[English] 日本語
Yorodumi
- PDB-7o2l: Yeast 20S proteasome in complex with the covalently bound inhibit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o2l
TitleYeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)
Components
  • (Proteasome endopeptidase ...) x 4
  • (Proteasome subunit beta type- ...) x 2
  • 20S proteasomeProteasome
  • BJ4_G0020160.mRNA.1.CDS.1
  • BJ4_G0021480.mRNA.1.CDS.1
  • BJ4_G0043800.mRNA.1.CDS.1
  • HLJ1_G0039880.mRNA.1.CDS.1
  • HLJ1_G0048980.mRNA.1.CDS.1
  • Probable proteasome subunit alpha type-7
  • Proteasome subunit beta
KeywordsHYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / b-lactone / Binding Analysis
Function / homology
Function and homology information


proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex ...proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm
Similarity search - Function
Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site ...Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Chem-V08 / PRE5 isoform 1 / PRE9 isoform 1 / SCL1 isoform 1 / PRE7 isoform 1 / Proteasome subunit beta / PRE6 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 / PUP3 isoform 1 ...Chem-V08 / PRE5 isoform 1 / PRE9 isoform 1 / SCL1 isoform 1 / PRE7 isoform 1 / Proteasome subunit beta / PRE6 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 / PUP3 isoform 1 / : / PRE8 isoform 1 / : / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShi, Y.M. / Hirschmann, M. / Shi, Y.N. / Shabbir, A. / Abebew, D. / Tobias, N.J. / Gruen, P. / Crames, J.J. / Poeschel, L. / Kuttenlochner, W. ...Shi, Y.M. / Hirschmann, M. / Shi, Y.N. / Shabbir, A. / Abebew, D. / Tobias, N.J. / Gruen, P. / Crames, J.J. / Poeschel, L. / Kuttenlochner, W. / Richter, C. / Herrmann, J. / Mueller, R. / Thanwisai, A. / Pidot, S.J. / Stinear, T.P. / Groll, M. / Kim, Y. / Bode, H.
CitationJournal: Nat.Chem. / Year: 2022
Title: Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria.
Authors: Shi, Y.M. / Hirschmann, M. / Shi, Y.N. / Ahmed, S. / Abebew, D. / Tobias, N.J. / Grun, P. / Crames, J.J. / Poschel, L. / Kuttenlochner, W. / Richter, C. / Herrmann, J. / Muller, R. / ...Authors: Shi, Y.M. / Hirschmann, M. / Shi, Y.N. / Ahmed, S. / Abebew, D. / Tobias, N.J. / Grun, P. / Crames, J.J. / Poschel, L. / Kuttenlochner, W. / Richter, C. / Herrmann, J. / Muller, R. / Thanwisai, A. / Pidot, S.J. / Stinear, T.P. / Groll, M. / Kim, Y. / Bode, H.B.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLJ1_G0039880.mRNA.1.CDS.1
B: BJ4_G0021480.mRNA.1.CDS.1
C: HLJ1_G0048980.mRNA.1.CDS.1
D: 20S proteasome
E: BJ4_G0043800.mRNA.1.CDS.1
F: Probable proteasome subunit alpha type-7
G: BJ4_G0020160.mRNA.1.CDS.1
H: Proteasome endopeptidase complex
I: Proteasome endopeptidase complex
J: Proteasome subunit beta
K: Proteasome subunit beta type-5
L: Proteasome endopeptidase complex
M: Proteasome subunit beta type-7
N: Proteasome endopeptidase complex
O: HLJ1_G0039880.mRNA.1.CDS.1
P: BJ4_G0021480.mRNA.1.CDS.1
Q: HLJ1_G0048980.mRNA.1.CDS.1
R: 20S proteasome
S: BJ4_G0043800.mRNA.1.CDS.1
T: Probable proteasome subunit alpha type-7
U: BJ4_G0020160.mRNA.1.CDS.1
V: Proteasome endopeptidase complex
W: Proteasome endopeptidase complex
X: Proteasome subunit beta
Y: Proteasome subunit beta type-5
Z: Proteasome endopeptidase complex
a: Proteasome subunit beta type-7
b: Proteasome endopeptidase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,27744
Polymers731,05128
Non-polymers1,22616
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, AU contains one biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.120, 301.500, 144.250
Angle α, β, γ (deg.)90.000, 112.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99956, -0.002515, 0.029542), (-0.002675, -0.984681, -0.174346), (0.029528, -0.174348, 0.984241)67.333443, -289.954102, -26.671921

-
Components

-
Protein , 8 types, 16 molecules AOBPCQDRESFTGUJX

#1: Protein HLJ1_G0039880.mRNA.1.CDS.1 / Proteasome subunit alpha type-2


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1BIF8
#2: Protein BJ4_G0021480.mRNA.1.CDS.1 / Proteasome subunit alpha type-3


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXC6
#3: Protein HLJ1_G0048980.mRNA.1.CDS.1 / Proteasome subunit alpha type-4


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q273
#4: Protein 20S proteasome / Proteasome


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379
#5: Protein BJ4_G0043800.mRNA.1.CDS.1 / Proteasome subunit alpha type-6


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTH4
#6: Protein Probable proteasome subunit alpha type-7


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q4M4
#7: Protein BJ4_G0020160.mRNA.1.CDS.1 / HLJ1_G0019920.mRNA.1.CDS.1 / Proteasome subunit alpha type-1


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYC9
#10: Protein Proteasome subunit beta /


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q0W2, proteasome endopeptidase complex

-
Proteasome endopeptidase ... , 4 types, 8 molecules HVIWLZNb

#8: Protein Proteasome endopeptidase complex /


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q449, proteasome endopeptidase complex
#9: Protein Proteasome endopeptidase complex /


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6L0YA22, proteasome endopeptidase complex
#12: Protein Proteasome endopeptidase complex /


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q0P3, proteasome endopeptidase complex
#14: Protein Proteasome endopeptidase complex /


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6L0ZSP2, proteasome endopeptidase complex

-
Proteasome subunit beta type- ... , 2 types, 4 molecules KYMa

#11: Protein Proteasome subunit beta type-5 / PSMB5


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6V8RU78, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30657

-
Non-polymers , 4 types, 142 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-V08 / (2 {R},3 {S})-3-methanoyl-4-methyl-2-hydroxy-pentanoic acid


Mass: 160.168 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H12O4 / Feature type: SUBJECT OF INVESTIGATION
#18: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 203690 / % possible obs: 96.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2 / Num. unique obs: 19450

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZ4

5cz4


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 43.994 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 10176 5 %RANDOM
Rwork0.1779 ---
obs0.1798 193349 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 217.19 Å2 / Biso mean: 90.54 Å2 / Biso min: 38.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å2-0 Å2-2.11 Å2
2---3.1 Å20 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49300 0 76 126 49502
Biso mean--107.26 62.47 -
Num. residues----6334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01350264
X-RAY DIFFRACTIONr_bond_other_d0.0010.01746846
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.64368004
X-RAY DIFFRACTIONr_angle_other_deg1.1541.582108720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99756304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10922.8022534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.673158734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.54515284
X-RAY DIFFRACTIONr_chiral_restr0.0350.26650
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0256512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210356
X-RAY DIFFRACTIONr_rigid_bond_restr0.331397110
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3063TIGHT POSITIONAL00.05
1A3185TIGHT POSITIONAL00.05
1A3389TIGHT POSITIONAL00.05
1A3487TIGHT POSITIONAL0.010.05
1A2941TIGHT POSITIONAL00.05
1A3765TIGHT THERMAL9.030.5
2B3714TIGHT THERMAL8.530.5
3C3685TIGHT THERMAL10.740.5
4D3540TIGHT THERMAL8.440.5
5E3459TIGHT THERMAL8.30.5
6F3693TIGHT THERMAL7.840.5
7G3724TIGHT THERMAL7.580.5
8H3373TIGHT THERMAL7.070.5
9I3091TIGHT THERMAL6.360.5
10J3063TIGHT THERMAL6.520.5
11K3185TIGHT THERMAL6.320.5
12L3389TIGHT THERMAL6.320.5
13M3487TIGHT THERMAL6.370.5
14N2941TIGHT THERMAL5.660.5
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 762 -
Rwork0.354 14467 -
all-15229 -
obs--98.7 %
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)
10.9425-0.37730.36990.94640.03240.5362-0.07090.0793-0.025-0.02280.0283-0.2241-0.1643-0.00810.04270.5893-0.097-0.0140.1767-0.04350.563566.5052-92.186845.796
20.59250.2225-0.29980.2240.18651.6519-0.11250.0320.0093-0.1277-0.0021-0.0598-0.20070.15380.11470.6599-0.07690.07350.15950.06430.475259.2662-87.991516.2035
30.78750.29450.06790.2892-0.32370.8636-0.00530.10170.0718-0.09270.06790.0133-0.00440.0815-0.06260.7522-0.0153-0.05540.18640.06960.427432.0204-87.61530.8994
40.82730.2071-0.09970.3122-0.03530.8634-0.0557-0.07920.0064-0.13820.05310.2652-0.08930.07290.00260.64890.1146-0.23530.08770.11750.63622.8195-90.352313.3927
50.57480.28420.25090.4473-0.19650.9159-0.1528-0.13750.0446-0.09180.03680.2226-0.1721-0.07720.1160.4510.12880.03290.1722-0.00420.7628-3.6807-94.856945.2981
60.90580.15430.05630.4439-0.32240.3123-0.0417-0.05480.15020.1631-0.02760.1086-0.0316-0.02870.06930.67890.03790.18620.2451-0.12320.46214.8227-95.405469.4694
70.77850.154-0.11640.67250.04121.18720.0430.04210.01910.2099-0.0272-0.0879-0.012-0.0401-0.01580.7499-0.0269-0.08930.1318-0.06430.41247.2366-93.668770.7848
80.0958-0.0662-0.04490.41190.2010.13930.0380.0030.02350.13080.017-0.2452-0.05030.0529-0.05510.57250.0037-0.08450.294-0.03710.600467.59-129.663747.1727
90.8272-0.151-0.11731.81870.23690.37620.0227-0.07260.0238-0.13790.037-0.2955-0.10460.0153-0.05970.5577-0.01960.15680.2292-0.02210.546768.2168-127.3520.7226
100.95020.00210.2541.80160.06840.42750.0484-0.05190.0845-0.43750.01050.0376-0.0302-0.0289-0.0590.7771-0.02790.080.22310.02220.312644.5426-126.912-0.8714
110.6050.72310.3571.62390.04120.5977-0.00480.06980.0242-0.2250.07070.2801-0.06110.015-0.06590.68940.0518-0.22110.18850.03410.509610.8318-131.28972.4098
120.44780.18720.16081.1370.25880.81630.0459-0.14240.0228-0.0990.03490.3458-0.04910.0168-0.08080.44110.0564-0.09780.17920.06960.6978-4.6108-134.982328.1508
130.77390.25570.04541.6965-0.09450.27440.0659-0.05710.05220.2622-0.09120.18190.01490.01530.02530.5587-0.01420.13230.26260.00250.48717.465-137.425859.8406
141.2078-0.3608-0.61151.60540.05040.68570.0045-0.00730.060.3170.0041-0.0660.06770.0858-0.00860.7136-0.0228-0.08090.2709-0.04820.361739.696-134.373970.4131
150.6079-0.3001-0.2390.50770.50710.68-0.01490.05530.0059-0.0653-0.00170.1710.2346-0.07580.01660.6543-0.1635-0.19110.06960.09960.62872.4352-207.371436.8239
161.3479-0.00660.37160.4582-0.2740.9418-0.02560.00830.0117-0.1004-0.02380.08890.0506-0.10780.04940.7237-0.0253-0.26010.0655-0.0770.48528.8538-206.37286.7704
170.60960.37060.04050.54080.07950.69810.09740.0298-0.0588-0.32380.06230.1870.09250.0241-0.15980.98930.0639-0.25410.0781-0.08650.419235.9544-204.2838-9.0653
181.20810.13850.42950.1525-0.09420.55640.043-0.12180.0466-0.2351-0.0607-0.18310.16060.0080.01770.84710.24550.20530.1376-0.09680.51365.3721-203.65463.1457
190.62650.187-0.42780.5161-0.22210.79580.0231-0.0535-0.0085-0.0263-0.006-0.29240.22990.0591-0.01710.52480.2356-0.15680.1326-0.09930.777872.6135-204.4835.0994
201.06940.32690.11070.12550.07440.2760.0924-0.1408-0.27720.1612-0.0338-0.16260.1543-0.0229-0.05860.84850.0964-0.32040.08450.10550.545954.6557-208.102259.4095
210.4988-0.15450.18410.5711-0.31271.10720.0312-0.0435-0.05420.0904-0.00060.12690.05040.0545-0.03060.8251-0.0335-0.11140.05220.0950.434122.3168-210.270461.0941
220.3031-0.0106-0.0580.42730.06020.03680.03480.0054-0.04510.1427-0.00440.24140.086-0.0055-0.03040.5808-0.0419-0.02930.21940.08520.59081.5018-170.63744.4878
231.2967-0.26670.21371.8027-0.71320.5749-0.0499-0.0984-0-0.23270.09660.26420.1145-0.0191-0.04670.588-0.0293-0.24910.1502-0.0050.57590.2706-168.46118.0057
241.06740.1139-0.16891.89650.2490.28210.03350.0095-0.1102-0.31910.0157-0.00960.00470.0515-0.04920.82350.0166-0.19850.1547-0.02810.316723.4427-165.1991-3.8814
250.25210.46920.13121.3898-0.04110.48060.08150.0439-0.072-0.29250.0679-0.12430.05580.1034-0.14940.72980.08650.17350.2218-0.09610.437357.2247-161.3683-0.6746
260.45410.0667-0.44911.2591-0.20030.58560.0598-0.1229-0.0289-0.0717-0.0414-0.32220.05840.0469-0.01830.52420.10980.02570.2376-0.09150.661873.263-162.07624.944
270.64-0.0172-0.00751.40140.05060.26480.0406-0.0336-0.03940.255-0.0293-0.230.0488-0.0935-0.01130.63960.0571-0.21770.2401-0.01010.507761.929-165.062456.8873
281.5089-0.16390.27061.7112-0.29920.55190.086-0.0350.01330.32770.0040.0990.0865-0.0406-0.090.7453-0.0294-0.0260.2290.05530.326229.9436-169.901767.5579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 228
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 228
28X-RAY DIFFRACTION28b1 - 196

+
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