[English] 日本語
Yorodumi
- PDB-1sqq: Crystal Structure Analysis of Bovine Bc1 with Methoxy Acrylate St... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sqq
TitleCrystal Structure Analysis of Bovine Bc1 with Methoxy Acrylate Stilbene (MOAS)
Components
  • (Ubiquinol-cytochrome c reductase complex ...) x 5
  • (Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...) x 2
  • (Ubiquinol-cytochrome-c reductase complex core protein ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / cytochrome bc1 / Qo inhibitor / membrane protein / electron transport
Function / homology
Function and homology information


mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain ...mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / 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 b-c1 complex subunit 10 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / 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 b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 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 / 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 / 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 / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / Chem-OST / UBIQUINONE-2 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 ...FE2/S2 (INORGANIC) CLUSTER / HEME C / Chem-OST / UBIQUINONE-2 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsEsser, L. / Quinn, B. / Li, Y.F. / Zhang, M. / Elberry, M. / Yu, L. / Yu, C.A. / Xia, D.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex.
Authors: Esser, L. / Quinn, B. / Li, Y.F. / Zhang, M. / Elberry, M. / Yu, L. / Yu, C.A. / Xia, D.
#1: Journal: Science / Year: 1997
Title: Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria.
Authors: Xia, D. / Yu, C.A. / Kim, H. / Xia, J.Z. / Kachurin, A.M. / Zhang, L. / Yu, L. / Deisenhofer, J.
#2: Journal: Biochemistry / Year: 2002
Title: The crystal structure of mitochondrial cytochrome bc1 in complex with famoxadone: the role of aromatic-aromatic interaction in inhibition.
Authors: Gao, X. / Wen, X. / Yu, C. / Esser, L. / Tsao, S. / Quinn, B. / Zhang, L. / Yu, L. / Xia, D.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_type.id / _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
Revision 2.1Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor
B: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome c reductase complex 11 kDa protein
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,93817
Polymers241,29311
Non-polymers2,6446
Water3,279182
1
A: Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor
B: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome c reductase complex 11 kDa protein
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
hetero molecules

A: Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor
B: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome c reductase complex 11 kDa protein
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,87534
Polymers482,58722
Non-polymers5,28812
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area102110 Å2
ΔGint-660 kcal/mol
Surface area164760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.677, 153.677, 598.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

-
Ubiquinol-cytochrome-c reductase complex core protein ... , 2 types, 2 molecules AB

#1: Protein Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor


Mass: 49266.254 Da / Num. of mol.: 1 / Fragment: core protein 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor / Complex III subunit II


Mass: 46575.469 Da / Num. of mol.: 1 / Fragment: core protein 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase

-
Protein , 2 types, 2 molecules CD

#3: Protein Cytochrome b /


Mass: 42620.340 Da / Num. of mol.: 1 / Fragment: cytochrome b / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00157
#4: Protein Cytochrome c1, heme protein, mitochondrial / / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 1 / Fragment: cytochrome c1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125

-
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ... , 2 types, 2 molecules EI

#5: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]


Mass: 21640.580 Da / Num. of mol.: 1 / Fragment: iron sulfur protein / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272
#9: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]


Mass: 7964.259 Da / Num. of mol.: 1 / Fragment: subunit 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272

-
Ubiquinol-cytochrome c reductase complex ... , 5 types, 5 molecules FGHJK

#6: Protein Ubiquinol-cytochrome c reductase complex 14 kDa protein / Complex III subunit VI


Mass: 13371.190 Da / Num. of mol.: 1 / Fragment: subunit 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129, quinol-cytochrome-c reductase
#7: Protein Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Complex III subunit VII


Mass: 9606.027 Da / Num. of mol.: 1 / Fragment: subunit 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271, quinol-cytochrome-c reductase
#8: Protein Ubiquinol-cytochrome c reductase complex 11 kDa protein / Mitochondrial hinge protein / Cytochrome C1 / nonheme 11 kDa protein / Complex III subunit VIII


Mass: 9189.116 Da / Num. of mol.: 1 / Fragment: subunit 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126, quinol-cytochrome-c reductase
#10: Protein Ubiquinol-cytochrome c reductase complex 7.2 kDa protein / Cytochrome C1 / nonheme 7 kDa protein / Complex III subunit X


Mass: 7209.311 Da / Num. of mol.: 1 / Fragment: subunit 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein Ubiquinol-cytochrome c reductase complex 6.4 kDa protein / Complex III subunit XI


Mass: 6527.604 Da / Num. of mol.: 1 / Fragment: subunit 11 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07552, quinol-cytochrome-c reductase

-
Non-polymers , 5 types, 188 molecules

#12: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#13: Chemical ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O4
#14: Chemical ChemComp-OST / METHYL (2Z)-3-METHOXY-2-{2-[(E)-2-PHENYLVINYL]PHENYL}ACRYLATE


Mass: 294.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O3
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.2
Details: 20mM ammonium acetate, 20% glycerol, 12% PEG4000, 0.5M KCl, 0.1% diheptanoyl-phosphatidylcholine , pH 7.2, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.736 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2001 / Details: mirrors
RadiationMonochromator: SAGITTALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.736 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 67802 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.08 Å / % possible all: 90.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1QCR

1qcr


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / SU B: 18.766 / SU ML: 0.352 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29485 2113 3 %RANDOM
Rwork0.22815 ---
obs0.2302 67802 96.84 %-
all-67802 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.643 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.02 Å2
Refine analyzeLuzzati coordinate error free: 0.458 Å / Luzzati sigma a free: 0.357 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16527 0 178 182 16887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02117551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.98423785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.105102093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1690.22590
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0213067
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.28600
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5080.410484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4063.80116868
X-RAY DIFFRACTIONr_scbond_it5.09937064
X-RAY DIFFRACTIONr_scangle_it7.5124.56909
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.079 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.417 135
Rwork0.301 4948
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78160.04860.60911.1362-1.15171.93730.0794-0.01540.1139-0.10420.08450.63250.0313-0.6842-0.16390.3647-0.08080.0310.4905-0.02270.60231.597887.107294.2101
20.1585-0.2274-0.05071.548-0.03530.74590.058-0.06760.20010.1837-0.06140.2604-0.116-0.26510.00350.3513-0.15230.1180.2504-0.02570.319448.650893.3883116.1592
30.7835-0.29060.19631.93850.1951.90560.08010.0680.2415-0.144600.0678-0.305-0.147-0.08010.2516-0.09840.00570.03890.00640.194368.6841104.324893.1372
41.233-0.82060.092.743-0.04491.33040.03660.0439-0.0761-0.24470.01720.39270.0469-0.2332-0.05380.2616-0.0711-0.06660.1275-0.00930.263656.856486.266374.6031
50.7911-0.05820.32740.32950.85550.7590.1344-0.35810.02770.3844-0.1065-0.0019-0.0559-0.139-0.02790.7258-0.34730.07910.37760.02710.291764.571368.6239155.5975
6-0.41360.8260.36920.21660.19262.66620.011-0.56730.18580.6155-0.0231-0.4750.11740.44590.01211.0185-0.3579-0.13450.63370.15550.572480.907256.5542173.7292
71.1971-0.04320.1860.46670.32522.73430.1847-0.3943-0.11790.3617-0.0137-0.08060.25970.0974-0.1710.7336-0.36050.03780.34720.09720.432964.600345.036154.4328
80000000000000000.5582000.558200.5582000
90.6535-0.1539-1.2480.2459-0.52315.06470.0992-0.29570.03170.4392-0.05790.1781-0.141-0.5479-0.04140.8108-0.37590.21780.48570.0140.427245.001271.5107160.5007
101.41350.17650.34492.30350.71981.5847-0.0231-0.4659-0.14260.70630.0972-0.03030.1011-0.1373-0.07411.3853-0.41970.22541.1490.06480.566954.285767.5365194.0892
111.44250.99211.59181.41641.88273.81770.2378-0.38950.08440.3148-0.17610.18940.0412-0.7332-0.06170.5616-0.22720.26160.4723-0.02340.493743.032582.0168142.8662
1210.1382.5693-1.591916.00893.281412.7893-0.04690.15070.67010.08110.1289-0.43820.09-0.1659-0.0821.14710.0009-0.03391.3352-0.18831.087970.6374111.4253190.7281
133.6504-1.1415-1.09871.5134-0.01621.1313-0.0619-0.2394-0.36790.20230.01210.21750.4495-0.18540.04980.536-0.30360.02150.23930.01960.246258.71346.9066123.5702
140.18150.098-0.30040.8799-1.02032.67320.0586-0.4236-0.07970.3723-0.06540.0970.1719-0.23590.00680.607-0.35080.11710.48610.06440.461447.824554.6462146.0128
154.6235-3.5586-2.28596.98171.17267.0140.3171-0.3303-0.3172-0.1475-0.3210.17990.0498-0.42250.00390.8667-0.33030.0690.99490.17540.839739.006141.9344196.5194
166.8395-11.5247-4.547225.1133-2.23197.0006-0.1540.0971-0.0240.16660.15580.02670.4156-0.7861-0.00180.8541-0.34940.1140.872-0.05440.72539.558949.9336188.8704
170000000000000000.5582000.558200.5582000
185.6314.28567.75044.18946.206712.853-0.30280.5225-0.014-0.1699-0.58040.58360.0108-2.37720.88310.5751-0.01050.14610.5463-0.15990.614160.38594.728789.6323
1911.21-1.82769.78155.4812-4.361313.47330.8395-0.5424-0.48120.2137-0.31830.291.0112-0.6452-0.52120.61230.04070.07570.7232-0.06690.732654.356580.750894.9735
20117.3058-7.0285-28.927348.215520.605126.6496-2.64445.3556-0.4295-0.50231.85550.58550.4177-0.92370.78880.5586-0.0005-0.00410.5589-0.00790.561846.783298.4128105.1981
212.07390.96210.00033.0287-0.6255.33010.1458-0.521-0.00040.7560.00620.2389-0.5608-1.0718-0.1520.8261-0.0870.27540.7642-0.10310.580438.722689.1815162.5846
221.84081.5514-4.15314.7041-5.301716.910.0776-0.51390.10920.3560.0066-0.0395-0.2835-0.1179-0.08420.6603-0.1480.02810.575-0.23620.60852.1779104.1906149.6405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2311 - 231
2X-RAY DIFFRACTION2AA232 - 446232 - 446
3X-RAY DIFFRACTION3BB17 - 23517 - 235
4X-RAY DIFFRACTION4BB236 - 439236 - 439
5X-RAY DIFFRACTION5CC3 - 1333 - 133
6X-RAY DIFFRACTION5CC173 - 264173 - 264
7X-RAY DIFFRACTION5CL - M381 - 382
8X-RAY DIFFRACTION6CC134 - 172134 - 172
9X-RAY DIFFRACTION7CC265 - 379265 - 379
10X-RAY DIFFRACTION8CL381
11X-RAY DIFFRACTION9DD173 - 241173 - 241
12X-RAY DIFFRACTION10DD1 - 1721 - 172
13X-RAY DIFFRACTION10DP242
14X-RAY DIFFRACTION11EE1 - 711 - 71
15X-RAY DIFFRACTION12EE72 - 19672 - 196
16X-RAY DIFFRACTION13FF6 - 1106 - 110
17X-RAY DIFFRACTION14GG1 - 751 - 75
18X-RAY DIFFRACTION15HH9 - 529 - 52
19X-RAY DIFFRACTION16HH53 - 7853 - 78
20X-RAY DIFFRACTION17HH49 - 7849 - 78
21X-RAY DIFFRACTION18II2 - 262 - 26
22X-RAY DIFFRACTION19II27 - 5127 - 51
23X-RAY DIFFRACTION20II52 - 5752 - 57
24X-RAY DIFFRACTION21JJ3 - 613 - 61
25X-RAY DIFFRACTION22KK1 - 541 - 54

+
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