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- PDB-5msj: Mouse PA28alpha -

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Basic information

Entry
Database: PDB / ID: 5msj
TitleMouse PA28alpha
ComponentsProteasome activator complex subunit 1
KeywordsSTRUCTURAL PROTEIN / proteasome activator / regulator / heptamer / REGalpha / interferon-gamma / hydrolase
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome activator complex / 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 ...Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome activator complex / 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 / 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 / positive regulation of endopeptidase activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / antigen processing and presentation of exogenous antigen / 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 / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / nucleoplasm / cytoplasm
Similarity search - Function
Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator pa28 alpha subunit / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit
Similarity search - Domain/homology
Proteasome activator complex subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Structure / Year: 2017
Title: The Mammalian Proteasome Activator PA28 Forms an Asymmetric alpha 4 beta 3 Complex.
Authors: Huber, E.M. / Groll, M.
History
DepositionJan 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome activator complex subunit 1
B: Proteasome activator complex subunit 1
C: Proteasome activator complex subunit 1
D: Proteasome activator complex subunit 1
E: Proteasome activator complex subunit 1
F: Proteasome activator complex subunit 1
G: Proteasome activator complex subunit 1
H: Proteasome activator complex subunit 1
I: Proteasome activator complex subunit 1
J: Proteasome activator complex subunit 1
K: Proteasome activator complex subunit 1
L: Proteasome activator complex subunit 1
M: Proteasome activator complex subunit 1
N: Proteasome activator complex subunit 1
O: Proteasome activator complex subunit 1
P: Proteasome activator complex subunit 1
Q: Proteasome activator complex subunit 1
R: Proteasome activator complex subunit 1
S: Proteasome activator complex subunit 1
T: Proteasome activator complex subunit 1
U: Proteasome activator complex subunit 1
V: Proteasome activator complex subunit 1
W: Proteasome activator complex subunit 1
X: Proteasome activator complex subunit 1
Y: Proteasome activator complex subunit 1
Z: Proteasome activator complex subunit 1
a: Proteasome activator complex subunit 1
b: Proteasome activator complex subunit 1


Theoretical massNumber of molelcules
Total (without water)804,10328
Polymers804,10328
Non-polymers00
Water0
1
A: Proteasome activator complex subunit 1
B: Proteasome activator complex subunit 1
C: Proteasome activator complex subunit 1
D: Proteasome activator complex subunit 1
E: Proteasome activator complex subunit 1
F: Proteasome activator complex subunit 1
G: Proteasome activator complex subunit 1


Theoretical massNumber of molelcules
Total (without water)201,0267
Polymers201,0267
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27350 Å2
ΔGint-122 kcal/mol
Surface area61820 Å2
MethodPISA
2
H: Proteasome activator complex subunit 1
I: Proteasome activator complex subunit 1
J: Proteasome activator complex subunit 1
K: Proteasome activator complex subunit 1
L: Proteasome activator complex subunit 1
M: Proteasome activator complex subunit 1
N: Proteasome activator complex subunit 1


Theoretical massNumber of molelcules
Total (without water)201,0267
Polymers201,0267
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27930 Å2
ΔGint-124 kcal/mol
Surface area61750 Å2
MethodPISA
3
O: Proteasome activator complex subunit 1
P: Proteasome activator complex subunit 1
Q: Proteasome activator complex subunit 1
R: Proteasome activator complex subunit 1
S: Proteasome activator complex subunit 1
T: Proteasome activator complex subunit 1
U: Proteasome activator complex subunit 1


Theoretical massNumber of molelcules
Total (without water)201,0267
Polymers201,0267
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26890 Å2
ΔGint-123 kcal/mol
Surface area61340 Å2
MethodPISA
4
V: Proteasome activator complex subunit 1
W: Proteasome activator complex subunit 1
X: Proteasome activator complex subunit 1
Y: Proteasome activator complex subunit 1
Z: Proteasome activator complex subunit 1
a: Proteasome activator complex subunit 1
b: Proteasome activator complex subunit 1


Theoretical massNumber of molelcules
Total (without water)201,0267
Polymers201,0267
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27290 Å2
ΔGint-127 kcal/mol
Surface area61260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.790, 119.800, 196.670
Angle α, β, γ (deg.)94.21, 98.52, 87.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Proteasome activator complex subunit 1 / 11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / ...11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / Proteasome activator 28 subunit alpha / PA28alpha


Mass: 28717.973 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psme1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P97371

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes, 25 % PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 92743 / % possible obs: 93.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.1
Reflection shellResolution: 3.5→3.6 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1.9 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVO
Resolution: 3.5→29.65 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.903 / SU B: 103.857 / SU ML: 0.658 / Cross valid method: THROUGHOUT / ESU R Free: 0.746 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28279 4638 5 %RANDOM
Rwork0.24953 ---
obs0.25122 88105 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0.56 Å2-0.21 Å2
2--4.02 Å20.71 Å2
3----4.58 Å2
Refinement stepCycle: 1 / Resolution: 3.5→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46128 0 0 0 46128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01946967
X-RAY DIFFRACTIONr_bond_other_d0.0010.0244998
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.98263461
X-RAY DIFFRACTIONr_angle_other_deg0.8483104918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.58155667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60825.472278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.559158845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.96915239
X-RAY DIFFRACTIONr_chiral_restr0.0470.27190
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02151096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028555
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_it0.6117.29222836
X-RAY DIFFRACTIONr_mcbond_other0.6117.29222835
X-RAY DIFFRACTIONr_mcangle_it1.14710.92928447
X-RAY DIFFRACTIONr_mcangle_other1.14710.92928448
X-RAY DIFFRACTIONr_scbond_it0.3287.2424131
X-RAY DIFFRACTIONr_scbond_other0.3287.2424132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.68210.87235015
X-RAY DIFFRACTIONr_long_range_B_refined2.63485.8752228
X-RAY DIFFRACTIONr_long_range_B_other2.63485.86952228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 339 -
Rwork0.35 6433 -
obs--93.59 %
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)
10.41360.15340.57030.75690.03482.7171-0.02360.12710.04370.0637-0.0441-0.0495-0.14730.28630.06780.3520.0226-0.04480.24280.03290.10941.486424.54362.3975
20.58860.2007-0.3590.09360.02561.29340.00790.03620.07050.00190.00850.0420.2571-0.1136-0.01640.43210.0316-0.06840.2680.05010.0702-18.913517.6118-0.8942
31.7377-0.9244-2.00112.01421.84022.75430.00560.0874-0.00880.1357-0.0155-0.1354-0.0082-0.08340.00990.3661-0.0041-0.08220.2384-0.00390.0737-25.7004-3.3416-3.6599
42.1582-0.4735-1.42790.6846-0.05571.1805-0.0554-0.016-0.01410.01470.0570.04630.0527-0.0371-0.00160.41-0.04550.04860.3267-0.14830.0764-13.5068-22.2775-2.7336
50.728-0.12130.74740.2409-0.0661.2326-0.04980.0281-0.24580.0413-0.0995-0.04420.0520.12470.14940.41370.02970.12290.3020.0660.49077.1124-24.88741.0687
60.1411-0.0370.38311.9849-2.00243.0657-0.00140.0351-0.0830.0615-0.0033-0.2031-0.0769-0.13420.00470.32790.0501-0.00150.30510.00190.117222.9679-8.33624.0539
71.3111-0.26210.9481.5288-1.10933.6662-0.0958-0.0255-0.13110.0706-0.0188-0.1731-0.0050.06750.11450.2772-0.01010.01720.1739-0.01510.098919.924413.02045.5923
81.71260.160.73960.63920.49724.0954-0.0938-0.05310.30020.1065-0.0549-0.2795-0.0687-0.05850.14870.32410.0226-0.09150.17380.10130.261827.6217-40.8823100.6432
91.18821.0339-0.17692.25781.00861.4539-0.0905-0.08670.27240.04030.07850.2210.0073-0.04310.0120.29330.0564-0.07040.30810.10920.17197.9202-49.728496.863
102.3607-1.034-1.75741.16671.1713.3625-0.14940.0550.1369-0.07380.06830.0546-0.2641-0.21870.08110.3019-0.0611-0.01070.20790.05480.07233.9185-71.290192.5222
110.25230.2394-0.15290.6609-0.3290.1889-0.13610.0197-0.2295-0.15130.0211-0.11420.0539-0.06490.11490.2798-0.0190.16970.4353-0.07750.245217.9219-88.680493.009
121.34391.0436-0.59611.3079-1.13981.18910.0428-0.0134-0.12730.0602-0.0429-0.0868-0.0560.05380.00010.2836-0.02740.19140.2786-0.13190.198239.6768-88.591797.7549
130.0980.2849-0.07333.0952-1.92341.4042-0.04090.0799-0.11030.13540.0552-0.2228-0.0798-0.0127-0.01420.209-0.03870.06880.43210.01080.162352.5338-71.325102.7976
141.1238-0.23441.14010.4548-0.97964.0578-0.1415-0.0244-0.0240.02450.0795-0.1847-0.0221-0.1270.0620.2609-0.0346-0.01280.21020.04370.169947.1546-50.6947104.3131
150.9383-0.4076-0.5460.55990.98592.1284-0.0744-0.0218-0.1632-0.0377-0.03810.1184-0.11850.19070.11250.33980.00810.07470.2809-0.03940.1154-6.7224-88.7266157.2195
161.08590.49970.24021.22380.61993.4273-0.09630.1356-0.0233-0.05080.01460.18610.17390.03730.08170.23850.04380.09050.2078-0.0220.1597-11.5318-67.8782157.7968
170.732-0.15790.77760.6796-0.63481.1673-0.0255-0.05360.22250.005-0.06740.1428-0.06650.0040.09280.41590.00980.07990.2687-0.06690.14621.6253-50.1897162.7647
180.8458-0.13880.29290.7963-1.17341.7787-0.051-0.14610.24790.068-0.0619-0.0504-0.0811-0.03140.11290.5101-0.0102-0.05050.2476-0.09690.090223.5761-50.8897168.3071
190.2309-0.05320.04420.2499-0.190.1502-0.1078-0.1465-0.01020.0874-0.0066-0.1485-0.11280.01760.11450.4249-0.0225-0.03250.33960.09110.111737.1548-68.0468169.34
201.80220.5399-1.73830.4002-0.2672.1477-0.08140.0167-0.24310.109-0.0317-0.1896-0.0257-0.06980.11320.38810.0221-0.04480.31560.14130.140632.8198-88.7755165.8882
211.08850.2871-0.64240.13630.02261.14230.09280.025-0.30150.015-0.1209-0.126-0.0848-0.21640.0280.3870.05280.08460.30350.09020.149411.3537-98.0484162.6582
220.3478-0.11590.39891.11030.52761.1610.0811-0.0198-0.0764-0.0626-0.0924-0.0357-0.1032-0.10080.01130.28320.01350.0070.22750.0250.139-34.268-18.34262.4064
231.172-0.18580.40420.12210.39743.07350.05350.0574-0.11320.0514-0.03140.05780.0704-0.0612-0.02210.3833-0.00930.03050.2097-0.02030.0934-36.43093.095762.9478
240.69190.11520.85310.3874-0.35271.77330.0244-0.05890.1995-0.0239-0.10120.1492-0.00820.17640.07670.361-0.02560.01220.3188-0.09110.101-20.791819.109266.8786
251.4913-0.3087-0.13251.6507-1.25371.07660.13230.00470.1375-0.033-0.10860.01250.03170.0007-0.02370.4239-0.0624-0.02980.2816-0.05830.03250.556416.35569.9788
260.41130.5412-0.7581.7546-1.20541.4595-0.0482-0.0134-0.0308-0.0547-0.014-0.08920.01-0.02270.06210.3866-0.0286-0.0840.32570.10590.054512.1059-2.13770.7106
271.4065-0.3756-1.60920.6769-0.2823.0495-0.11230.0368-0.08920.0948-0.2344-0.28280.02380.00570.34670.2673-0.0271-0.03910.27940.19690.2184.8689-23.053168.8866
280.9067-0.2496-1.60630.87430.59453.1833-0.07810.0752-0.33520.0201-0.3378-0.0391-0.0449-0.23530.41590.25730.00420.03050.21130.07050.2538-15.208-30.513264.6196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 243
2X-RAY DIFFRACTION2B5 - 243
3X-RAY DIFFRACTION3C5 - 243
4X-RAY DIFFRACTION4D7 - 243
5X-RAY DIFFRACTION5E3 - 244
6X-RAY DIFFRACTION6F8 - 241
7X-RAY DIFFRACTION7G6 - 244
8X-RAY DIFFRACTION8H4 - 243
9X-RAY DIFFRACTION9I6 - 244
10X-RAY DIFFRACTION10J4 - 242
11X-RAY DIFFRACTION11K4 - 242
12X-RAY DIFFRACTION12L5 - 243
13X-RAY DIFFRACTION13M7 - 241
14X-RAY DIFFRACTION14N3 - 243
15X-RAY DIFFRACTION15O8 - 243
16X-RAY DIFFRACTION16P4 - 244
17X-RAY DIFFRACTION17Q6 - 243
18X-RAY DIFFRACTION18R8 - 241
19X-RAY DIFFRACTION19S8 - 242
20X-RAY DIFFRACTION20T4 - 243
21X-RAY DIFFRACTION21U7 - 242
22X-RAY DIFFRACTION22V8 - 243
23X-RAY DIFFRACTION23W5 - 243
24X-RAY DIFFRACTION24X8 - 243
25X-RAY DIFFRACTION25Y6 - 243
26X-RAY DIFFRACTION26Z4 - 243
27X-RAY DIFFRACTION27a4 - 243
28X-RAY DIFFRACTION28b4 - 242

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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

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