[English] 日本語
Yorodumi
- PDB-9qb4: Yeast 20S proteasome mutant: beta5_T3M in complex with Carfilzomib -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qb4
TitleYeast 20S proteasome mutant: beta5_T3M in complex with Carfilzomib
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Carfilzomib
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Proteasome / Proteasome Associated Autoinflammatory Syndromes / Mutation / Assembly / Maturation
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / 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 / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 alpha5 / Proteasome subunit alpha6 / 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 alpha5 / Proteasome subunit alpha6 / 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-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: 2.7 Å
AuthorsHuber, E.M. / Heinemeyer, W. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035, project no.201302640, A02 Germany
CitationJournal: Structure / Year: 2025
Title: Proteasome-associated autoinflammatory syndromes: The impact of mutations in proteasome subunits on particle assembly, structure, and activity.
Authors: Huber, E.M. / Heinemeyer, W. / Groll, M.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 2.0Apr 9, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_modification_feature / pdbx_refine_tls_group / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _pdbx_refine_tls_group.beg_auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 8, 2025Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.src_method / _struct_ref_seq_dif.details
Revision 2.2Oct 15, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
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
e: Carfilzomib
f: Carfilzomib
g: Carfilzomib
h: Carfilzomib
i: Carfilzomib
j: Carfilzomib
hetero molecules


Theoretical massNumber of molelcules
Total (without water)736,83449
Polymers735,74134
Non-polymers1,09315
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, AU contains one biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130250 Å2
ΔGint-497 kcal/mol
Surface area211460 Å2
Unit cell
Length a, b, c (Å)135.200, 300.160, 144.670
Angle α, β, γ (deg.)90.00, 112.84, 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: 25013.355 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: 23254.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
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 / 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 FTefghij

#15: Protein/peptide
Carfilzomib


Mass: 839.029 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 , 4 types, 306 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#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.: 291 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.76 %
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: Oct 24, 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: 2.7→30 Å / Num. obs: 285103 / % possible obs: 98.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2 / Num. unique obs: 29360 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 26.301 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20651 14173 5 %RANDOM
Rwork0.17271 ---
obs0.1749 269275 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å2-0.94 Å2
2---2.33 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49610 0 59 291 49960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01350587
X-RAY DIFFRACTIONr_bond_other_d0.0010.01747212
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.6568448
X-RAY DIFFRACTIONr_angle_other_deg1.161.594109582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06256306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79622.7912530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.301158740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.74615284
X-RAY DIFFRACTIONr_chiral_restr0.0380.26680
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0256662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210442
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_it3.3916.20925313
X-RAY DIFFRACTIONr_mcbond_other3.3916.20925312
X-RAY DIFFRACTIONr_mcangle_it4.8729.30631588
X-RAY DIFFRACTIONr_mcangle_other4.8729.30631589
X-RAY DIFFRACTIONr_scbond_it3.3036.61225274
X-RAY DIFFRACTIONr_scbond_other3.3036.61225272
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6989.76236861
X-RAY DIFFRACTIONr_long_range_B_refined6.39171.27553164
X-RAY DIFFRACTIONr_long_range_B_other6.37971.26953146
X-RAY DIFFRACTIONr_rigid_bond_restr0.498397799
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
10103063tight positional0.010.05
11113278tight positional0.010.05
12123389tight positional0.010.05
13133564tight positional0.010.05
14143030tight positional0.010.05
113765tight thermal7.730.5
223714tight thermal7.560.5
333685tight thermal12.920.5
443540tight thermal10.010.5
553459tight thermal8.650.5
663693tight thermal8.650.5
773723tight thermal70.5
883397tight thermal5.840.5
993091tight thermal5.960.5
10103063tight thermal5.610.5
11113278tight thermal5.320.5
12123389tight thermal5.710.5
13133564tight thermal5.240.5
14143030tight thermal4.960.5
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 1011 -
Rwork0.309 19206 -
obs--97.6 %
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)
10.0359-0.0149-0.00630.02670.02060.0181-0.00760.02350.0052-0.0040.0028-0.0094-0.00630.00590.00480.1467-0.0111-0.0120.0311-0.00370.126667.0627-92.007845.974
20.0630.03840.0380.05570.0640.0764-0.00290.01820.0052-0.00980.00580.0004-0.00740.0118-0.00290.1226-0.00970.01060.03980.01360.10259.7977-87.785516.3982
30.09730.0764-0.03840.0649-0.05290.14790.010.018900.00380.0173-0.00090.02020.0058-0.02730.13960.0102-0.00650.03350.00660.11532.4946-87.38141.1978
40.01730.00860.00370.01160.01160.0498-0.0158-0.00580.0244-0.01040.00280.0347-0.03140.01430.0130.13520.0234-0.00530.01650.01390.11773.3912-89.945213.6886
50.00410.00450.00090.00660.00290.0034-0.0154-0.00180.015-0.0075-0.00150.02780.006-0.00590.01690.12140.02170.01010.0384-0.00460.1332-3.0082-94.25345.6514
60.0026-0.0016-0.00160.001900.00330.00210.0004-0.01370.008-0.00220.0133-0.0060.00670.00010.12480.01260.02440.0269-0.01980.102715.5071-94.839969.7893
70.00260.0027-0.00830.0869-0.04360.04780.00590.00510.00110.0134-0.0061-0.01160.005-0.01560.00020.1449-0.0039-0.00110.018-0.01810.108447.8937-93.363271.0221
80.00310.0016-0.00480.01740.00110.00830.0090.0084-0.00380.0263-0.0045-0.0376-0.0133-0.0138-0.00450.1354-0.009-0.00980.0348-0.00860.111167.5106-130.04947.9939
90.05570.0038-0.02990.06920.04240.04670.0134-0.0009-0.0151-0.0298-0.0106-0.0179-0.0261-0.0139-0.00280.1537-0.0068-0.00170.03020.00070.121668.3975-127.439620.967
100.0244-0.006-0.00610.0639-0.04060.03140.00010.00630.0245-0.02080.0128-0.01070.0101-0.0155-0.01290.153-0.00310.00310.0460.01120.097644.8533-126.5231-0.5141
110.0124-0.02270.0170.0865-0.04670.04240.01940.01040.0121-0.023-0.01770.03420.00510.0316-0.00170.14560.0064-0.01040.03490.01140.111911.1614-130.7822.884
120.0156-0.01550.02250.0242-0.03040.04360.0093-0.0028-0.00730.01750.00170.0258-0.0170.0056-0.0110.1390.008-0.00640.0310.01060.1278-4.2983-134.092128.7779
130.0454-0.02770.00790.1770.01970.00530.0003-0.00180.00660.0143-0.00180.01270.00250.00160.00150.13890.00220.0080.0323-0.0040.11848.066-137.724960.4251
140.04040.0296-0.03210.1813-0.00420.03570.0143-0.00360.00080.0054-0.0020.02720.010.0141-0.01220.15130.0014-0.00160.0385-0.00720.106540.1964-134.077970.3414
150.0750.0339-0.01350.0172-0.0080.0047-0.00350.01370.0035-0.01180.00210.00590.01130.00210.00140.1398-0.022-0.02010.03420.01150.13221.8919-206.227636.826
160.0250.00210.01740.0042-0.00370.0217-0.0129-0.0058-0.0080.0080.0099-0.0023-0.0048-0.02220.00310.147-0.0046-0.01950.0365-0.00570.11578.3154-205.20656.7899
170.0142-0.00580.00830.0038-0.00620.01050.0363-0.003-0.0221-0.0105-0.00170.02010.01130.0045-0.03470.15710.0104-0.02050.0236-0.02160.122835.5372-203.1206-8.9035
180.0012-0.0030.00290.0116-0.00560.01150.0006-0.00050.0097-0.0309-0.0088-0.02410.00950.00120.00820.11790.03540.01510.0174-0.0240.12464.8679-202.67873.4393
190.0092-0.0032-0.01860.0267-0.01470.07360.0070.00020.01160.01450.0102-0.03710.0070.0041-0.01710.11640.0296-0.00740.0313-0.03210.134271.9938-203.859935.3305
200.07560.0247-0.03180.0088-0.00920.01650.0161-0.0004-0.01770.0043-0.0058-0.01330.0011-0.0041-0.01030.16110.0088-0.03590.01270.00890.127154.0115-207.504859.5465
210.051-0.0330.02460.0528-0.04060.04410.0026-0.0013-0.00980.00040.00470.0242-0.01840.0137-0.00730.1492-0.0084-0.00990.02350.01830.116721.7156-209.392761.1598
220.00070.00190.00070.0110.00040.00190.0087-0.00140.00090.023-0.0040.02710.01230.002-0.00470.1478-0.0154-0.00430.01880.01120.11381.6365-169.135645.3708
230.01130.0292-0.00190.1183-0.02010.00740.0196-0.0018-0.0016-0.0007-0.01120.01040.00680.0047-0.00840.1329-0.0116-0.01370.02970.00060.12950.1238-167.040918.2362
240.0143-0.01440.01280.0201-0.00540.02820.0094-0.0017-0.0088-0.01970.0089-0.0105-0.01520.0199-0.01820.15320.003-0.02630.0406-0.0080.112523.17-164.1948-3.5956
250.0038-0.00680.00320.0276-0.00040.00450.0106-0.0078-0.0041-0.03070.0032-0.01780.0088-0.0088-0.01380.1490.00770.00690.0432-0.00690.111356.9412-160.5537-0.1694
260.00370.01-0.00390.0865-0.03420.01620.0145-0.0013-0.0042-0.0281-0.0035-0.01260.0067-0.0019-0.0110.13510.00970.00620.0423-0.00970.127872.9712-161.723125.5545
270.0436-0.0490.02450.0897-00.05510.01220.0049-0.0187-0.0065-0.0049-0.0142-0.0053-0.0022-0.00720.1330.0039-0.00770.0310.00380.114261.3591-163.619157.6156
280.0460.02830.04350.02030.0240.0451-0.0004-0.00480.00090.00870.0062-0.0043-0.012-0.0146-0.00580.1569-0.0053-0.0030.04020.00230.111229.4641-168.992667.4636
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 DIFFRACTION7G3 - 242
8X-RAY DIFFRACTION8H2 - 222
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K2 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N2 - 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 DIFFRACTION21U3 - 242
22X-RAY DIFFRACTION22V2 - 222
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y2 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b2 - 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