[English] 日本語
Yorodumi
- PDB-4qxj: yCP beta5-M45A mutant in complex with the epoxyketone inhibitor O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qxj
TitleyCP beta5-M45A mutant in complex with the epoxyketone inhibitor ONX 0914
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cancer / Proteasome / Bortezomib / Drug Resistance / Binding Analysis / HYDROLASE-HYDROLASE INHIBITOR complex
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
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / 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 ...1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuber, E.M. / Heinemeyer, W. / Groll, M.
CitationJournal: Structure / Year: 2015
Title: Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and ONX 0914.
Authors: Huber, E.M. / Heinemeyer, W. / Groll, M.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)735,43646
Polymers730,93128
Non-polymers4,50618
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120570 Å2
ΔGint-422 kcal/mol
Surface area214580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.490, 299.730, 145.610
Angle α, β, γ (deg.)90.00, 113.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999647, -0.001045, 0.02655), (-0.003562, -0.984936, -0.172882), (0.026331, -0.172916, 0.984585)68.86047, -287.76123, -25.77637

-
Components

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

#1: Protein Proteasome subunit alpha type-2


Mass: 27191.828 Da / Num. of mol.: 2 / Mutation: M45A / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein 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) / Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein 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) / Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein 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) / Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein 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) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex

-
Protein , 1 types, 2 molecules FT

#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) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex

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

#8: Protein Proteasome subunit beta type-2


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-4


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5


Mass: 23265.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRE2, DOA3, PRG1, YPR103W, P8283.10 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7


Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

-
Non-polymers , 5 types, 295 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / 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-04C / 1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 584.704 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H44N4O7
References: 1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL
#18: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
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, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2013
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / 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. all: 265266 / Num. obs: 259961 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.8 / % possible all: 99.2

-
Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RYP

1ryp


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 29.122 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22235 12998 5 %RANDOM
Rwork0.18773 ---
obs0.18945 246963 98.1 %-
all-259961 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.3 Å20 Å2-0.45 Å2
2---7.51 Å2-0 Å2
3---3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49198 0 308 277 49783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950427
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248187
X-RAY DIFFRACTIONr_angle_refined_deg0.8911.9768241
X-RAY DIFFRACTIONr_angle_other_deg0.8073.003110969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05256294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07824.4052243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17158711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.93515284
X-RAY DIFFRACTIONr_chiral_restr0.0510.27677
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257102
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0211302
X-RAY DIFFRACTIONr_mcbond_it2.9826.16925266
X-RAY DIFFRACTIONr_mcbond_other2.9816.16925265
X-RAY DIFFRACTIONr_mcangle_it3.9489.23531530
X-RAY DIFFRACTIONr_mcangle_other3.9489.23531531
X-RAY DIFFRACTIONr_scbond_it2.9026.56425161
X-RAY DIFFRACTIONr_scbond_other2.9026.56425161
X-RAY DIFFRACTIONr_scangle_other3.6719.68236712
X-RAY DIFFRACTIONr_long_range_B_refined4.51847.95353768
X-RAY DIFFRACTIONr_long_range_B_other4.51147.95353747
X-RAY DIFFRACTIONr_rigid_bond_restr1.44398614
X-RAY DIFFRACTIONr_sphericity_free30.1625193
X-RAY DIFFRACTIONr_sphericity_bonded19.833597786
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 935 -
Rwork0.304 17780 -
obs--99.2 %
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)
10.0110.0055-0.01460.0044-0.00620.02220.00370.0088-0.0104-0.0017-0.0018-0.0171-0.0093-0.0021-0.00190.1237-0.00850.00340.1012-0.00490.1267.8446-91.601846.1725
20.00210.00480.0080.01650.02740.0519-0.00880.0009-0.0054-0.01090.00330.00860.00430.00860.00540.1216-0.00670.02350.10560.00650.108660.6739-87.437316.4972
30.04630.028-0.02080.0198-0.01460.01160.0044-0.00250.0095-0.00580.00860.02090.01050.0027-0.0130.13310.00650.00330.09990.00910.11333.3211-86.79211.0815
40.03140.02560.03080.06070.040.0372-0.01920.01750.0015-0.0324-0.00010.0637-0.01880.02020.01930.08360.02830.00750.04450.01010.1263.9482-89.45613.5666
50.0008-0.0016-0.00010.0045-0.0020.00370.0021-0.0047-0.00850.00470.00550.0254-0.00270.0148-0.00750.05320.01650.03220.0871-0.00320.1431-2.4194-93.675245.602
60.00080.00020.00120.0007-0.00010.00260.00610.0006-0.00140.0045-0.00680.00450.01350.0080.00080.10490.00430.04910.0847-0.0120.087515.9886-94.304969.9098
70.0078-0.0051-0.00160.0082-0.00030.00150.01020.01870.00680.0119-0.0155-0.0173-0.002-0.00830.00520.1578-0.00360.0090.07-0.01990.092948.5291-92.845271.2599
80.0041-0.0006-0.00470.0210.00380.00680.01240.01390.00290.0254-0.0102-0.038-0.0038-0.023-0.00210.104-0.0092-0.0030.0883-0.01370.109768.1278-129.602648.2712
90.00940.0224-0.00980.0764-0.01770.01520.0082-0.0020.0035-0.0246-0.0033-0.0166-0.0219-0.0157-0.00490.1083-0.00610.0220.0999-0.00230.118569.2016-127.089220.983
100.04120.0140.00140.017-0.00150.0020.0148-0.01790.0215-0.0345-0.00510.00620.00890.0063-0.00980.1474-0.00030.01540.09730.0050.093845.6097-126.0382-0.5265
110.02580.0023-0.01250.0015-0.00170.00660.015-0.00360.018-0.0062-0.00260.012-0.00350.0074-0.01230.12040.0072-0.02020.08470.01670.119511.7242-130.14342.5021
120.0359-0.010.03930.0199-0.01890.0540.0069-0.00650.00510.02390.00560.0368-0.00280.0173-0.01250.08320.00650.00690.09350.00670.1451-3.7957-133.506228.639
130.46990.14060.01490.131-0.09090.11620.02950.018-0.027-0.0039-0.0210.00990.02430.063-0.00850.11150.00320.02570.0857-0.00620.118.2305-136.170860.3848
140.00120.0041-0.00050.0837-0.02320.00840.01060.00650.00240.0393-0.007-0.00520.00280.0043-0.00360.1569-0.00870.00240.0945-0.00830.095240.5913-133.486970.6908
150.0081-0.0074-0.0040.00890.0070.01390.00190.01440.0041-0.0028-0.0020.00330.02090.01140.00020.1037-0.0146-0.00910.09610.00930.13112.2118-205.644936.9002
160.0021-0.00080.00090.0013-0.00030.0004-0.0036-0.00670.0146-0.0084-0.0022-0.0073-0.0027-0.00180.00590.1287-0.0007-0.02540.0988-0.00640.12318.5636-204.51176.7948
170.0094-0.00330.0020.0023-0.0020.00930.0194-0.0006-0.0208-0.0155-0.00410.0062-0.00170.023-0.01530.1430.02420.00470.0743-0.02260.077535.9616-202.6585-9.1077
180.0106-0.00830.00810.0455-0.03960.04090.008-0.01360.023-0.0277-0.0185-0.03580.03370.0110.01040.09790.01960.02580.0428-0.02230.095265.4716-202.12763.3879
190.00340.00250.00040.00290.00160.00570.01450.0041-0.0040.01040.0021-0.0146-0.0001-0.0115-0.01660.07530.0197-0.00410.045-0.00990.135572.5148-203.358235.3157
200.01260.0019-0.00530.0036-0.00190.00890.02360.0033-0.00890.0093-0.0172-0.02-0.0133-0.0202-0.00640.1367-0.0044-0.04660.059-0.00010.111254.611-206.996359.6123
210.00570.005-0.0090.0092-0.02430.07310.00340.01690.00910.00380.00740.00780.00440.013-0.01080.1484-0.0079-0.00660.08350.00610.110322.1498-208.910761.2714
220.00280.00440.00370.0396-0.00170.00980.0140.0024-0.00520.0172-0.00510.03740.01720.0213-0.00890.107-0.00610.00970.0860.0060.13072.0938-168.599145.5049
230.02810.03160.02790.04450.03370.03880.0079-0.00880.0021-0.0105-0.00210.0250.01280.019-0.00580.1148-0.0039-0.01250.07820.01260.13230.4382-166.349618.1895
240.0021-0.0016-0.00080.00640.00130.00090.0004-0.0098-0.0103-0.02930.00220.0108-0.00570.0082-0.00270.15040-0.01690.0945-0.00340.107423.6453-163.6317-3.6372
250.0025-0.00430.00210.0195-0.00310.0030.0081-0.0062-0.007-0.01850.004-0.00170.01020.0047-0.01210.12160.00850.02680.1009-0.00910.098157.5603-160.0868-0.4914
260.00410.0144-0.00470.0614-0.02520.01690.0088-0.0017-0.0067-0.0082-0.0072-0.02550.0134-0.0114-0.00160.09060.00960.01450.101-0.00380.131473.5574-161.251725.5165
270.0165-0.0235-0.01080.05890.01670.00960.00270.0152-0.01490.0248-0.0056-0.01610.0081-0.02110.00290.13280.0015-0.01330.08720.00870.111462.3092-164.387557.3867
280.0071-0.00020.00040.00410.00040.00040.01660.0167-0.00930.0203-0.01010.01080.0047-0.0035-0.00650.1626-0.00790.01080.09090.00690.099330.0874-168.589167.7492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301 - 316
5X-RAY DIFFRACTION3C1 - 240
6X-RAY DIFFRACTION3C301 - 309
7X-RAY DIFFRACTION4D1 - 242
8X-RAY DIFFRACTION4D301 - 303
9X-RAY DIFFRACTION5E3 - 233
10X-RAY DIFFRACTION5E301 - 303
11X-RAY DIFFRACTION6F2 - 244
12X-RAY DIFFRACTION6F301 - 309
13X-RAY DIFFRACTION7G2 - 242
14X-RAY DIFFRACTION7G301 - 302
15X-RAY DIFFRACTION7G401 - 407
16X-RAY DIFFRACTION8H1 - 222
17X-RAY DIFFRACTION8H301 - 302
18X-RAY DIFFRACTION8H401 - 411
19X-RAY DIFFRACTION9I1 - 204
20X-RAY DIFFRACTION9I301
21X-RAY DIFFRACTION9I401 - 410
22X-RAY DIFFRACTION10J1 - 195
23X-RAY DIFFRACTION10J201 - 215
24X-RAY DIFFRACTION11K1 - 212
25X-RAY DIFFRACTION11K301 - 303
26X-RAY DIFFRACTION11K401 - 415
27X-RAY DIFFRACTION12L1 - 222
28X-RAY DIFFRACTION12L301 - 320
29X-RAY DIFFRACTION13M1 - 228
30X-RAY DIFFRACTION13M301 - 312
31X-RAY DIFFRACTION14N1 - 196
32X-RAY DIFFRACTION14N201 - 202
33X-RAY DIFFRACTION14N301 - 309
34X-RAY DIFFRACTION15O1 - 250
35X-RAY DIFFRACTION15O301 - 306
36X-RAY DIFFRACTION16P1 - 244
37X-RAY DIFFRACTION16P301 - 308
38X-RAY DIFFRACTION17Q1 - 240
39X-RAY DIFFRACTION17Q301 - 307
40X-RAY DIFFRACTION18R1 - 242
41X-RAY DIFFRACTION18R301 - 307
42X-RAY DIFFRACTION19S3 - 233
43X-RAY DIFFRACTION19S301 - 303
44X-RAY DIFFRACTION20T2 - 244
45X-RAY DIFFRACTION20T301 - 305
46X-RAY DIFFRACTION21U2 - 242
47X-RAY DIFFRACTION21U301
48X-RAY DIFFRACTION21U401 - 409
49X-RAY DIFFRACTION22V1 - 222
50X-RAY DIFFRACTION22V301 - 303
51X-RAY DIFFRACTION22V401 - 409
52X-RAY DIFFRACTION23W1 - 204
53X-RAY DIFFRACTION23W301 - 305
54X-RAY DIFFRACTION24X1 - 195
55X-RAY DIFFRACTION24X201 - 216
56X-RAY DIFFRACTION25Y1 - 212
57X-RAY DIFFRACTION25Y301 - 303
58X-RAY DIFFRACTION25Y401 - 416
59X-RAY DIFFRACTION26Z1 - 222
60X-RAY DIFFRACTION26Z301 - 316
61X-RAY DIFFRACTION27a1 - 226
62X-RAY DIFFRACTION27a301 - 315
63X-RAY DIFFRACTION28b1 - 196
64X-RAY DIFFRACTION28b201
65X-RAY DIFFRACTION28b301 - 312

+
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