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- PDB-1kb9: YEAST CYTOCHROME BC1 COMPLEX -

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Entry
Database: PDB / ID: 1kb9
TitleYEAST CYTOCHROME BC1 COMPLEX
Components
  • (UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ...) x 6
  • CYTOCHROME B
  • CYTOCHROME C1, HEME PROTEIN
  • HEAVY CHAIN (VH) OF FV-FRAGMENT
  • LIGHT CHAIN (VL) OF FV-FRAGMENT
  • UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / oxidoreductase / ubiquinone / stigmatellin / cardiolipin / phosphatidylinositol / phosphatidylcholin / phosphatidylethanolamin / undecyl-maltopyranoside / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / cellular respiration / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista ...matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / cellular respiration / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / metal ion binding / cytosol
Similarity search - Function
Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 ...Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 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 / 3-layer Sandwich / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / STIGMATELLIN A / Chem-UQ6 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / STIGMATELLIN A / Chem-UQ6 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLange, C. / Nett, J.H. / Trumpower, B.L. / Hunte, C.
Citation
Journal: EMBO J. / Year: 2001
Title: SPECIFIC ROLES OF PROTEIN-PHOSPHOLIPID INTERACTIONS IN THE YEAST CYTOCHROME BC1 COMPLEX STRUCTURE
Authors: Lange, C. / Nett, J.H. / Trumpower, B.L. / Hunte, C.
#1: Journal: Structure / Year: 2000
Title: Structure Of The Yeast Cytochrome Bc1 Complex Co-Crystallized With An Antibody Fv-Fragment
Authors: Hunte, C. / Koepke, J. / Lange, C. / Rossmanith, T. / Michel, H.
History
DepositionNov 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
B: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
C: CYTOCHROME B
D: CYTOCHROME C1, HEME PROTEIN
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
F: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
G: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
H: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
I: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
J: HEAVY CHAIN (VH) OF FV-FRAGMENT
K: LIGHT CHAIN (VL) OF FV-FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,22323
Polymers244,17611
Non-polymers8,04712
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.473, 163.921, 147.276
Angle α, β, γ (deg.)90.00, 117.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ... , 6 types, 6 molecules ABFGHI

#1: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I


Mass: 47445.242 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07256, quinol-cytochrome-c reductase
#2: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 38751.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07257, quinol-cytochrome-c reductase
#6: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN / MITOCHONDRIAL HINGE PROTEIN / COMPLEX III POLYPEPTIDE VI


Mass: 8854.792 Da / Num. of mol.: 1 / Fragment: RESIDUES 74-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P00127, quinol-cytochrome-c reductase
#7: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN / COMPLEX III SUBUNIT VII


Mass: 14355.443 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P00128, quinol-cytochrome-c reductase
#8: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN / COMPLEX III SUBUNIT VIII


Mass: 10856.314 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P08525, quinol-cytochrome-c reductase
#9: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN / COMPLEX III POLYPEPTIDE IX


Mass: 6301.232 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P22289, quinol-cytochrome-c reductase

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Protein , 3 types, 3 molecules CDE

#3: Protein CYTOCHROME B /


Mass: 43674.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P00163
#4: Protein CYTOCHROME C1, HEME PROTEIN /


Mass: 27521.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 62-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07143
#5: Protein UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / RIESKE IRON-SULFUR PROTEIN / RISP


Mass: 20122.955 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P08067, quinol-cytochrome-c reductase

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Antibody , 2 types, 2 molecules JK

#10: Antibody HEAVY CHAIN (VH) OF FV-FRAGMENT


Mass: 14365.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#11: Antibody LIGHT CHAIN (VL) OF FV-FRAGMENT


Mass: 11926.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83

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Non-polymers , 10 types, 333 molecules

#12: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Dipalmitoylphosphatidylcholine


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P
#13: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#14: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#15: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O7
#16: Chemical 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


Mass: 592.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H60O4
#17: Chemical ChemComp-PIE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL


Mass: 836.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H80O13P
#18: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#19: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#21: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 73.83 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8 / Details: PEG4000, pH 8, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Method: unknown / Details: Hunte, C., (2000) Structure, 8, 669.

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Data collection

DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→14.96 Å / Num. all: 168517 / Num. obs: 168517 / Observed criterion σ(F): 0 / Biso Wilson estimate: 31.9 Å2 / Limit h max: 82 / Limit h min: -93 / Limit k max: 71 / Limit k min: -93 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 3621196.32 / Observed criterion F min: 18.17
Reflection
*PLUS
Highest resolution: 2.3 Å

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.3→14.96 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4240 2.5 %RANDOM
Rwork0.218 ---
all-199019 --
obs-168517 84.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 38.6265 Å2 / ksol: 0.273859 e/Å3
Displacement parametersBiso max: 157.38 Å2 / Biso mean: 69.92 Å2 / Biso min: 20.92 Å2
Baniso -1Baniso -2Baniso -3
1--12.03 Å20 Å2-7.27 Å2
2--6.16 Å20 Å2
3---5.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.41 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17227 0 492 321 18040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23
X-RAY DIFFRACTIONx_torsion_impr_deg1.18
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.3434481.80.342174260.016248601787471.9
2.4-2.530.2934541.80.293185210.014248701897576.3
2.53-2.690.27150720.273194270.012248521993480.2
2.69-2.890.24649120.248200630.011248032055482.9
2.89-3.180.2355492.20.235208530.01248742140286
3.18-3.640.225322.10.218216890.01248912222189.3
3.64-4.560.1996392.60.196230340.008249452367394.9
4.56-14.960.196202.50.19232640.008250962388495.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2parhcsdx_iub.+lip_trun.bc1tophcsdx_iub.+lip_trun.bc1
X-RAY DIFFRACTION3water.1.paramwater_mod.1.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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