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- PDB-4h44: 2.70 A Cytochrome b6f Complex Structure From Nostoc PCC 7120 -

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Basic information

Entry
Database: PDB / ID: 4h44
Title2.70 A Cytochrome b6f Complex Structure From Nostoc PCC 7120
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6
  • Cytochrome b6-f complex iron-sulfur subunit 1
KeywordsPHOTOSYNTHESIS / Alpha helix / beta-sheet / Plastoquinol-plastocyanin oxidoreductase / Plastocyanin / Thylakoid membranes
Function / homology
Function and homology information


cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / : / plasma membrane-derived thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / : / plasma membrane-derived thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis / respiratory electron transport chain / monooxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 ...Single helix bin / plastocyanin oxidoreductase / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Iron-sulfur subunit PetC transmembrane anchor / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / : / : / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / 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 / Rudiment single hybrid motif / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-7PH / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OPC ...Chem-7PH / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OPC / Chem-SQD / Cytochrome b6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit 6 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit 1 / Cytochrome b6-f complex subunit 4
Similarity search - Component
Biological speciesNostoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHasan, S.S. / Yamashita, E. / Baniulis, D. / Cramer, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex
Authors: Hasan, S.S. / Yamashita, E. / Baniulis, D. / Cramer, W.A.
History
DepositionSep 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 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 b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit 1
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,45328
Polymers106,2428
Non-polymers10,21120
Water1,838102
1
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit 1
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules

A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit 1
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,90656
Polymers212,48416
Non-polymers20,42240
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area90010 Å2
ΔGint-970 kcal/mol
Surface area75600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.127, 159.127, 364.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein Cytochrome b6


Mass: 24291.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: P0A384
#3: Protein Apocytochrome f


Mass: 31178.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: Q93SW9
#4: Protein Cytochrome b6-f complex iron-sulfur subunit 1 / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein 1 / ISP 1 / RISP 1 / Rieske iron- ...Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein 1 / ISP 1 / RISP 1 / Rieske iron-sulfur protein 1


Mass: 19216.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: Q93SX0, EC: 1.10.9.1

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Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17548.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: Q93SX1
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit PetL / Cytochrome b6-f complex subunit VI


Mass: 3227.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: Q8YVQ2
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit PetM / Cytochrome b6-f complex subunit VII


Mass: 3547.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: P0A3Y1
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit PetG / Cytochrome b6-f complex subunit V


Mass: 3997.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: P58246
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit PetN / Cytochrome b6-f complex subunit VIII


Mass: 3234.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc (bacteria) / Strain: PCC 7120 / References: UniProt: P61048

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Non-polymers , 13 types, 122 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#11: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#12: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#13: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical ChemComp-OPC / (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE / DIOLEOYL-PHOSPHATIDYLCHOLINE


Mass: 801.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H87NO8P / Comment: phospholipid*YM
#15: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H57O8P
#16: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#17: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#18: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#19: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#20: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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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: 6.27 Å3/Da / Density % sol: 80.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→39.55 Å / Num. obs: 74395 / Biso Wilson estimate: 69.65 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2ZT9

2zt9


Resolution: 2.7→39.547 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2465 3733 5.04 %
Rwork0.2195 --
obs0.2208 74023 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.66 Å2 / Biso mean: 81.9901 Å2 / Biso min: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7364 0 662 102 8128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048262
X-RAY DIFFRACTIONf_angle_d0.99711269
X-RAY DIFFRACTIONf_dihedral_angle_d15.7423013
X-RAY DIFFRACTIONf_chiral_restr0.1911245
X-RAY DIFFRACTIONf_plane_restr0.0031337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6988-2.73290.34431260.312569269599
2.7329-2.76890.29311120.301126162728100
2.7689-2.80680.32951340.27425882722100
2.8068-2.84690.29281380.26422624276299
2.8469-2.88940.25841250.27242586271199
2.8894-2.93450.33391540.26112579273399
2.9345-2.98260.30561550.25482563271899
2.9826-3.0340.2811420.25822597273999
3.034-3.08920.31551480.23622576272499
3.0892-3.14860.26681290.23552613274299
3.1486-3.21280.26251440.2262609275399
3.2128-3.28260.25911120.2312620273299
3.2826-3.3590.25641290.22292619274899
3.359-3.44290.24361540.2212573272799
3.4429-3.53590.25991390.21342619275899
3.5359-3.63990.25221270.22462609273699
3.6399-3.75730.26561530.22872592274599
3.7573-3.89150.26761460.20712602274899
3.8915-4.04720.2451510.21222599275098
4.0472-4.23120.23791380.20492616275498
4.2312-4.45390.20141360.20322629276598
4.4539-4.73260.21721570.19852586274398
4.7326-5.09730.2081480.19412636278498
5.0973-5.6090.21841300.20332656278698
5.609-6.41760.25391450.22662662280798
6.4176-8.07420.21881360.20652678281496
8.0742-39.5510.25711250.22522474259983

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