEEYDNPL PRWWLWTFYA TIVWGVLYLI AYPAIPLVNG ATQGLLGQNY RSDVAAEIQR FNEANAPIQA KLVETPLEEI A ADPELANY ...String:
MADTDDEHAS PQNPDNRIEL ERQAADEAHK AKILAHPPEG PGGDPLHPPV TPRPGATRVV RDRKGGRRVV EVPSTGHSWD GIEEYDNPL PRWWLWTFYA TIVWGVLYLI AYPAIPLVNG ATQGLLGQNY RSDVAAEIQR FNEANAPIQA KLVETPLEEI A ADPELANY TANAGAAIFR TWCAQCHGSG AGGATGYPSL LDNDWLWGGT LEEIHTTVMH GIRDPKDADT RYSEMPRFGI DG LLENAQI SQVVNHVLEL GGLPHDAALA AEGVEVFADN CSSCHAEDGT GDRAQGAPDL TDAVWLYGSD PATITRIVRD GPF GVMPAW TGRLSEADIV AVAAYVHSLG GGE

UniProtKB: Cbb3-type cytochrome c oxidase subunit CcoP

+
Macromolecule #33: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 33 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #34: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 34 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

+
Macromolecule #35: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 35 / Number of copies: 4 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #36: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 36 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

+
Macromolecule #37: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13...

MacromoleculeName: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
type: ligand / ID: 37 / Number of copies: 3 / Formula: DU0
Molecular weightTheoretical: 516.752 Da
Chemical component information

ChemComp-DU0:
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol

+
Macromolecule #38: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 38 / Number of copies: 5 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

+
Macromolecule #39: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 39 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #40: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 40 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

+
Macromolecule #41: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 41 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #42: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 42 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #43: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 43 / Number of copies: 5 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #44: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 44 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

+
Macromolecule #45: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 45 / Number of copies: 3 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

+
Macromolecule #46: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 46 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

+
Macromolecule #47: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 47 / Number of copies: 2 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4238
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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