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- PDB-2fyn: Crystal Structure Analysis of the double mutant Rhodobacter Sphae... -

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Basic information

Entry
Database: PDB / ID: 2fyn
TitleCrystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Transmembrane helices / functional dimer
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 / 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 / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-LOP / STIGMATELLIN A / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsEsser, L. / Xia, D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex.
Authors: Esser, L. / Gong, X. / Yang, S. / Yu, L. / Yu, C.A. / Xia, D.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_asym_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_asym_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
M: Cytochrome b
N: Cytochrome c1
O: Ubiquinol-cytochrome c reductase iron-sulfur subunit
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)615,89854
Polymers596,68718
Non-polymers19,21136
Water00
1
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,29918
Polymers198,8966
Non-polymers6,40412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32340 Å2
ΔGint-353 kcal/mol
Surface area69660 Å2
MethodPISA
2
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,29918
Polymers198,8966
Non-polymers6,40412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32290 Å2
ΔGint-345 kcal/mol
Surface area69930 Å2
MethodPISA
3
M: Cytochrome b
N: Cytochrome c1
O: Ubiquinol-cytochrome c reductase iron-sulfur subunit
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,29918
Polymers198,8966
Non-polymers6,40412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32470 Å2
ΔGint-351 kcal/mol
Surface area69870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)351.300, 147.130, 160.830
Angle α, β, γ (deg.)90.00, 103.94, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe asymmetric unit contains three independent dimers (biological assembly)

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Components

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Protein , 3 types, 18 molecules ADGJMPBEHKNQCFILOR

#1: Protein
Cytochrome b


Mass: 50157.539 Da / Num. of mol.: 6 / Fragment: cytochrome b / Mutation: S287R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petB, fbcB / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q02761
#2: Protein
Cytochrome c1


Mass: 29373.953 Da / Num. of mol.: 6 / Fragment: cytochrome c1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petC, fbcC / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q02760
#3: Protein
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 19916.322 Da / Num. of mol.: 6 / Fragment: Rieske Iron sulfur protein / Mutation: V135S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q02762, quinol-cytochrome-c reductase

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Non-polymers , 4 types, 36 molecules

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


Mass: 616.487 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H42O7
#6: Chemical
ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#7: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2

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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: 2

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 288.2 K / Method: evaporation / pH: 7.5
Details: 10% PEG400, 0.2 M NaCl, 0.2 M Histidine, 0.1M Tris, 10% Glycerol, 5 mM NaN3, 10% Glycerol, 2mM DHPC, 0.5% beta-octyl glucopyranoside, 0.06% sucrose monocarprate, 10mM Sr(NO3)2, pH 7.5, ...Details: 10% PEG400, 0.2 M NaCl, 0.2 M Histidine, 0.1M Tris, 10% Glycerol, 5 mM NaN3, 10% Glycerol, 2mM DHPC, 0.5% beta-octyl glucopyranoside, 0.06% sucrose monocarprate, 10mM Sr(NO3)2, pH 7.5, EVAPORATION, temperature 288.2K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 22-ID21
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDFeb 5, 2005mirrors
MARRESEARCH2CCDFeb 5, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 160039 / Num. obs: 155528 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.37 / Num. unique all: 13841 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1qcr

1qcr


Resolution: 3.2→18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 111061.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2102 1.7 %RANDOM
Rwork0.224 ---
all0.224 130217 --
obs0.224 123993 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.4667 Å2 / ksol: 0.285271 e/Å3
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1--12.98 Å20 Å2-9.87 Å2
2---5.76 Å20 Å2
3---18.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40398 0 1290 0 41688
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.332
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.852.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 303 1.6 %
Rwork0.325 19137 -
obs-19137 89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3Ligand.parLigand.top
X-RAY DIFFRACTION4cis_peptide.param

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