[English] 日本語
Yorodumi
- PDB-3unf: Mouse 20S immunoproteasome in complex with PR-957 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3unf
TitleMouse 20S immunoproteasome in complex with PR-957
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Proteasome / antigen presentation / drug development / protein degradation / HYDROLASE-HYDROLASE INHIBITOR complex
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 / spermatoproteasome complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / 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 / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / T cell proliferation / skeletal muscle tissue development / negative regulation of inflammatory response to antigenic stimulus / response to organonitrogen compound / Neutrophil degranulation / sarcomere / proteasome complex / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / response to bacterium / P-body / response to virus / protein catabolic process / cell morphogenesis / response to organic cyclic compound / nuclear matrix / positive regulation of NF-kappaB transcription factor activity / peptidase activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / nuclear body / ribosome / centrosome / synapse / ubiquitin protein ligase binding / mitochondrion / proteolysis / 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
1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / IODIDE ION / : / Proteasome subunit beta type-1 / Proteasome subunit beta type-10 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-8 / Proteasome subunit beta type-9 ...1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / IODIDE ION / : / Proteasome subunit beta type-1 / Proteasome subunit beta type-10 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-8 / Proteasome subunit beta type-9 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-7 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / 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: 2.9 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 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 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_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn_type.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)722,17794
Polymers715,94528
Non-polymers6,23166
Water17,745985
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.300, 194.600, 157.700
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999738, -0.022464, 0.004418), (-0.022605, 0.999137, -0.034849), (-0.003632, -0.03494, -0.999383)58.36053, 0.74754, -2.69464
DetailsThe AU contains 28 subunits forming one biological assembly (dimer)

-
Components

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

#1: Protein Proteasome subunit alpha type-2


Mass: 25955.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: P49722
#2: Protein Proteasome subunit alpha type-4


Mass: 29512.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9R1P0
#3: Protein Proteasome subunit alpha type-7


Mass: 27897.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9Z2U0
#4: Protein Proteasome subunit alpha type-5


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9Z2U1
#5: Protein Proteasome subunit alpha type-1


Mass: 29586.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9R1P4
#6: Protein Proteasome subunit alpha type-3


Mass: 28442.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: O70435
#7: Protein Proteasome subunit alpha type-6


Mass: 27405.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9QUM9

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

#8: Protein Proteasome subunit beta type-10


Mass: 24830.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: P70195, UniProt: O35955*PLUS
#9: Protein Proteasome subunit beta type-3


Mass: 22988.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9R1P1
#10: Protein Proteasome subunit beta type-2


Mass: 22935.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q9R1P3
#11: Protein Proteasome subunit beta type-8


Mass: 22674.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: O55234, UniProt: P28063*PLUS
#12: Protein Proteasome subunit beta type-1


Mass: 23576.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: O09061
#13: Protein Proteasome subunit beta type-4


Mass: 24384.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: P99026
#14: Protein Proteasome subunit beta type-9


Mass: 21345.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090 / References: UniProt: Q60692, UniProt: P28076*PLUS

-
Non-polymers , 5 types, 1051 molecules

#15: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Cl
#16: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE STARTING EPOXIDE RING OF AN EPOXOMICIN-LIKE INHIBITOR UNDERGOES RE-CYCLIZATION REACTION WITH ...THE STARTING EPOXIDE RING OF AN EPOXOMICIN-LIKE INHIBITOR UNDERGOES RE-CYCLIZATION REACTION WITH THE SIDE CHAIN OF N-TERMINAL RESIDUE THR-1 (CHAINS V,H,b,N,K, and Y) AND THE FINAL PRODUCT 04C IS OBSERVED. SEE ALSO LINK RECORDS AND REMARK 630.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.81 %
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: 2.9→30 Å / Num. all: 149421 / Num. obs: 145087 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2 / % possible all: 89.8

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IRU

1iru


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.869 / SU B: 55.113 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27498 7255 5 %RANDOM
Rwork0.23527 ---
obs0.23724 137832 97.12 %-
all-145087 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.703 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-1.21 Å2
2--4.56 Å20 Å2
3----3.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48508 0 312 985 49805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0249662
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.97367120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90456210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84223.7972186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.645158642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.40915350
X-RAY DIFFRACTIONr_chiral_restr0.0620.27556
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02137046
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr0.765349662
X-RAY DIFFRACTIONr_sphericity_free28.2095472
X-RAY DIFFRACTIONr_sphericity_bonded34.324549333
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 448 -
Rwork0.328 8502 -
obs--85.31 %
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)
10.0190.0440.06520.28230.15060.4489-0.01520.0238-0.0115-0.03950.00120.049-0.05030.03210.0140.1576-0.0544-0.02790.24960.02490.082713.93-58.542-64.253
20.12190.0509-0.07660.26840.0060.0694-0.08380.0770.0149-0.05810.05240.0710.0094-0.0220.03140.2247-0.0691-0.06520.22330.04540.106318.821-27.494-64.073
30.2181-0.00190.27360.31660.31570.7263-0.09260.09050.0999-0.01630.0150.0179-0.11640.03080.07760.1859-0.0684-0.02170.22960.1090.160546-12.113-55.452
40.3174-0.01640.54190.02380.02211.0416-0.08990.18320.1026-0.0014-0.0568-0.0293-0.15660.1860.14670.214-0.0947-0.02010.26290.06030.131872.679-26.192-47.193
50.50450.09420.10740.05810.08280.3603-0.06590.0897-0.011-0.05490.044-0.04460.00720.06860.0220.1618-0.02930.01950.2071-0.01150.126779.955-56.498-44.506
60.2338-0.03690.07340.14970.01770.0292-0.03280.0847-0.0626-0.02940.0588-0.0426-0.01550.0389-0.0260.1923-0.04680.03490.1948-0.04630.12662.653-81.352-50.373
70.1772-0.0148-0.03690.6360.18240.0686-0.04740.0906-0.024-0.04240.02040.04240.0293-0.04680.02710.2139-0.09670.01160.1951-0.02170.082832.194-82.132-60.388
80.0923-0.03910.07810.0495-0.0410.089-0.03250.04250.0030.00080.03260.022-0.0074-0.0252-0.00010.1579-0.0353-0.02190.22450.01560.11282.876-63.613-27.393
90.4784-0.3495-0.220.4079-0.01370.3222-0.01880.08470.0215-0.01070.0013-0.00330.0485-0.070.01760.13-0.0235-0.01620.18910.03060.11151.655-35.465-28.123
100.68280.13760.13070.0727-0.08220.2944-0.03490.010.0748-0.02240.02580.00660.0112-0.06040.00910.18610.0131-0.01810.03210.00630.156523.93-13.273-21.515
110.40570.05440.46590.30970.26670.686-0.02260.0406-0.0155-0.05430.0151-0.0139-0.07260.03330.00740.1619-0.0224-0.01840.0660.00910.146155.24-16.511-11.135
120.0238-0.0785-0.0050.27610.01360.2106-0.0086-0.0024-0.02160.00960.00840.0356-0.00480.16920.00010.161-0.0088-0.01070.1364-0.00650.116769.78-43.328-5.011
130.10810.1363-0.12140.1905-0.10720.5173-0.0203-0.0173-0.0245-0.0438-0.0092-0.00240.12090.05070.02950.18280.00740.00450.0407-0.00260.147458.64-74.573-6.983
140.4440.2152-0.0860.1072-0.04280.0992-0.02840.0401-0.0084-0.02820.0352-0.01080.0366-0.0619-0.00670.1935-0.024-0.01120.1366-0.00190.122829.975-85.59-18.328
150.5257-0.1356-0.16670.331-0.03650.07460.0388-0.0331-0.01090.0016-0.0474-0.0142-0.02330.02590.00870.159-0.0223-0.01410.153-0.00560.070345.992-56.08763.387
160.06640.1307-0.06440.3716-0.06640.26820.0062-0.02620.0160.048-0.01-0.0308-0.0198-0.03250.00380.1667-0.0084-0.00710.0944-0.02530.097640.366-25.25462.428
170.58390.2724-0.05630.4921-0.10420.03950.0598-0.09140.13730.0658-0.05040.0079-0.0365-0.0283-0.00940.18710.01370.01580.124-0.04520.136713.118-10.5353.195
180.07430.05320.1390.1651-0.10880.6184-0.0325-0.11460.0792-0.0071-0.13460.0357-0.0327-0.15530.1670.14740.0168-0.00830.2347-0.07590.1579-13.29-25.25645.126
190.6447-0.07710.350.0737-0.02440.3537-0.0413-0.08640.02860.0120.00410.0195-0.034-0.11390.03720.1419-0.00410.00790.2095-0.01950.0951-20.31-55.89743.71
200.45440.21340.04230.17090.02210.02620.0251-0.0289-0.0047-0.0222-0.01890.03330.0178-0.0587-0.00620.1617-0.0176-0.00940.1501-0.00020.1032-2.592-80.19450.483
210.3213-0.1074-0.09150.5291-0.06840.10910.024-0.086-0.07770.0011-0.0265-0.02140.0214-0.00560.00250.1677-0.0084-0.00830.11750.01310.101728.038-80.21260.178
220.16850.0637-0.03570.1165-0.08430.06680.0309-0.10830.0025-0.0256-0.0523-0.00320.00260.03590.02140.1747-0.0091-0.0090.0893-0.00330.1356.886-62.36326.712
230.10940.1643-0.03530.46260.09730.11880.0085-0.0550.02140.0283-0.01810.03750.01930.05420.00960.15180.0192-0.00090.1074-0.00230.114957.866-34.21426.615
240.5745-0.2425-0.25790.13420.10860.1473-0.01230.02880.04520.00650.00660.0403-0.0211-0.03730.00570.1699-0.0123-0.02020.03740.01570.135235.255-12.47119.329
250.32590.01870.3290.1222-0.1040.45830.0082-0.02180.0317-0.00980.00090.05220.0293-0.0209-0.00920.17230.0336-0.00220.13070.00240.13643.988-16.569.015
260.22740.0279-0.22190.22080.05590.2506-0.01390.03310.0029-0.00190.01760.01390.002-0.0421-0.00380.15180.0056-0.01680.19390.01830.1061-10.314-43.7153.721
270.2956-0.1306-0.26180.0930.0380.4819-0.00320.0235-0.01210.0049-0.01430.00860.1106-0.03980.01750.168-0.03260.00490.1523-0.01220.10421.146-74.876.71
280.7683-0.1391-0.2960.20260.16510.1866-0.04610.04240.00550.04880.0353-0.00240.0466-0.00080.01080.2082-0.0105-0.01380.0577-0.00640.127930.047-84.99918.401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1A401 - 443
4X-RAY DIFFRACTION2B1 - 248
5X-RAY DIFFRACTION2B301
6X-RAY DIFFRACTION2B401 - 442
7X-RAY DIFFRACTION3C1 - 238
8X-RAY DIFFRACTION3C301 - 329
9X-RAY DIFFRACTION4D1 - 233
10X-RAY DIFFRACTION4D301
11X-RAY DIFFRACTION4D401 - 424
12X-RAY DIFFRACTION5E1 - 238
13X-RAY DIFFRACTION5E301
14X-RAY DIFFRACTION5E401 - 439
15X-RAY DIFFRACTION6F1 - 244
16X-RAY DIFFRACTION6F301 - 337
17X-RAY DIFFRACTION7G1 - 243
18X-RAY DIFFRACTION7G301
19X-RAY DIFFRACTION7G401 - 444
20X-RAY DIFFRACTION8H1 - 219
21X-RAY DIFFRACTION8H301 - 303
22X-RAY DIFFRACTION8H401 - 440
23X-RAY DIFFRACTION9I1 - 204
24X-RAY DIFFRACTION9I301 - 302
25X-RAY DIFFRACTION9I401 - 425
26X-RAY DIFFRACTION10J1 - 196
27X-RAY DIFFRACTION10J301
28X-RAY DIFFRACTION10J401 - 428
29X-RAY DIFFRACTION11K2 - 201
30X-RAY DIFFRACTION11K301 - 303
31X-RAY DIFFRACTION11K401 - 432
32X-RAY DIFFRACTION12L1 - 213
33X-RAY DIFFRACTION12L301 - 303
34X-RAY DIFFRACTION12L401 - 443
35X-RAY DIFFRACTION13M1 - 216
36X-RAY DIFFRACTION13M301 - 305
37X-RAY DIFFRACTION13M401 - 450
38X-RAY DIFFRACTION14N2 - 199
39X-RAY DIFFRACTION14N201 - 203
40X-RAY DIFFRACTION14N301 - 329
41X-RAY DIFFRACTION15O1 - 230
42X-RAY DIFFRACTION15O301 - 302
43X-RAY DIFFRACTION15O401 - 444
44X-RAY DIFFRACTION16P1 - 248
45X-RAY DIFFRACTION16P301
46X-RAY DIFFRACTION16P401 - 438
47X-RAY DIFFRACTION17Q1 - 238
48X-RAY DIFFRACTION17Q301 - 304
49X-RAY DIFFRACTION17Q401 - 413
50X-RAY DIFFRACTION18R1 - 233
51X-RAY DIFFRACTION18R301 - 303
52X-RAY DIFFRACTION18R401 - 424
53X-RAY DIFFRACTION19S1 - 238
54X-RAY DIFFRACTION19S301 - 303
55X-RAY DIFFRACTION19S401 - 440
56X-RAY DIFFRACTION20T1 - 244
57X-RAY DIFFRACTION20T301 - 332
58X-RAY DIFFRACTION21U1 - 243
59X-RAY DIFFRACTION21U301
60X-RAY DIFFRACTION21U401 - 438
61X-RAY DIFFRACTION22V2 - 219
62X-RAY DIFFRACTION22V301 - 306
63X-RAY DIFFRACTION22V401 - 439
64X-RAY DIFFRACTION23W1 - 204
65X-RAY DIFFRACTION23W301
66X-RAY DIFFRACTION23W401 - 439
67X-RAY DIFFRACTION24X1 - 196
68X-RAY DIFFRACTION24X301 - 304
69X-RAY DIFFRACTION24X401 - 420
70X-RAY DIFFRACTION25Y2 - 201
71X-RAY DIFFRACTION25Y301 - 302
72X-RAY DIFFRACTION25Y401 - 436
73X-RAY DIFFRACTION26Z1 - 213
74X-RAY DIFFRACTION26Z301 - 304
75X-RAY DIFFRACTION26Z401 - 449
76X-RAY DIFFRACTION27a1 - 216
77X-RAY DIFFRACTION27a301 - 305
78X-RAY DIFFRACTION27a401 - 435
79X-RAY DIFFRACTION28b2 - 199
80X-RAY DIFFRACTION28b201 - 203
81X-RAY DIFFRACTION28b301 - 333

+
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