[English] 日本語
Yorodumi
- PDB-6zp6: Yeast 20S proteasome in complex with glidobactin-like natural pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zp6
TitleYeast 20S proteasome in complex with glidobactin-like natural product HB334
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Inhibitor / 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / 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 / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / 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
: / Chem-QOB / 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 ...: / Chem-QOB / 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 S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhao, L. / Le Chapelain, C. / Brachmann, A.O. / Kaiser, M. / Groll, M. / Bode, H.B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
CitationJournal: Chembiochem / Year: 2021
Title: Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-like Proteasome Inhibitors from Photorhabdus laumondii.
Authors: Zhao, L. / Le Chapelain, C. / Brachmann, A.O. / Kaiser, M. / Groll, M. / Bode, H.B.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 25, 2024Group: Source and taxonomy / Structure summary / Category: entity_src_nat / pdbx_molecule_features / Item: _entity_src_nat.pdbx_organism_scientific

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)733,33542
Polymers731,05128
Non-polymers2,28414
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.720, 301.640, 144.360
Angle α, β, γ (deg.)90.000, 113.080, 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(-0.999537, -0.000453, 0.03042), (-0.004812, -0.98495, -0.172775), (0.03004, -0.172841, 0.984491)68.033318, -290.128326, -26.245331

-
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 S288C (yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P21243, proteasome endopeptidase complex

-
Protein , 1 types, 2 molecules FT

#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 S288C (yeast)
References: UniProt: P21242, proteasome endopeptidase complex

-
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 S288C (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 S288C (yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#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 S288C (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 S288C (yeast)
References: UniProt: P23724, 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 S288C (yeast)
References: UniProt: P30657, proteasome endopeptidase complex
#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 S288C (yeast)
References: UniProt: P38624, proteasome endopeptidase complex

-
Non-polymers , 4 types, 380 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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-QOB / ~{N}-[(2~{S},3~{R})-1-[[(5~{S},8~{S},10~{S})-5-methyl-10-oxidanyl-2,7-bis(oxidanylidene)-1,6-diazacyclododec-8-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-5-phenyl-pentanamide / Syrbactin inhibitor / HB334


Class: Inhibitor / Mass: 504.619 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H40N4O6 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002580
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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 / 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 PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2015
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: 2.8→30 Å / Num. obs: 255091 / % possible obs: 97.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.36
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 25704 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZ4

5cz4


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 30.433 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 12674 5 %RANDOM
Rwork0.1744 ---
obs0.1758 240805 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 222.61 Å2 / Biso mean: 80.187 Å2 / Biso min: 30.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å2-0 Å2-0.91 Å2
2---5.18 Å20 Å2
3---2.5 Å2
Refinement stepCycle: final / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49333 0 154 366 49853
Biso mean--64.72 57.67 -
Num. residues----6339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01950383
X-RAY DIFFRACTIONr_bond_other_d0.0020.0246945
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.96668155
X-RAY DIFFRACTIONr_angle_other_deg0.8723.001108934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72956309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28224.422251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.529158743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.26715284
X-RAY DIFFRACTIONr_chiral_restr0.0640.27678
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0256237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210119
X-RAY DIFFRACTIONr_rigid_bond_restr0.818397328
X-RAY DIFFRACTIONr_sphericity_free31.1325273
X-RAY DIFFRACTIONr_sphericity_bonded7.468596525
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3063TIGHT POSITIONAL0.010.05
1A3232TIGHT POSITIONAL0.010.05
1A3389TIGHT POSITIONAL0.010.05
1A3494TIGHT POSITIONAL0.010.05
1A2919TIGHT POSITIONAL0.010.05
1A3765TIGHT THERMAL3.60.5
2B3714TIGHT THERMAL4.420.5
3C3685TIGHT THERMAL10.430.5
4D3538TIGHT THERMAL5.760.5
5E3459TIGHT THERMAL4.670.5
6F3693TIGHT THERMAL3.820.5
7G3724TIGHT THERMAL3.90.5
8H3420TIGHT THERMAL3.20.5
9I3091TIGHT THERMAL2.690.5
10J3063TIGHT THERMAL3.60.5
11K3232TIGHT THERMAL2.990.5
12L3389TIGHT THERMAL2.50.5
13M3494TIGHT THERMAL3.290.5
14N2919TIGHT THERMAL2.490.5
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 919 -
Rwork0.331 17468 -
all-18387 -
obs--98.56 %
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)
10.4005-0.03380.12930.26050.06790.1173-0.03390.0427-0.04660.0760.0308-0.0626-0.0608-0.04940.00320.4386-0.0641-0.0550.1813-0.04250.341366.8033-92.277845.8139
20.17120.10580.15580.07440.10890.1641-0.11030.0031-0.0137-0.07940.03030.0429-0.07530.01320.080.4934-0.07710.07330.24470.06530.32359.5197-87.99216.2189
30.39870.3752-0.11570.3975-0.17430.192-0.0230.00990.0468-0.02120.06640.07530.01180.04-0.04340.55060.0096-0.03150.22570.09220.292232.2428-87.6910.9347
40.2674-0.0218-0.21140.074-0.01240.2387-0.0057-0.0988-0.0407-0.1209-0.00050.1525-0.01790.11550.00620.42450.072-0.18560.1340.10740.42423.025-90.454713.4002
50.04210.04980.060.10140.14090.2516-0.0968-0.00570.0056-0.07970.01990.1102-0.10960.03090.07680.2730.09350.05680.08950.05340.4791-3.4336-94.956945.3236
60.58970.04550.07550.0147-0.01970.1215-0.02090.02190.06940.0419-0.02760.0308-0.04430.0540.04860.51570.03610.18590.1325-0.07930.260915.0849-95.518269.4808
70.3683-0.1248-0.08480.30910.35890.45460.01690.15880.01660.0648-0.015-0.0650.0451-0.0163-0.00190.5328-0.0216-0.05880.0835-0.03630.172347.4982-93.777970.8199
80.0658-0.1104-0.09990.42450.29690.23910.06370.08010.03860.0473-0.0319-0.1515-0.0592-0.0669-0.03180.35430.0049-0.11630.1916-0.02960.325167.7253-129.779647.1281
90.2444-0.207-0.00260.65140.16820.06410.0716-0.0361-0.0036-0.073-0.0634-0.072-0.0328-0.0652-0.00820.3858-0.00390.08930.2705-0.01210.365768.5422-127.559920.689
100.14670.19640.13020.48760.21160.15110.0485-0.0780.0182-0.18950.0160.05010.0061-0.0296-0.06440.536-0.00840.05660.27920.02670.234844.8148-126.9339-0.7911
110.59020.85430.14611.34980.3180.4494-0.0319-0.0590.0948-0.0970.03210.28950.00940.1726-0.00020.37540.0644-0.22940.17850.07450.349511.1265-131.41242.5892
120.01410.06170.04280.53060.3340.24370.01060.00990.0163-0.0219-0.0650.202-0.01210.04370.05440.2770.0462-0.02380.20990.06380.5197-4.4041-135.096928.1959
130.2418-0.24030.03920.33440.01920.04640.01420.11250.0160.099-0.03720.02590.03750.0770.02290.38450.00260.14240.16580.00560.26587.7093-137.623159.8751
140.316-0.1046-0.22520.33970.11580.19010.0320.08610.01780.11850.0088-0.05850.0237-0.0008-0.04080.5414-0.0032-0.04220.1776-0.04070.125739.883-134.435570.5506
150.4701-0.0331-0.08260.17020.09080.0855-0.02430.05350.07650.14160.00430.03140.12260.03460.020.4894-0.0926-0.09520.16330.06640.45032.4414-207.330936.7207
160.06680.0985-0.0510.1518-0.08180.0488-0.049-0.01980.0065-0.10270.0024-0.02020.0570.00290.04660.4765-0.0536-0.18630.1551-0.07990.36658.8491-206.37056.6499
170.28710.2504-0.03610.32030.04130.38650.0848-0.01760.0342-0.1523-0.01930.14670.01670.0807-0.06550.64640.0819-0.24280.0683-0.12230.284236.1408-204.2418-9.1729
180.8128-0.08170.21410.37360.12390.14010.0994-0.10030.0249-0.2484-0.11-0.132-0.0011-0.08460.01060.50690.15660.14110.1474-0.06410.244565.5668-203.58923.2281
190.57580.39140.00160.3136-0.06430.3470.03290.0243-0.19490.05820.0776-0.23910.1293-0.028-0.11050.32150.1678-0.17270.1279-0.14410.627272.6907-204.460235.0163
200.33020.1352-0.13610.064-0.05190.06030.0352-0.0389-0.11970.0864-0.0366-0.1008-0.00970.00050.00150.64070.0528-0.34550.07860.09340.387854.727-208.1259.2799
210.1458-0.1127-0.08110.1550.02980.13990.0080.0516-0.03880.0671-0.01120.07530.08910.02060.00310.6628-0.0068-0.09930.11140.07910.313422.3664-210.275761.0047
220.1884-0.06020.23560.1092-0.09250.29910.08850.0943-0.0460.0297-0.02440.11150.09730.1279-0.0640.3261-0.03160.03510.17230.07910.38311.6948-170.587144.3861
230.2733-0.1636-0.09620.5902-0.19070.17550.0123-0.0078-0.007-0.1023-0.01590.08340.01730.06750.00370.3834-0.0011-0.18190.20480.01730.43490.2991-168.257617.9146
240.33710.2082-0.0220.4891-0.18360.1230.0333-0.13-0.0829-0.11090.04930.0502-0.017-0.0161-0.08260.53580.0255-0.14240.1893-0.03790.200823.5517-165.1976-3.8746
250.29120.40040.16911.5975-0.18070.3077-0.0006-0.053-0.0344-0.12740.0828-0.1347-0.0159-0.0407-0.08230.39610.07740.16820.2119-0.08710.223357.2993-161.3422-0.4423
260.3001-0.0951-0.18320.5424-0.05960.17310.03930.06840.01440.0341-0.0408-0.18160.0147-0.08580.00150.29950.075-0.00640.2246-0.04850.399873.3532-162.026725.0403
270.23080.02850.06090.4353-0.06350.19650.02050.1318-0.04710.173-0.0157-0.0926-0.0222-0.087-0.00480.44570.0375-0.18990.1786-0.00960.309961.8631-164.353557.0881
280.1587-0.04320.07610.13850.01060.05080.06790.1041-0.00750.1442-0.0480.02070.08010.0192-0.01980.5841-0.0162-0.00990.17660.05420.195430.0691-169.993367.6485
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 - 229
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 - 232
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