[English] 日本語
Yorodumi
- PDB-3unh: Mouse 20S immunoproteasome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3unh
TitleMouse 20S immunoproteasome
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / 20S proteasome comprises 28 subunits / Protease / Cytosol
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex ...Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Degradation of AXIN / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / spermatoproteasome complex / Degradation of DVL / UCH proteinases / Orc1 removal from chromatin / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Hedgehog ligand biogenesis / TNFR2 non-canonical NF-kB pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Separation of Sister Chromatids / Downstream TCR signaling / KEAP1-NFE2L2 pathway / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome core complex / immune system process / myofibril / proteasome binding / fat cell differentiation / antigen processing and presentation / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / T cell proliferation / skeletal muscle tissue development / negative regulation of inflammatory response to antigenic stimulus / : / Neutrophil degranulation / sarcomere / proteasome complex / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / response to bacterium / P-body / protein catabolic process / response to virus / cell morphogenesis / response to organic cyclic compound / nuclear matrix / positive regulation of NF-kappaB transcription factor activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ribosome / centrosome / ubiquitin protein ligase binding / synapse / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome subunit alpha 1 / 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 subunit alpha 1 / 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
IODIDE ION / : / Proteasome subunit beta type-1 / Proteasome subunit beta type-10 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-8 / Proteasome subunit beta type-9 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-6 ...IODIDE ION / : / Proteasome subunit beta type-1 / Proteasome subunit beta type-10 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-8 / Proteasome subunit beta type-9 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-7 / Proteasome subunit alpha type-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHuber, E. / Basler, M. / Schwab, R. / Heinemeyer, W. / Kirk, C. / Groettrup, M. / Groll, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Immuno- and constitutive proteasome crystal structures reveal differences in substrate and inhibitor specificity.
Authors: Huber, E.M. / Basler, M. / Schwab, R. / Heinemeyer, W. / Kirk, C.J. / Groettrup, M. / Groll, M.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-10
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-8
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-9
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-10
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-8
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,92875
Polymers715,94528
Non-polymers2,98347
Water9,638535
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.280, 205.220, 161.940
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999989, -0.004188, 0.002276), (-0.00403, 0.997845, 0.065492), (-0.002545, 0.065482, -0.99785)18.76788, -5.33349, 168.7892

-
Components

-
Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25955.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P49722, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29512.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9R1P0, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1


Mass: 27897.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9Z2U0, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9Z2U1, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-1 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / ...Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29586.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9R1P4, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / ...Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / Proteasome subunit K


Mass: 28442.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: O70435, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-6 / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27405.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9QUM9, proteasome endopeptidase complex

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

#8: Protein Proteasome subunit beta type-10 / Low molecular mass protein 10 / Macropain subunit MECl-1 / Multicatalytic endopeptidase complex ...Low molecular mass protein 10 / Macropain subunit MECl-1 / Multicatalytic endopeptidase complex subunit MECl-1 / Proteasome MECl-1 / Proteasome subunit beta-2i


Mass: 24830.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: O35955, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22988.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9R1P1, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22935.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9R1P3, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-8 / Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit ...Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit C13 / Proteasome component C13 / Proteasome subunit beta-5i


Mass: 22674.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P28063, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23576.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: O09061, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / Proteasome beta chain / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic ...Proteasome beta chain / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome chain 3


Mass: 24384.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P99026, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-9 / LMP-2d / Low molecular mass protein 2 / Macropain chain 7 / Multicatalytic endopeptidase complex ...LMP-2d / Low molecular mass protein 2 / Macropain chain 7 / Multicatalytic endopeptidase complex chain 7 / Proteasome chain 7 / Proteasome subunit beta-1i / Really interesting new gene 12 protein


Mass: 21345.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P28076, proteasome endopeptidase complex

-
Non-polymers , 4 types, 582 molecules

#15: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#16: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M NaI, 40% MPD, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 12, 2011
RadiationMonochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 122308 / Num. obs: 121329 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.4
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1IRU
Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.888 / SU B: 65.629 / SU ML: 0.473 / Cross valid method: THROUGHOUT / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25395 6067 5 %RANDOM
Rwork0.23862 ---
obs0.23938 115261 99.2 %-
all-121328 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.186 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å20 Å2-0.64 Å2
2--7.62 Å20 Å2
3----4.75 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48502 0 47 535 49084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01949380
X-RAY DIFFRACTIONr_angle_refined_deg0.8511.96566718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.39856216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89223.7972186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.551158648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.96915350
X-RAY DIFFRACTIONr_chiral_restr0.0560.27484
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02137046
X-RAY DIFFRACTIONr_rigid_bond_restr0.809349380
X-RAY DIFFRACTIONr_sphericity_free22.2945296
X-RAY DIFFRACTIONr_sphericity_bonded2.911548789
LS refinement shellResolution: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 419 -
Rwork0.337 7996 -
obs--99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4521-0.3431-0.36221.44250.20910.3207-0.22550.29370.0719-0.06120.21740.05310.2601-0.3130.00820.4226-0.4616-0.10530.83670.05570.0757-8.913-55.52318.779
20.479-0.4974-0.45320.94370.55760.4953-0.12130.19410.218-0.09480.2060.03860.1348-0.1123-0.08470.2983-0.1631-0.13470.64460.36050.3233-3.447-24.64920.322
31.2614-0.6305-0.26741.08010.53160.37540.07460.19980.45630.02450.0506-0.1550.1871-0.061-0.12520.3143-0.06830.06350.25830.27450.524523.873-9.82928.741
40.036-0.00720.09480.26470.47611.6918-0.02370.0804-0.0337-0.00870.04350.11580.1340.0945-0.01970.1357-0.10010.05660.36170.1360.375450.9-24.15235.47
50.64630.35250.4880.20510.25850.5626-0.20640.0183-0.0578-0.09230.0381-0.07490.10310.05380.16830.41250.09410.23350.49090.07090.434258.205-54.60736.503
60.0861-0.11130.03790.9921-0.41710.4265-0.15920.0826-0.1298-0.01220.0613-0.06230.2946-0.00810.09780.77360.00850.32660.2455-0.17610.34540.351-79.04430.208
70.67610.5894-0.45341.1145-0.40920.3091-0.39410.3512-0.1159-0.03090.3002-0.22810.2265-0.23480.09390.9699-0.43290.13860.3661-0.18440.13659.527-79.39821.294
80.4218-0.1824-0.13370.16450.03650.1005-0.17610.16670.22150.03620.1381-0.04850.1951-0.18860.0380.4747-0.3398-0.05860.6046-0.0120.3319-18.369-62.37356.23
90.4912-0.3032-0.50020.21610.20151.1309-0.03590.07250.15060.00180.0627-0.09230.3022-0.2987-0.02670.1976-0.0311-0.04250.45480.14570.4447-19.391-34.38756.629
100.9986-0.1057-1.15960.19270.11571.37320.11330.04280.11270.00790.1378-0.0351-0.1197-0.0789-0.25110.35370.03530.0120.12110.10840.67053.222-12.58663.609
111.06140.13390.40580.0730.21970.67390.2081-0.0018-0.1154-0.01740.0309-0.0532-0.0770.0954-0.2390.3273-0.07830.00140.17060.00530.642534.962-16.34773.02
120.07130.12810.00740.33980.10790.56440.0083-0.12910.0246-0.1032-0.09980.12480.11930.41810.09150.21020.01720.01350.59420.04890.488249.553-43.23277.179
130.2917-0.025-0.40460.5302-0.46311.3851-0.0574-0.1762-0.0211-0.2491-0.09040.0410.33080.2440.14780.4890.17480.14480.1950.07920.523638.194-74.36974.072
140.75950.0286-0.43030.0973-0.1260.3719-0.1515-0.02120.0283-0.17480.0656-0.11510.2526-0.07530.08590.7234-0.11780.10960.0601-0.08110.54958.994-84.63463.254
150.7523-0.2465-0.44581.78690.08630.47750.0983-0.0174-0.11530.14-0.191-0.290.1169-0.0450.09270.2401-0.1293-0.12860.82730.18120.154628.265-59.787146.346
160.04770.1426-0.01281.19050.0960.0293-0.0113-0.0830.05770.18640.0814-0.12490.06230.047-0.07020.2413-0.1908-0.14250.8855-0.14290.19922.673-28.867146.858
172.27550.7180.00560.3657-0.04950.030.1311-0.45390.5013-0.0654-0.1970.10270.0861-0.02840.06590.311-0.15150.11640.5594-0.36880.3741-4.78-13.61139.408
180.3075-0.22330.66960.2043-0.53781.52290.0606-0.1202-0.0445-0.0494-0.02050.01790.1287-0.1331-0.040.0778-0.03120.11270.6619-0.25270.4212-31.687-27.587131.796
190.7878-0.08870.28180.2885-0.23210.79480.0262-0.13860.0893-0.0178-0.04470.11820.0335-0.13720.01850.1649-0.20720.05750.7508-0.0740.2867-38.846-57.909128.716
200.54370.15430.07520.62260.6340.83490.0134-0.2009-0.08520.0108-0.038-0.00720.20480.03580.02450.4841-0.28810.0420.52190.13520.2159-20.89-82.73133.384
210.5461-0.2572-0.22021.17980.15390.09560.001-0.1974-0.1859-0.0431-0.0974-0.01050.05040.04380.09640.4663-0.1365-0.06660.65440.24810.1439.947-83.584142.227
220.47220.5182-0.08740.609-0.13420.0674-0.0186-0.17470.0337-0.1289-0.1017-0.0340.11470.05660.12030.32890.0637-0.00410.54720.14980.412137.77-64.04108.586
230.51640.2027-0.53310.1099-0.2620.69610.1188-0.33450.0624-0.0417-0.1150.07040.08170.3323-0.00380.2551-0.1042-0.03010.6465-0.02010.342338.7-36.088110.009
241.3262-0.2916-1.2560.07980.26251.22520.2142-0.19250.2278-0.08340.03810.0295-0.15720.1004-0.25220.3287-0.14290.02570.2821-0.15490.590115.984-13.975104.464
250.53990.1975-0.0570.1242-0.16840.47330.2031-0.0822-0.04930.06310.00330.0931-0.0777-0.1348-0.20640.36170.0740.00910.3742-0.04910.6958-15.735-17.1394.846
260.089-0.1672-0.04540.42290.07450.95720.0507-0.00440.07050.0264-0.0601-0.06680.0971-0.32670.00940.2303-0.0818-0.02710.48790.03180.4809-30.221-43.7688.914
270.3544-0.3459-0.14540.39160.20071.0011-0.11280.07680.09110.01190.0364-0.1220.3323-0.18640.07640.499-0.3080.01230.3806-0.04190.3712-18.739-75.01489.957
280.0244-0.0896-0.12150.51530.60250.7441-0.0627-0.032-0.01640.0291-0.0290.01560.13830.04530.09170.5579-0.00110.03450.27870.16010.499910.493-85.878100.094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1A234 - 235
3X-RAY DIFFRACTION1A236 - 529
4X-RAY DIFFRACTION2B1 - 248
5X-RAY DIFFRACTION2B261
6X-RAY DIFFRACTION2B262 - 534
7X-RAY DIFFRACTION3C1 - 238
8X-RAY DIFFRACTION3C248 - 249
9X-RAY DIFFRACTION3C250 - 530
10X-RAY DIFFRACTION4D1 - 233
11X-RAY DIFFRACTION4D234 - 235
12X-RAY DIFFRACTION4D236 - 514
13X-RAY DIFFRACTION5E1 - 238
14X-RAY DIFFRACTION5E261 - 263
15X-RAY DIFFRACTION5E264 - 502
16X-RAY DIFFRACTION6F1 - 244
17X-RAY DIFFRACTION6F255
18X-RAY DIFFRACTION6F256 - 508
19X-RAY DIFFRACTION7G1 - 243
20X-RAY DIFFRACTION7G246
21X-RAY DIFFRACTION7G247 - 531
22X-RAY DIFFRACTION8H1 - 219
23X-RAY DIFFRACTION8H235 - 237
24X-RAY DIFFRACTION8H238 - 442
25X-RAY DIFFRACTION9I1 - 204
26X-RAY DIFFRACTION9I205
27X-RAY DIFFRACTION9I206 - 527
28X-RAY DIFFRACTION10J1 - 196
29X-RAY DIFFRACTION10J202 - 511
30X-RAY DIFFRACTION11K1 - 201
31X-RAY DIFFRACTION11K205 - 207
32X-RAY DIFFRACTION11K208 - 499
33X-RAY DIFFRACTION12L1 - 213
34X-RAY DIFFRACTION12L214
35X-RAY DIFFRACTION12L215 - 522
36X-RAY DIFFRACTION13M1 - 216
37X-RAY DIFFRACTION13M220
38X-RAY DIFFRACTION13M221 - 512
39X-RAY DIFFRACTION14N1 - 199
40X-RAY DIFFRACTION14N200 - 203
41X-RAY DIFFRACTION14N204 - 533
42X-RAY DIFFRACTION15O1 - 230
43X-RAY DIFFRACTION15O234
44X-RAY DIFFRACTION15O235 - 438
45X-RAY DIFFRACTION16P1 - 248
46X-RAY DIFFRACTION16P261
47X-RAY DIFFRACTION16P262 - 532
48X-RAY DIFFRACTION17Q1 - 238
49X-RAY DIFFRACTION17Q248 - 249
50X-RAY DIFFRACTION17Q250 - 505
51X-RAY DIFFRACTION18R1 - 233
52X-RAY DIFFRACTION18R234
53X-RAY DIFFRACTION18R235 - 535
54X-RAY DIFFRACTION19S1 - 238
55X-RAY DIFFRACTION19S261 - 262
56X-RAY DIFFRACTION19S263 - 506
57X-RAY DIFFRACTION20T1 - 244
58X-RAY DIFFRACTION20T255
59X-RAY DIFFRACTION20T256 - 519
60X-RAY DIFFRACTION21U1 - 243
61X-RAY DIFFRACTION21U246
62X-RAY DIFFRACTION21U247 - 507
63X-RAY DIFFRACTION22V1 - 219
64X-RAY DIFFRACTION22V235 - 237
65X-RAY DIFFRACTION22V238 - 465
66X-RAY DIFFRACTION23W1 - 204
67X-RAY DIFFRACTION23W205
68X-RAY DIFFRACTION23W206 - 493
69X-RAY DIFFRACTION24X1 - 196
70X-RAY DIFFRACTION24X202 - 521
71X-RAY DIFFRACTION25Y1 - 201
72X-RAY DIFFRACTION25Y205 - 206
73X-RAY DIFFRACTION25Y207 - 526
74X-RAY DIFFRACTION26Z1 - 213
75X-RAY DIFFRACTION26Z214
76X-RAY DIFFRACTION26Z215 - 525
77X-RAY DIFFRACTION27a1 - 216
78X-RAY DIFFRACTION27a220 - 221
79X-RAY DIFFRACTION27a222 - 483
80X-RAY DIFFRACTION28b1 - 199
81X-RAY DIFFRACTION28b200 - 203
82X-RAY DIFFRACTION28b204 - 520

+
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