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- PDB-3cxh: Structure of yeast complex III with isoform-2 cytochrome c bound ... -

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Entry
Database: PDB / ID: 3cxh
TitleStructure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer.
Components
  • (Cytochrome b-c1 complex subunit ...) x 7
  • Cytochrome b
  • Cytochrome c iso-2
  • Cytochrome c1, heme protein, mitochondrial
  • HEAVY CHAIN (VH) OF FV-FRAGMENT
  • LIGHT CHAIN (VL) OF FV-FRAGMENT
KeywordsOXIDOREDUCTASE / COMPLEX III / CYTOCHROME C ISOFORM-2 / ELECTRON TRANSFER COMPLEX / CYTOCHROME BC1 COMPLEX / MITOCHONDRIALTRANSMEMBRANE COMPLEX / RESPIRATORY CHAIN / TRANSIENT PROTEIN-PROTEIN INTERACTION / Electron transport / Inner membrane / Mitochondrion / Transit peptide / Transport / Phosphoprotein / Heme / Iron / Metal-binding / Iron-sulfur
Function / homology
Function and homology information


matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / cellular respiration / quinol-cytochrome-c reductase ...matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / 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, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / respirasome / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity / 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 c, class IA/ IB / 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 / Cytochrome c / 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
sucrose / Chem-6PH / Chem-7PH / Chem-8PE / Chem-9PE / Chem-CN6 / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / STIGMATELLIN A / Cytochrome c isoform 2 ...sucrose / Chem-6PH / Chem-7PH / Chem-8PE / Chem-9PE / Chem-CN6 / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / STIGMATELLIN A / Cytochrome c isoform 2 / 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 speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSolmaz, S.R.N. / Hunte, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.
Authors: Solmaz, S.R. / Hunte, C.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 6
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9
J: HEAVY CHAIN (VH) OF FV-FRAGMENT
K: LIGHT CHAIN (VL) OF FV-FRAGMENT
L: Cytochrome b-c1 complex subunit 1, mitochondrial
M: Cytochrome b-c1 complex subunit 2, mitochondrial
N: Cytochrome b
O: Cytochrome c1, heme protein, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 6
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 9
U: HEAVY CHAIN (VH) OF FV-FRAGMENT
V: LIGHT CHAIN (VL) OF FV-FRAGMENT
W: Cytochrome c iso-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,74247
Polymers520,29523
Non-polymers13,44824
Water9,872548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.540, 162.970, 194.230
Angle α, β, γ (deg.)90.00, 104.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Cytochrome b-c1 complex subunit ... , 7 types, 14 molecules ALBMEPFQGRHSIT

#1: Protein Cytochrome b-c1 complex subunit 1, mitochondrial / Ubiquinol- cytochrome-c reductase complex core protein 1 / Core protein I / Complex III subunit 1


Mass: 47445.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07256, quinol-cytochrome-c reductase
#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Ubiquinol- cytochrome-c reductase complex core protein 2 / Core protein II / Complex III subunit 2


Mass: 38751.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07257, quinol-cytochrome-c reductase
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex ...Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex III subunit 5


Mass: 20122.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 6 / Ubiquinol-cytochrome c reductase complex 17 kDa protein / Cytochrome c1 non-heme 17 kDa protein / ...Ubiquinol-cytochrome c reductase complex 17 kDa protein / Cytochrome c1 non-heme 17 kDa protein / Mitochondrial hinge protein / Complex III subunit 6 / Complex III subunit VI


Mass: 17144.879 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-147 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00127, quinol-cytochrome-c reductase
#7: Protein Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome c reductase c reductase complex 14 kDa protein / Complex III subunit 7 / ...Ubiquinol-cytochrome c reductase c reductase complex 14 kDa protein / Complex III subunit 7 / Complex III subunit VII


Mass: 14452.557 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-127 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00128, quinol-cytochrome-c reductase
#8: Protein Cytochrome b-c1 complex subunit 8 / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C / Ubiquinol-cytochrome c ...Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C / Ubiquinol-cytochrome c reductase complex 11 kDa protein / Complex III subunit VII / Complex III subunit 8


Mass: 10856.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08525, quinol-cytochrome-c reductase
#9: Protein Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome c reductase complex 7.3 kDa protein / Cytochrome c1 non-heme 7.3 kDa protein / ...Ubiquinol-cytochrome c reductase complex 7.3 kDa protein / Cytochrome c1 non-heme 7.3 kDa protein / Complex III subunit X / Complex III subunit 9


Mass: 7354.140 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-66 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22289, quinol-cytochrome-c reductase

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Protein , 3 types, 5 molecules CNDOW

#3: Protein Cytochrome b / / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit / Cytochrome b-c1 complex subunit 3 / ...Ubiquinol-cytochrome-c reductase complex cytochrome b subunit / Cytochrome b-c1 complex subunit 3 / Complex III subunit 3 / Complex III subunit III / Complex III subunit CYTB / Cytochrome b-c1 complex subunit CYTB


Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00163, quinol-cytochrome-c reductase
#4: Protein Cytochrome c1, heme protein, mitochondrial / / Cytochrome c-1 / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex ...Cytochrome c-1 / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Complex III subunit 4 / Complex III subunit IV


Mass: 27807.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07143, quinol-cytochrome-c reductase
#12: Protein Cytochrome c iso-2


Mass: 12466.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00045

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Antibody , 2 types, 4 molecules JUKV

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


Mass: 14365.817 Da / Num. of mol.: 2
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
#11: Antibody LIGHT CHAIN (VL) OF FV-FRAGMENT


Mass: 11926.350 Da / Num. of mol.: 2
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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Sugars , 1 types, 1 molecules

#13: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 10 types, 571 molecules

#14: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#15: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#16: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42O7
#17: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#18: Chemical ChemComp-CN6 / (2R,5R,11S,14R)-2-(butanoyloxy)-5,8,11-trihydroxy-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate


Mass: 764.730 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H58O17P2
#19: Chemical ChemComp-9PE / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 593.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H60NO8P / Comment: phospholipid*YM
#20: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 564.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H57O8P
#21: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#22: Chemical ChemComp-6PH / (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 592.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61O8P
#23: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.35 %
Crystal growTemperature: 277 K / Method: microbatch (paraffin oil) / pH: 7.5
Details: 1M Sucrose, 10% DMSO, 20mM Tris pH 7.5, 80mM NaCl, 0.05 % UM, 1 M stigmatellin, 5% PEG 4000, Microbatch (Paraffin oil), temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 290829 / Num. obs: 289871 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.66 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.38 / % possible all: 77.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DNAdata collection
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1KB9 and 1YEA

1kb9

1yea


Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5660991.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 14494 5 %RANDOM
Rwork0.225 ---
all0.225 290829 --
obs0.225 289871 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8991 Å2 / ksol: 0.323322 e/Å3
Displacement parametersBiso mean: 57.9 Å2
Baniso -1Baniso -2Baniso -3
1-18.67 Å20 Å24.94 Å2
2---9.65 Å20 Å2
3----9.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35342 0 904 548 36794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 2131 5 %
Rwork0.338 40490 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water_mod.paramwater.top
X-RAY DIFFRACTION3parhcsdx.sozannei202.bc1tophcsdx.sozannei202.bc1
X-RAY DIFFRACTION4protein.link

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