[English] 日本語
Yorodumi
- PDB-6nhh: Rhodobacter sphaeroides bc1 with azoxystrobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nhh
TitleRhodobacter sphaeroides bc1 with azoxystrobin
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Mitochondrial respiratory chain complex / cytochrome bc1 / inhibitors / electron transfer
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 / membrane / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / 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 ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / 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
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8SP / Chem-AZO / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / STRONTIUM ION / : / : / : ...1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8SP / Chem-AZO / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / STRONTIUM ION / : / : / : / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsXia, D. / Zhou, F. / Yu, C.A.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structure of bacterial cytochromebc1in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit.
Authors: Esser, L. / Zhou, F. / Yu, C.A. / Xia, D.
History
DepositionDec 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
E: Cytochrome b
F: Cytochrome c1
G: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,76325
Polymers199,2106
Non-polymers7,55319
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31530 Å2
ΔGint-386 kcal/mol
Surface area72000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.309, 154.655, 100.939
Angle α, β, γ (deg.)90.000, 95.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain E
12(chain B and resid 1 through 256)
22(chain F and resid 1 through 256)
13chain C
23chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA3 - 2010
211chain EE3 - 2010
112(chain B and resid 1 through 256)B1 - 256
212(chain F and resid 1 through 256)F1 - 256
113chain CC13 - 1001
213chain GG13 - 1001

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 3 types, 6 molecules AEBFCG

#1: Protein Cytochrome b


Mass: 50087.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Expressed as one natural part of a complex in the bacterium rhodobacter sphaeroides
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / References: UniProt: A0A344Q9J3, UniProt: Q3IY10*PLUS
#2: Protein Cytochrome c1


Mass: 29589.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / References: UniProt: A0A344Q9J2, UniProt: Q3IY11*PLUS
#3: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 19928.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
References: UniProt: A0A344Q9J4, UniProt: Q3IY09*PLUS, quinol-cytochrome-c reductase

-
Sugars , 1 types, 2 molecules

#9: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 7 types, 17 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-AZO / METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE / AZOXYSTROBIN


Mass: 403.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17N3O5
#6: Chemical ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 410.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H33NO8P
#7: Chemical ChemComp-8SP / O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine


Type: L-peptide linking / Mass: 511.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H42NO10P
#8: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sr
#10: Chemical ChemComp-HEC / HEME C


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.86 % / Description: red plates
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 57 mg/ml protein incubated with 3.5 mM azoxystrobin (ChemService). Diluted with 50 mM Tris 7.5 pH, 200 mM NaCl, 200 mM Histidine, 0.5% b-OG, 10 % glycerol, 5 mM NaN3 and 1.25 mM NaAscorbate. ...Details: 57 mg/ml protein incubated with 3.5 mM azoxystrobin (ChemService). Diluted with 50 mM Tris 7.5 pH, 200 mM NaCl, 200 mM Histidine, 0.5% b-OG, 10 % glycerol, 5 mM NaN3 and 1.25 mM NaAscorbate. This solution is treated with 0.12-0.30% SMC and 5-8% PEG400 and 10 mM Sr(NO3)2
Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 54693 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.096 / Rrim(I) all: 0.197 / Χ2: 0.993 / Net I/σ(I): 4.4 / Num. measured all: 396134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3-3.076.836580.60.6860.943100
3.07-3.156.836080.7120.570.947100
3.15-3.236.936170.7280.4880.983100
3.23-3.33736410.8140.40.9711000.984
3.33-3.43736710.8520.341.0181000.8410.908
3.43-3.567.136070.9060.2591.0341000.6450.696
3.56-3.77.236440.950.1951.0271000.4860.524
3.7-3.877.236490.9720.1441.0351000.3610.389
3.87-4.077.336100.9830.1091.0461000.2740.295
4.07-4.337.436510.9890.0841.0241000.2140.23
4.33-4.667.436370.9920.0651.0221000.1670.179
4.66-5.137.636650.9950.0581.0041000.1490.16
5.13-5.877.636580.9930.0610.9891000.1560.168
5.87-7.397.736770.9960.0470.8941000.1210.13
7.39-507.637000.9990.020.96799.50.0510.055

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXdev_3339refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementResolution: 3→39.285 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.82 / Phase error: 30.58
RfactorNum. reflection% reflection
Rfree0.2816 1996 3.66 %
Rwork0.2639 --
obs0.2646 54537 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.11 Å2 / Biso mean: 73.7896 Å2 / Biso min: 6.55 Å2
Refinement stepCycle: final / Resolution: 3→39.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13436 0 911 0 14347
Biso mean--38.67 --
Num. residues----1722
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4052X-RAY DIFFRACTION2.937TORSIONAL
12E4052X-RAY DIFFRACTION2.937TORSIONAL
21B2442X-RAY DIFFRACTION2.937TORSIONAL
22F2442X-RAY DIFFRACTION2.937TORSIONAL
31C1632X-RAY DIFFRACTION2.937TORSIONAL
32G1632X-RAY DIFFRACTION2.937TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.07510.37081420.38283736387899
3.0751-3.15820.38611400.352337123852100
3.1582-3.25110.31011430.32237523895100
3.2511-3.3560.35131430.313537503893100
3.356-3.47580.29681420.298837363878100
3.4758-3.61490.28571430.280437453888100
3.6149-3.77930.30631410.267837423883100
3.7793-3.97840.25651420.233737183860100
3.9784-4.22740.24791430.225337783921100
4.2274-4.55330.2051430.22137623905100
4.5533-5.01070.27691430.208137583901100
5.0107-5.73390.30591420.234237553897100
5.7339-7.21670.28731430.258437803923100
7.2167-39.28860.25741460.276638173963100
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)
10.0162-0.02880.02560.0428-0.04150.0291-0.21430.1475-0.3857-0.1526-0.1944-0.81880.88730.422300.931-0.04480.18891.43590.3591.076936.38350.326621.1868
20.222-0.20710.0547-0.0307-0.31080.63550.0428-0.1325-0.1353-0.0139-0.09460.0247-0.11790.0189-0.05990.2704-0.0386-0.00430.66050.06840.4158.341.289738.6942
30.2119-0.0214-0.18090.74690.18780.17150.2006-0.3367-0.15640.2162-0.27280.0601-0.23230.1033-0.05370.4519-0.0649-0.03351.09930.14680.36517.72294.942760.3801
42.6785-0.9749-1.00660.6384-0.18311.3008-0.5506-0.1412-0.48540.1353-0.4253-0.2609-0.04250.7076-1.73110.38570.027-0.12721.51390.3470.734331.6535-7.71857.75
50.31730.07830.23760.2471-0.18160.43060.0577-0.03570.0166-0.03930.0603-0.05420.01850.14730.18290.49240.250.13440.58140.07160.1882-1.11866.974446.7473
60.28020.00660.01890.2599-0.1830.3953-0.181-0.2332-0.31480.07880.1012-0.38470.0646-0.4109-0.0120.4041-0.0922-0.10040.81450.12760.8198-22.2918-15.841334.3475
71.2138-0.11640.12311.50710.13670.7497-0.0787-0.0808-0.14750.05640.04340.2185-0.1012-0.3003-00.4234-0.0159-0.01421.2680.13720.6962-25.4822-7.657939.8694
80.02870.0434-0.06590.023-0.0990.21590.014-0.0530.1941-0.10030.1004-0.15950.2279-0.16130.00830.2885-0.02320.02240.80640.040.6118-8.9017-19.350133.1761
90.10160.1322-0.15390.76330.16110.39990.10080.3435-1.3137-0.30730.0350.28230.2035-0.02760.00010.6492-0.01940.0381.2441-0.02370.96343.3681-11.00817.1195
100.2996-0.2322-0.10980.15790.07710.029-0.42960.47770.9321-0.70610.29190.2183-0.40980.07230.33340.9017-0.2991-0.52580.62110.22790.8955-25.97244.0321-8.8664
110.02020.02270.00340.0253-0.01740.0243-0.2465-0.10990.37140.0386-0.1124-0.5744-0.46130.3681-00.7802-0.0249-0.1161.62130.35591.015736.001818.196336.7264
120.01310.0366-0.08930.0175-0.17380.30380.06150.0472-0.0224-0.0081-0.0949-0.0526-0.1504-0.09-0.01720.3634-0.00680.02030.67510.14850.388910.159124.976517.7606
13-0.0370.19860.00130.07870.02840.23220.09280.1044-0.074-0.0527-0.31580.32150.01370.1039-1.76770.2674-0.11350.03010.18190.22270.061815.65417.448413.8087
140.425-0.0142-0.23380.0506-0.1080.3843-0.00170.08980.1165-0.3837-0.10150.0624-0.0099-0.1581-0.07490.64470.02390.03161.17180.14160.43421.165316.7812-3.0126
150.14650.01970.13090.1645-0.13260.16560.0354-0.0098-0.0493-0.10630.01070.0347-0.02730.11380.12620.5472-0.03890.15930.73730.12230.351418.176719.3269-5.9608
160.20180.22190.10370.38220.14660.0652-0.0599-0.0997-0.0029-0.1839-0.3154-0.2248-0.0766-0.0415-1.47510.674-0.21310.40691.32750.24910.582939.210126.35470.0542
170.2826-0.0939-0.09370.0932-0.04370.12140.0623-0.01850.00620.0086-0.0286-0.00940.01940.01880.07370.715-0.1369-0.09690.68970.08330.09283.426716.00434.576
180.17720.15980.06420.37160.17320.1079-0.08130.06830.0221-0.02470.2907-0.2035-0.066-0.260.09610.6270.1045-0.08260.59450.22590.6076-16.765541.35913.0834
190.3680.0372-0.24080.09810.04960.2612-0.0144-0.14790.329-0.17860.0630.150.26340.14560.05120.62640.113-0.05810.88290.21760.5389-20.451235.90767.9187
200.1042-0.0016-0.27870.00180.0050.76640.14350.03640.22080.0550.0673-0.2102-0.1707-0.19090.04630.839-0.232-0.08110.38110.17220.793717.922441.957623.0096
210.05080.0392-0.02780.14350.03920.0202-0.42470.02640.24890.14950.2667-0.03210.262-0.01210.00330.52850.04290.00460.5754-0.12580.5744.478533.679934.698
221.2830.17180.81890.56840.18030.5280.0641-0.394-0.27020.48980.09110.28910.4168-0.2612-0.09240.73180.03890.25870.29180.06960.5501-31.490122.433253.897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 33 )A3 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 295 or resseq 1001 or resseq 1002)A34 - 295
3X-RAY DIFFRACTION2chain 'A' and (resid 34 through 295 or resseq 1001 or resseq 1002)A1001
4X-RAY DIFFRACTION2chain 'A' and (resid 34 through 295 or resseq 1001 or resseq 1002)A1002
5X-RAY DIFFRACTION3chain 'A' and (resid 296 through 405 )A296 - 405
6X-RAY DIFFRACTION4chain 'A' and (resid 406 through 432 )A406 - 432
7X-RAY DIFFRACTION5chain 'A' and resid 1003A1003
8X-RAY DIFFRACTION6chain 'B' and (resid 1 through 46 )B1 - 46
9X-RAY DIFFRACTION7chain 'B' and (resid 47 through 183 )B47 - 183
10X-RAY DIFFRACTION8chain 'B' and (resid 184 through 256 )B184 - 256
11X-RAY DIFFRACTION9chain 'C' and (resid 13 through 51 )C13 - 51
12X-RAY DIFFRACTION10chain 'C' and (resid 52 through 187 or resid 1001)C52 - 187
13X-RAY DIFFRACTION10chain 'C' and (resid 52 through 187 or resid 1001)C1001
14X-RAY DIFFRACTION11chain 'E' and (resid 3 through 33 )E3 - 33
15X-RAY DIFFRACTION12chain 'E' and (resid 34 through 118 )E34 - 118
16X-RAY DIFFRACTION13chain 'E' and (resid 119 through 269 or resseq 1001 or resseq 1002)E119 - 269
17X-RAY DIFFRACTION13chain 'E' and (resid 119 through 269 or resseq 1001 or resseq 1002)E1001
18X-RAY DIFFRACTION13chain 'E' and (resid 119 through 269 or resseq 1001 or resseq 1002)E1002
19X-RAY DIFFRACTION14chain 'E' and (resid 270 through 327 )E270 - 327
20X-RAY DIFFRACTION15chain 'E' and (resid 328 through 405 )E328 - 405
21X-RAY DIFFRACTION16chain 'E' and (resid 406 through 432 )E406 - 432
22X-RAY DIFFRACTION17chain 'E' and resid 1003E1003
23X-RAY DIFFRACTION18chain 'F' and (resid 1 through 46 )F1 - 46
24X-RAY DIFFRACTION19chain 'F' and (resid 47 through 222 )F47 - 222
25X-RAY DIFFRACTION20chain 'F' and (resid 223 through 256 )F223 - 256
26X-RAY DIFFRACTION21chain 'G' and (resid 13 through 51 )G13 - 51
27X-RAY DIFFRACTION22chain 'G' and (resid 52 through 187 or resid 1001)G52 - 187
28X-RAY DIFFRACTION22chain 'G' and (resid 52 through 187 or resid 1001)G1001

+
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