[English] 日本語
Yorodumi
- PDB-1ppj: Bovine cytochrome bc1 complex with stigmatellin and antimycin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ppj
TitleBovine cytochrome bc1 complex with stigmatellin and antimycin
Components
  • (Ubiquinol-cytochrome C reductase complex ...) x 6
  • (Ubiquinol-cytochrome C reductase iron-sulfur subunit, ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEASE / MPP UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / STIGMATELLIN / ANTIMYCIN
Function / homology
Function and homology information


Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane ...Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C ...Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / 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 8 superfamily / 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 b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / 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 / 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
Chem-ANY / AZIDE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / hexyl beta-D-glucopyranoside / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / STIGMATELLIN A ...Chem-ANY / AZIDE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / hexyl beta-D-glucopyranoside / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / STIGMATELLIN A / 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: 2.1 Å
AuthorsHuang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding Pattern.
Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A.
History
DepositionJun 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 29, 2014Group: Other
Revision 2.0Dec 20, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _struct_site.details
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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 / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial
B: Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
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
J: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
N: Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial
O: Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial
P: Cytochrome b
Q: Cytochrome c1, heme protein, mitochondrial
R: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
S: Ubiquinol-cytochrome C reductase complex 14 kDa protein
T: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
U: Ubiquinol-cytochrome C reductase complex 11 kDa protein
V: Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial
W: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,10165
Polymers469,44420
Non-polymers18,65845
Water24,6811370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area108550 Å2
ΔGint-711 kcal/mol
Surface area146890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.530, 168.748, 231.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.601077, 0.24814, 0.759692), (0.24814, -0.845651, 0.472547), (0.759692, 0.472547, 0.446729)
Vector: -7.75066, 110.47308, -32.01405)

-
Components

-
Ubiquinol-cytochrome C reductase complex ... , 6 types, 12 molecules ANBOFSGTHUJW

#1: Protein Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial / CYTOCHROME BC1 COMPLEX / COMPLEX III


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


Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase
#6: Protein Ubiquinol-cytochrome C reductase complex 14 kDa protein / Complex III subunit VI


Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase

-
Protein , 2 types, 4 molecules CPDQ

#3: Protein Cytochrome b / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00157, quinol-cytochrome-c reductase
#4: Protein Cytochrome c1, heme protein, mitochondrial / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00125, quinol-cytochrome-c reductase

-
Ubiquinol-cytochrome C reductase iron-sulfur subunit, ... , 2 types, 4 molecules ERIV

#5: Protein Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial / Rieske iron-sulfur protein / RISP / Complex III subunit IX


Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#9: Protein Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial / Rieske iron-sulfur protein / RISP / Complex III subunit IX


Mass: 7920.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase

-
Sugars , 1 types, 9 molecules

#11: Sugar
ChemComp-JZR / hexyl beta-D-glucopyranoside / hexyl beta-D-glucoside / hexyl D-glucoside / hexyl glucoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H24O6

-
Non-polymers , 11 types, 1406 molecules

#12: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#13: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N3
#14: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#15: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / 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-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
#18: Chemical ChemComp-ANY / 2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2-HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL-4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER / ANTIMYCIN


Mass: 562.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H42N2O9
#19: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#20: 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
#21: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1370 / 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: 2.74 Å3/Da / Density % sol: 54.7 % / Description: IRON-SULFUR PROTEINS, HEME PROTEINS
Crystal growTemperature: 277 K / pH: 6.7
Details: PEG-3350, JEFFAMINE, GLYCEROL, CACODYLATE, HEXYLGLUCOSIDE , pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.70

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-110.97977
SYNCHROTRONALS 5.0.121
SYNCHROTRONALS 5.0.231.1
SYNCHROTRONALS 8.2.241.1808
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEJun 26, 2002SI(311)MONOCHROMATOR (HORIZONTAL)
ADSC QUANTUM 42CCDJun 30, 2002TOROIDAL FUCUSING MIRROR
ADSC QUANTUM 2103CCDOct 6, 2002FLAT MIRROR(VERTICAL)
ADSC QUANTUM 2104CCDOct 15, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(311) BENTSINGLE WAVELENGTHMx-ray1
2SINGLE CRYSTAL SI(220)CYLINDRICALLY BENTSINGLE WAVELENGTHMx-ray1
3DOUBLE CYRSTAL SI(111)SINGLE WAVELENGTHMx-ray1
4DOUBLE CYRSTAL SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979771
211
31.11
41.18081
ReflectionResolution: 2.1→250 Å / Num. obs: 285923 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.63 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 18.689
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 2.819 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BE3 2BCC

1be3

2bcc


Resolution: 2.1→93.53 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5660254.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: A NUMBER OF DIFFERENT DATASETS WERE USED IN THE STRUCTURE DETERMINATION IN ADDITION TO THE DATASET USED FOR THE FINAL REFINEMENT PRESENTED HERE. THE ORIGINAL MOLECULAR REPLACEMENT WAS ...Details: A NUMBER OF DIFFERENT DATASETS WERE USED IN THE STRUCTURE DETERMINATION IN ADDITION TO THE DATASET USED FOR THE FINAL REFINEMENT PRESENTED HERE. THE ORIGINAL MOLECULAR REPLACEMENT WAS CARRIED OUT WITH A LOWER RESOLUTION DATASET. DUE TO LARGE VARIATIONS IN THE CELL PARAMETERS, EACH NEW DATASET WAS RE-SOLVED BY MOLECULAR REPLACEMENT USING A PREVIOUS MODEL. THE SAME R-FREE SET WAS USED IN ALL CASES. STRONG NCS RESTRAINTS WERE USED IN POSITIONAL REFINEMENT. THE COMPLEX WAS DIVIDED INTO 49 TWO-FOLD NCS GROUPS. SPECIFIC RESIDUES NOT OBEYING NCS WERE IDENTIFIED AND RELEASED FROM THE CONSTRAINT. NO NCS RESTRAINT ON B-FACTOR WAS USED. After refinement to convergence against the working set of reflections, the R- and R-Free values of 0.224 and 0.260 were obtained. A final round of positional minimization and restrained B-factor refinement was carried out with identical parameters but against all the data, giving an R-factor of 0.2359. The submitted coordinates are from this final non-cv refinement. Residue (GLU 12 ) and Residue (VAL 17 ) are linked together for chain B and O. Sequence assignment for this fragment is ambiguous. Sequence assignment is also ambiguous for chains I AND V.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 14181 5 %RANDOM
Rwork0.224 ---
obs0.224 285060 97.7 %-
all-288448 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.2121 Å2 / ksol: 0.390225 e/Å3
Displacement parametersBiso mean: 50.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.34 Å20 Å20 Å2
2---3.71 Å20 Å2
3----8.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.1→93.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31181 0 998 1370 33549
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it4.32.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.383 856 4.9 %
Rwork0.334 16565 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN_NOHYDROGEN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION3HETERO10.PARHETERO10.TOP
X-RAY DIFFRACTION4PROSTH4.PARPROSTH4.TOP

+
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