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- PDB-2ibz: Yeast Cytochrome BC1 Complex with Stigmatellin -

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Basic information

Entry
Database: PDB / ID: 2ibz
TitleYeast Cytochrome BC1 Complex with Stigmatellin
Components
  • (Ubiquinol-cytochrome c reductase complex ...) x 4
  • (Ubiquinol-cytochrome-c reductase complex core protein ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial precursor
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor
  • Variable Heavy chain of antibody fragment
  • Variable Light chain of antibody fragment
KeywordsOXIDOREDUCTASE / multisubunit membrane protein complex
Function / homology
Function and homology information


Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade ...Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / matrix side of mitochondrial inner membrane / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / protein processing involved in protein targeting to mitochondrion / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / Regulation of actin dynamics for phagocytic cup formation / Mitochondrial protein degradation / : / immunoglobulin complex / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / immunoglobulin mediated immune response / proton transmembrane transport / aerobic respiration / nuclear periphery / antigen binding / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / blood microparticle / heme binding / mitochondrion / proteolysis / extracellular region / metal ion binding / plasma membrane / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Helix Hairpins / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / STIGMATELLIN A / Chem-UQ6 / F30C7 light chain variable region / 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 ...FE2/S2 (INORGANIC) CLUSTER / HEME C / STIGMATELLIN A / Chem-UQ6 / F30C7 light chain variable region / 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 / Ig heavy chain V region 3-6 / Cytochrome b-c1 complex subunit 9, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsHunte, C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome bc(1) Complex.
Authors: Lancaster, C.R. / Hunte, C. / Kelley, J. / Trumpower, B.L. / Ditchfield, R.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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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 1
B: Ubiquinol-cytochrome-c reductase complex core protein 2
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial precursor
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor
H: Ubiquinol-cytochrome c reductase complex 17 kDa protein
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
I: Ubiquinol-cytochrome c reductase complex 7.3 kDa protein
X: Variable Heavy chain of antibody fragment
Y: Variable Light chain of antibody fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,14417
Polymers246,00611
Non-polymers3,1396
Water6,125340
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 core protein ... , 2 types, 2 molecules AB

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


Mass: 47445.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07256, quinol-cytochrome-c reductase
#2: Protein Ubiquinol-cytochrome-c reductase complex core protein 2 / Complex III subunit 2 / Cytochrome b-c1 complex subunit 2 / Ubiquinol:cytochrome-c oxidoreductase subunit II


Mass: 38751.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07257, quinol-cytochrome-c reductase

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Protein , 3 types, 3 molecules CDE

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


Mass: 43674.535 Da / Num. of mol.: 1 / 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 precursor / Ubiquinol- cytochrome-c reductase complex cytochrome c1 subunit / Complex III subunit CYT1 / ...Ubiquinol- cytochrome-c reductase complex cytochrome c1 subunit / Complex III subunit CYT1 / Cytochrome b-c1 complex subunit CYT1


Mass: 27807.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07143, quinol-cytochrome-c reductase
#5: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor / Complex III subunit RIP1 / Cytochrome b-c1 complex subunit RIP1 / Rieske iron-sulfur protein / RISP


Mass: 20122.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase

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Ubiquinol-cytochrome c reductase complex ... , 4 types, 4 molecules HFGI

#6: Protein Ubiquinol-cytochrome c reductase complex 17 kDa protein / Mitochondrial hinge protein / Complex III subunit 6 / Cytochrome b-c1 complex subunit 6 / Ubiquinol- ...Mitochondrial hinge protein / Complex III subunit 6 / Cytochrome b-c1 complex subunit 6 / Ubiquinol-cytochrome c reductase subunit VI


Mass: 8854.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00127, quinol-cytochrome-c reductase
#7: Protein Ubiquinol-cytochrome c reductase complex 14 kDa protein / Complex III subunit 7 / Cytochrome b-c1 complex subunit 7


Mass: 14583.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / 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 8 / Cytochrome b-c1 ...Ubiquinol-cytochrome c reductase complex 11 kDa protein / Complex III subunit 8 / Cytochrome b-c1 complex subunit 8


Mass: 10987.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08525, quinol-cytochrome-c reductase
#9: Protein Ubiquinol-cytochrome c reductase complex 7.3 kDa protein / Complex III subunit 9 / Cytochrome b-c1 complex subunit 9


Mass: 7485.334 Da / Num. of mol.: 1 / 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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Antibody , 2 types, 2 molecules XY

#10: Antibody Variable Heavy chain of antibody fragment


Mass: 14365.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: variable domain antibody heavy chain / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P18531*PLUS
#11: Antibody Variable Light chain of antibody fragment


Mass: 11926.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: variable domain antibody light chain / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: A0N6Y3*PLUS

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Non-polymers , 5 types, 346 molecules

#12: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#13: 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
#14: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O7
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 340 / 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: 17

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Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 73.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: precipitant PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3
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: 199019 / Num. obs: 168517 / % possible obs: 84.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.2 / Num. unique all: 23537 / % possible all: 72.9

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→14.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4240 -random
Rwork0.222 ---
all-199009 --
obs-168517 84.7 %-
Displacement parametersBiso mean: 69.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17227 0 213 340 17780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.349 593 -
Rwork0.33 --
obs-23537 72.9 %

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