[English] 日本語
Yorodumi
- PDB-8rhj: Yeast 20S proteasome in complex with a macrocyclic oxindole epoxy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rhj
TitleYeast 20S proteasome in complex with a macrocyclic oxindole epoxyketone (compound 5)
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Macrocyclic oxindole epoxyketone
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Proteasome / Epoxomicin / TMC-95A / Carfilzomib / Macrocycle / Binding Analysis
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
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
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsGoetz, M.G. / Godwin, K. / Price, R. / Dorn, R. / Merrill-Steskal, G. / Hansen, H. / Klemmer, W. / Produturi, G. / Rocha, M. / Palmer, M. ...Goetz, M.G. / Godwin, K. / Price, R. / Dorn, R. / Merrill-Steskal, G. / Hansen, H. / Klemmer, W. / Produturi, G. / Rocha, M. / Palmer, M. / Molacek, L. / Strater, Z. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/10-3 Germany
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome.
Authors: Gotz, M.G. / Godwin, K. / Price, R. / Dorn, R. / Merrill-Steskal, G. / Klemmer, W. / Hansen, H. / Produturi, G. / Rocha, M. / Palmer, M. / Molacek, L. / Strater, Z. / Groll, M.
History
DepositionDec 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Probable proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Probable proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
g: Macrocyclic oxindole epoxyketone
e: Macrocyclic oxindole epoxyketone
i: Macrocyclic oxindole epoxyketone
f: Macrocyclic oxindole epoxyketone
h: Macrocyclic oxindole epoxyketone
j: Macrocyclic oxindole epoxyketone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,66544
Polymers735,40034
Non-polymers26510
Water2,900161
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)135.690, 302.010, 144.240
Angle α, β, γ (deg.)90.00, 113.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

-
Components

-
Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639
#2: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303
#4: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


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 Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302
#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243

-
Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25451
#10: Protein Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22141
#11: Protein Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23724
#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
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex

-
Protein / Protein/peptide , 2 types, 8 molecules FTgeifhj

#15: Protein/peptide
Macrocyclic oxindole epoxyketone


Mass: 724.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21242

-
Non-polymers , 3 types, 171 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2020
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: 3.05→30 Å / Num. obs: 194819 / % possible obs: 96.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.8
Reflection shellResolution: 3.05→3.15 Å / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 18384 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 39.938 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21207 9733 5 %RANDOM
Rwork0.17596 ---
obs0.17728 184930 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.227 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-0 Å2-0.23 Å2
2---3.28 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49622 0 10 161 49793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01350550
X-RAY DIFFRACTIONr_bond_other_d0.0020.01747082
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.65168440
X-RAY DIFFRACTIONr_angle_other_deg1.1371.59109256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25556306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35822.7912530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.941158736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.97115284
X-RAY DIFFRACTIONr_chiral_restr0.040.26688
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0256744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210424
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1734.88225314
X-RAY DIFFRACTIONr_mcbond_other3.1734.88225313
X-RAY DIFFRACTIONr_mcangle_it4.7167.31431590
X-RAY DIFFRACTIONr_mcangle_other4.7167.31431591
X-RAY DIFFRACTIONr_scbond_it3.085.24125236
X-RAY DIFFRACTIONr_scbond_other3.085.24125236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5257.7336850
X-RAY DIFFRACTIONr_long_range_B_refined6.54155.84453007
X-RAY DIFFRACTIONr_long_range_B_other6.53955.8452992
X-RAY DIFFRACTIONr_rigid_bond_restr0.557397632
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1010J3063tight positional0.010.05
1111K3263tight positional0.010.05
1212L3389tight positional0.010.05
1313M3564tight positional0.010.05
1414N3019tight positional0.010.05
11A3765tight thermal9.640.5
22B3714tight thermal10.770.5
33C3685tight thermal13.780.5
44D3540tight thermal10.850.5
55E3459tight thermal12.110.5
66F3693tight thermal10.420.5
77G3724tight thermal9.340.5
88H3386tight thermal7.610.5
99I3091tight thermal7.430.5
1010J3063tight thermal7.230.5
1111K3263tight thermal7.460.5
1212L3389tight thermal80.5
1313M3564tight thermal7.230.5
1414N3019tight thermal6.910.5
LS refinement shellResolution: 3.05→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 729 -
Rwork0.285 13854 -
obs--98.53 %
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)
10.9382-0.1290.23450.57350.03170.2013-0.06140.09140.0637-0.00010.0338-0.1484-0.0927-0.03140.02760.3779-0.0608-0.04510.187-0.05260.444766.8368-92.248345.6828
20.7025-0.0750.06240.33190.2870.6529-0.1382-0.03450.0192-0.21830.0166-0.0229-0.16060.09420.12160.4681-0.06740.05840.2240.0850.356659.6436-88.056216.0346
30.59230.4544-0.1560.44650.1210.7442-0.07370.08130.0392-0.18020.1051-0.0037-0.08980.0651-0.03140.5760.0074-0.05690.2360.09460.373632.3794-87.79510.6626
40.6607-0.0830.16150.3284-0.25230.7928-0.0056-0.0795-0.0008-0.2159-0.0540.2278-0.05460.09430.05970.43970.0759-0.18960.12870.07240.49623.1298-90.450713.1222
50.5322-0.02260.07430.19080.03230.5228-0.1063-0.05990.072-0.10660.01120.1673-0.1333-0.02940.09510.27430.0926-0.03680.179-0.00830.5513-3.4233-94.940145.127
60.72930.1519-0.15060.4181-0.11980.29320.0401-0.03560.1090.1035-0.05060.0941-0.0321-0.00520.01050.43660.05040.1080.2163-0.10550.322815.0496-95.422669.4207
70.4429-0.0305-0.08570.9007-0.18870.33580.06370.04510.08420.1624-0.0675-0.1075-0.0205-0.04650.00370.508-0.0085-0.0890.1538-0.07660.306347.5136-93.65470.7861
80.1324-0.0719-0.05790.1060.04030.02790.04540.1390.05460.059-0.0063-0.17890.0099-0.0624-0.03910.3731-0.0013-0.11480.2693-0.06010.438467.5096-130.422947.7784
91.1751-0.2263-0.12741.33140.22660.3170.02840.0708-0.0434-0.0893-0.0215-0.1437-0.1342-0.0226-0.00690.3167-0.03360.07770.2141-0.01330.40668.4376-127.754420.571
100.61810.0562-0.09210.6408-0.08660.49280.01-0.01490.0259-0.24320.03190.0521-0.04550.0169-0.0420.5519-0.010.03720.27220.02130.267744.9341-127.0869-1.1107
110.35980.36220.19631.50890.18070.44010.05570.00360.0274-0.161-0.03810.2092-0.0560.0753-0.01760.45960.0229-0.2080.24090.050.387611.1953-131.53122.1854
120.3443-0.03610.29270.28170.2190.59110.0843-0.0545-0.0248-0.072-0.03250.1614-0.0445-0.0221-0.05180.29890.0246-0.08810.2420.04050.5521-4.3874-134.948628.1595
130.88640.530.01490.7114-0.10060.46240.09410.01960.04360.1234-0.10620.05080.04490.01490.01210.3513-0.01650.05520.2485-0.00370.32677.8428-138.487160.0201
141.2008-0.23420.01811.7311-0.22820.04090.0380.11030.08730.1062-0.0076-0.0460.03290.0273-0.03040.5045-0.0109-0.06970.2556-0.04550.191240.0441-134.605870.1956
150.6652-0.3289-0.22410.45110.1780.2047-0.05190.0885-0.00430.03610.02810.14320.1924-0.03490.02380.4473-0.108-0.20770.14090.07950.52092.3543-207.381536.3638
160.85770.14780.29630.48850.03030.842-0.0516-0.0151-0.0035-0.0061-0.01220.07210.0296-0.11770.06380.4954-0.005-0.2320.1489-0.07440.46378.8131-206.25526.3753
170.59520.360.24360.50560.27040.70090.19-0.0516-0.0002-0.2917-0.07540.30140.01310.0975-0.11450.76150.1213-0.38940.0598-0.12720.482936.3205-204.0799-9.5261
180.8746-0.08950.30470.74260.17130.640.0763-0.09060.0241-0.3518-0.141-0.11440.0799-0.04230.06470.5870.17090.07770.1319-0.1180.354865.5996-203.57243.0977
190.52950.3359-0.02010.6624-0.18430.80730.0682-0.0248-0.1501-0.03250.0575-0.38580.15450.0299-0.12570.26170.1375-0.18960.1073-0.1530.696772.5873-204.501134.9953
200.67970.336-0.00290.19890.13370.63720.1505-0.0572-0.22520.0893-0.0461-0.16550.0934-0.069-0.10440.54220.0376-0.38260.07180.09550.498154.5266-208.279359.2865
210.1789-0.14340.04950.53670.030.27250.02810.0283-0.03450.083-0.00130.0979-0.03280.0178-0.02670.5605-0.0304-0.17250.09810.10390.373422.1286-210.43360.8257
220.28470.00680.16150.06250.00460.09190.11880.1173-0.0892-0.0158-0.04880.13650.07440.06-0.070.4331-0.0447-0.08430.26110.04720.51381.8146-170.120944.9335
230.7305-0.2568-0.03091.2875-0.21030.14570.02190.07230.0208-0.17870.01750.21650.11460.0873-0.03940.3719-0.0288-0.20240.177-0.02310.42640.4436-168.077617.6228
240.54330.0693-0.08881.19110.42350.23730.05460.0336-0.1154-0.29590.0110.0345-0.0290.0756-0.06570.59830.013-0.18140.2236-0.02080.303523.634-164.9948-4.2404
250.63750.72-0.0221.7057-0.33180.29860.06470.1238-0.0518-0.18660.0469-0.10790.06260.0161-0.11160.46430.06140.07230.2734-0.09430.323657.422-161.1584-0.7432
260.20970.0035-0.26020.5596-0.23440.51730.06660.0016-0.0139-0.0458-0.0462-0.20890.0455-0.0046-0.02040.29150.079-0.0110.2626-0.09120.54173.3501-162.215325.1671
270.98870.21250.20630.63540.18310.61240.090.0966-0.02720.1667-0.0315-0.0857-0.0459-0.0387-0.05850.37230.0285-0.19580.17080.01030.341761.6668-164.195157.3727
280.7029-0.3003-0.2211.62390.61880.27320.06150.1359-0.05390.0906-0.040.0960.0023-0.0755-0.02150.5246-0.0327-0.07210.24070.07780.254929.6501-169.820767.2769
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 DIFFRACTION8H6 - 222
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K6 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N6 - 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 DIFFRACTION22V6 - 222
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y6 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b6 - 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://pdbjlvh1.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