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- PDB-4d6u: Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121 -

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Basic information

Entry
Database: PDB / ID: 4d6u
TitleCytochrome bc1 bound to the 4(1H)-pyridone GSK932121
Components
  • (CYTOCHROME B-C1 COMPLEX SUBUNIT ...) x 10
  • CYTOCHROME B
  • CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN / COMPLEX
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / Respiratory electron transport / pyramidal neuron development / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / Respiratory electron transport / pyramidal neuron development / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / metalloendopeptidase activity / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / 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 ...Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / 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 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / 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. / 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] domain / Rieske [2Fe-2S] iron-sulphur 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
Similarity search - Domain/homology
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / Chem-G8U / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / Chem-G8U / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / 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 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.09 Å
AuthorsCapper, M.J. / ONeill, P.M. / Fisher, N. / Strange, R.W. / Moss, D. / Ward, S.A. / Berry, N.G. / Lawrenson, A.S. / Hasnain, S.S. / Biagini, G.A. / Antonyuk, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome Bc1.
Authors: Capper, M.J. / O'Neill, P.M. / Fisher, N. / Strange, R.W. / Moss, D. / Ward, S.A. / Berry, N.G. / Lawrenson, A.S. / Hasnain, S.S. / Biagini, G.A. / Antonyuk, S.V.
History
DepositionNov 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
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.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_entry_details ...database_PDB_caveat / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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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 7
G: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
H: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
I: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
J: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
N: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
O: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
P: CYTOCHROME B
Q: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
R: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
S: CYTOCHROME B-C1 COMPLEX SUBUNIT 7
T: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
U: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
V: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
W: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,44047
Polymers558,93020
Non-polymers14,50927
Water00
1
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 7
G: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
H: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
I: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
J: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,74924
Polymers279,48610
Non-polymers7,26314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38940 Å2
ΔGint-244.2 kcal/mol
Surface area94800 Å2
MethodPQS
2
N: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
O: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
P: CYTOCHROME B
Q: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
R: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
S: CYTOCHROME B-C1 COMPLEX SUBUNIT 7
T: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
U: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
V: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
W: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,69123
Polymers279,44510
Non-polymers7,24613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37720 Å2
ΔGint-239.2 kcal/mol
Surface area101890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)129.490, 129.490, 719.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 10 types, 16 molecules ABEIRFSGTHUJWNOV

#1: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL / COMPLEX III SUBUNIT 1 / CORE PROTEIN I / UBIQUINOL-CYTOCHROME- C REDUCTASE COMPLEX CORE PROTEIN 1


Mass: 52796.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P31800
#2: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL / COMPLEX III SUBUNIT 2 / CORE PROTEIN II / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 48203.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P23004
#5: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL / COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / ...COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / COMPLEX III SUBUNIT IX / UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN


Mass: 29586.842 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 7 / COMPLEX III SUBUNIT 7 / COMPLEX III SUBUNIT VII / QP-C / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ...COMPLEX III SUBUNIT 7 / COMPLEX III SUBUNIT VII / QP-C / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN


Mass: 13502.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00129
#7: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 8 / COMPLEX III SUBUNIT 8 / COMPLEX III SUBUNIT VIII / UBIQUINOL- CYTOCHROME C REDUCTASE COMPLEX 9.5 ...COMPLEX III SUBUNIT 8 / COMPLEX III SUBUNIT VIII / UBIQUINOL- CYTOCHROME C REDUCTASE COMPLEX 9.5 KDA PROTEIN / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C


Mass: 9737.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P13271
#8: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL / COMPLEX III SUBUNIT 6 / COMPLEX III SUBUNIT VIII / CYTOCHROME C1 NON-HEME 11 KDA PROTEIN / ...COMPLEX III SUBUNIT 6 / COMPLEX III SUBUNIT VIII / CYTOCHROME C1 NON-HEME 11 KDA PROTEIN / MITOCHONDRIAL HINGE PROTEIN / UBIQUINOL- CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN


Mass: 10638.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00126
#9: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 9 / COMPLEX III SUBUNIT 9 / COMPLEX III SUBUNIT X / CYTOCHROME C1 NON-HEME 7 KDA PROTEIN / UBIQUINOL- ...COMPLEX III SUBUNIT 9 / COMPLEX III SUBUNIT X / CYTOCHROME C1 NON-HEME 7 KDA PROTEIN / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN


Mass: 7469.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00130
#10: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL / COMPLEX III SUBUNIT 1 / CORE PROTEIN I / UBIQUINOL-CYTOCHROME- C REDUCTASE COMPLEX CORE PROTEIN 1


Mass: 52768.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P31800
#11: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL / COMPLEX III SUBUNIT 2 / CORE PROTEIN II / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 48204.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P23004
#12: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL / COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / ...COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / COMPLEX III SUBUNIT IX / UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN


Mass: 29572.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase

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Protein , 2 types, 4 molecules CPDQ

#3: Protein CYTOCHROME B / COMPLEX III SUBUNIT 3 / COMPLEX III SUBUNIT III / CYTOCHROME B-C1 COMPLEX SUBUNIT 3 / UBIQUINOL- ...COMPLEX III SUBUNIT 3 / COMPLEX III SUBUNIT III / CYTOCHROME B-C1 COMPLEX SUBUNIT 3 / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME B SUBUNIT


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00157
#4: Protein CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL / COMPLEX III SUBUNIT 4 / COMPLEX III SUBUNIT IV / CYTOCHROME B-C1 COMPLEX SUBUNIT 4 / UBIQUINOL- ...COMPLEX III SUBUNIT 4 / COMPLEX III SUBUNIT IV / CYTOCHROME B-C1 COMPLEX SUBUNIT 4 / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME C1 SUBUNIT / CYTOCHROME C-1 / CYTOCHROME BC1


Mass: 35343.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE 4(1H)-PYRIDONE, GSK932121, BOUND IN THE QI SITE OF CYTOCHROME B
Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00125

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Non-polymers , 8 types, 27 molecules

#13: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#14: Chemical ChemComp-G8U / 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol


Mass: 425.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15ClF3NO4
#15: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#16: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#17: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#18: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#20: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Details

Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 34.7 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8
Details: SITTING DROP VAPOUR DIFFUSION 50 MM KPI, PH 6.8, 100 MM NACL, 3 MM NAN3, 10 - 13 % PEG4000,1.4% HECAMEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.09→42.1 Å / Num. obs: 42955 / % possible obs: 80.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 123.66 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6
Reflection shellResolution: 4.09→4.25 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.55 / % possible all: 51.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPJ

1ppj


Resolution: 4.09→50 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.852 / Cross valid method: THROUGHOUT / ESU R Free: 1.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27106 2147 5 %RANDOM
Rwork0.2233 ---
obs0.22573 40901 80.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 162.551 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å21.79 Å20 Å2
2--3.57 Å20 Å2
3----11.59 Å2
Refinement stepCycle: LAST / Resolution: 4.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30363 0 717 0 31080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01931844
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.98143255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98153845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50523.4031387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.504155132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.89515206
X-RAY DIFFRACTIONr_chiral_restr0.080.24710
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02124004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.095→4.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 88 -
Rwork0.334 1897 -
obs--50.39 %

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