[English] 日本語
Yorodumi
- PDB-3h4p: Proteasome 20S core particle from Methanocaldococcus jannaschii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h4p
TitleProteasome 20S core particle from Methanocaldococcus jannaschii
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE / 20S / Proteasome / core particle / Protease / Threonine protease
Function / homology
Function and homology information


proteasome core complex / proteasomal ubiquitin-independent protein catabolic process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / cytoplasm
Similarity search - Function
Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / 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 ...Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / 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
Similarity search - Domain/homology
Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsJeffrey, P.D. / Zhang, F. / Hu, M. / Tian, G. / Zhang, P. / Finley, D. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Insights into the Regulatory Particle of the Proteasome from Methanocaldococcus jannaschii.
Authors: Zhang, F. / Hu, M. / Tian, G. / Zhang, P. / Finley, D. / Jeffrey, P.D. / Shi, Y.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2016Group: Refinement description
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
a: Proteasome subunit beta
b: Proteasome subunit beta
c: Proteasome subunit beta
d: Proteasome subunit beta
e: Proteasome subunit beta
f: Proteasome subunit beta
g: Proteasome subunit beta
H: Proteasome subunit alpha
I: Proteasome subunit alpha
J: Proteasome subunit alpha
K: Proteasome subunit alpha
L: Proteasome subunit alpha
M: Proteasome subunit alpha
N: Proteasome subunit alpha
h: Proteasome subunit beta
i: Proteasome subunit beta
j: Proteasome subunit beta
k: Proteasome subunit beta
l: Proteasome subunit beta
m: Proteasome subunit beta
n: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)748,08728
Polymers748,08728
Non-polymers00
Water0
1
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
a: Proteasome subunit beta
b: Proteasome subunit beta
c: Proteasome subunit beta
d: Proteasome subunit beta
e: Proteasome subunit beta
f: Proteasome subunit beta
g: Proteasome subunit beta

H: Proteasome subunit alpha
I: Proteasome subunit alpha
J: Proteasome subunit alpha
K: Proteasome subunit alpha
L: Proteasome subunit alpha
M: Proteasome subunit alpha
N: Proteasome subunit alpha
h: Proteasome subunit beta
i: Proteasome subunit beta
j: Proteasome subunit beta
k: Proteasome subunit beta
l: Proteasome subunit beta
m: Proteasome subunit beta
n: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)748,08728
Polymers748,08728
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area98210 Å2
ΔGint-257 kcal/mol
Surface area212820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.720, 219.540, 149.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
12
22
32
42
52
62
72
82
92
102
112
122
132
142

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111segid AAA1
211segid AAA2
311segid AAA3
411segid AAA4
511segid AAA5
611segid AAA6
711segid AAA7
811segid AAB1
911segid AAB2
1011segid AAB3
1111segid AAB4
1211segid AAB5
1311segid AAB6
1411segid AAB7
112segid BBA1
212segid BBA2
312segid BBA3
412segid BBA4
512segid BBA5
612segid BBA6
712segid BBA7
812segid BBB1
912segid BBB2
1012segid BBB3
1112segid BBB4
1212segid BBB5
1312segid BBB6
1412segid BBB7

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Proteasome subunit alpha / / Multicatalytic endopeptidase complex subunit alpha / 20S proteasome subunit alpha


Mass: 29647.076 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: psmA, MJ0591 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60177, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / / Multicatalytic endopeptidase complex subunit beta


Mass: 23787.709 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: psmB, MJ1237 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58634, proteasome endopeptidase complex

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M Tris, pH 6.8, 0.2 M KCl and 33-36% MPD (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. all: 54076 / Num. obs: 54076 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.126 / Net I/σ(I): 9.5
Reflection shellResolution: 4.1→4.25 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.488 / % possible all: 100

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→49.975 Å / SU ML: 0.71 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3245 2737 5.09 %IN THIN RESOLUTION SHELLS
Rwork0.2536 ---
obs0.2573 53777 99.83 %-
all-53777 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 149.766 Å2 / ksol: 0.328 e/Å3
Refinement stepCycle: LAST / Resolution: 4.1→49.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46648 0 0 0 46648
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1814X-RAY DIFFRACTIONPOSITIONAL0.33
12B1814X-RAY DIFFRACTIONPOSITIONAL0.33
13C1814X-RAY DIFFRACTIONPOSITIONAL0.299
14D1814X-RAY DIFFRACTIONPOSITIONAL0.318
15E1814X-RAY DIFFRACTIONPOSITIONAL0.337
16F1814X-RAY DIFFRACTIONPOSITIONAL0.338
17G1814X-RAY DIFFRACTIONPOSITIONAL0.335
18H1814X-RAY DIFFRACTIONPOSITIONAL0.3
19I1814X-RAY DIFFRACTIONPOSITIONAL0.334
110J1814X-RAY DIFFRACTIONPOSITIONAL0.306
111K1814X-RAY DIFFRACTIONPOSITIONAL0.339
112L1814X-RAY DIFFRACTIONPOSITIONAL0.234
113M1814X-RAY DIFFRACTIONPOSITIONAL0.313
114N1814X-RAY DIFFRACTIONPOSITIONAL0.29
21a1520X-RAY DIFFRACTIONPOSITIONAL0.306
22b1520X-RAY DIFFRACTIONPOSITIONAL0.306
23c1520X-RAY DIFFRACTIONPOSITIONAL0.316
24d1520X-RAY DIFFRACTIONPOSITIONAL0.322
25e1520X-RAY DIFFRACTIONPOSITIONAL0.343
26f1520X-RAY DIFFRACTIONPOSITIONAL0.35
27g1520X-RAY DIFFRACTIONPOSITIONAL0.342
28h1520X-RAY DIFFRACTIONPOSITIONAL0.316
29i1520X-RAY DIFFRACTIONPOSITIONAL0.346
210j1520X-RAY DIFFRACTIONPOSITIONAL0.354
211k1520X-RAY DIFFRACTIONPOSITIONAL0.327
212l1520X-RAY DIFFRACTIONPOSITIONAL0.239
213m1520X-RAY DIFFRACTIONPOSITIONAL0.339
214n1520X-RAY DIFFRACTIONPOSITIONAL0.313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.17070.4181190.35342538X-RAY DIFFRACTION100
4.1707-4.24650.3661180.3112539X-RAY DIFFRACTION100
4.2465-4.32810.39841500.28952496X-RAY DIFFRACTION100
4.3281-4.41640.34311540.28382521X-RAY DIFFRACTION100
4.4164-4.51240.38121190.26252528X-RAY DIFFRACTION100
4.5124-4.61720.32671360.26552513X-RAY DIFFRACTION100
4.6172-4.73260.34391390.27512514X-RAY DIFFRACTION100
4.7326-4.86050.38081510.26472512X-RAY DIFFRACTION100
4.8605-5.00340.31641120.25452576X-RAY DIFFRACTION100
5.0034-5.16470.31161300.23952535X-RAY DIFFRACTION100
5.1647-5.34910.35681430.25872535X-RAY DIFFRACTION100
5.3491-5.5630.36291340.25782529X-RAY DIFFRACTION100
5.563-5.81580.31911300.262550X-RAY DIFFRACTION100
5.8158-6.1220.37311510.2662543X-RAY DIFFRACTION100
6.122-6.50470.3321470.26062553X-RAY DIFFRACTION100
6.5047-7.00570.33331370.24072576X-RAY DIFFRACTION100
7.0057-7.70850.26881300.19442587X-RAY DIFFRACTION100
7.7085-8.81860.23261390.14822592X-RAY DIFFRACTION100
8.8186-11.09050.17431550.13692590X-RAY DIFFRACTION100
11.0905-49.97890.31621430.28162713X-RAY DIFFRACTION99
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)
13.74330.3980.53763.0437-2.04060.0337-0.17620.27240.36280.25640.14561.1381-0.55580.0963-0.00031.99740.16940.04751.29180.01972.005831.5173141.270154.0883
20.592-0.1758-0.73780.629-1.36461.6045-0.0579-0.03851.0481-0.09980.24090.53560.6161-0.02090.00011.02670.02790.18151.4333-0.03912.262715.4483122.890574.4059
32.0628-0.6662-0.52990.8452-1.5672.7770.0214-0.3302-0.02620.1747-0.34530.57620.10940.0103-01.2825-0.26030.49971.5266-0.30071.699426.2399101.789595.9961
4-0.87750.252-0.48280.3644-0.62491.1656-0.05490.34130.09240.4265-0.11230.2327-0.11010.71650.00010.8066-0.18670.25031.07150.15340.470956.629295.337103.1108
51.5271-0.77621.83610.6347-0.00590.3147-0.2124-0.5520.0594-0.26940.78380.3864-0.09530.6169-0.00010.9087-0.10790.09341.81230.08960.616783.0394106.873790.7163
62.2704-0.0326-0.87530.96470.1062-2.31440.453-0.34470.0524-0.0577-0.41670.3426-0.08290.3195-0.00011.2966-0.42760.32391.5955-0.0590.830686.2805129.146767.8577
72.2549-0.1199-0.12064.6353-1.18132.02650.40680.10410.1295-0.4766-0.07370.2666-0.60880.2453-0.00021.7159-0.32370.28371.31180.00651.144263.3401144.390551.6775
83.0604-1.11830.06481.0715-2.21953.1694-0.1369-0.4614-0.04010.43730.03960.42570.0940.528902.20740.2170.06681.7305-0.00861.2557-46.450848.084728.0388
9-0.2047-0.18790.72520.1124-0.9402-0.8047-0.31920.134-0.23290.2227-0.0705-0.2545-0.3733-0.32530.00021.340.1823-0.29351.14060.16051.0353-19.876259.988415.2638
101.23470.28621.85891.3566-0.1091-1.0384-0.7274-0.00590.4658-0.04080.32570.04840.1949-0.0249-0.00420.92920.0218-0.32730.92210.08831.3605-17.056181.9805-7.9055
112.29722.11310.48484.3251-2.67880.744-0.49320.30420.5632-0.015-0.14360.307-0.18210.2639-0.00021.44420.054-0.46741.15810.18951.9378-40.202297.0103-23.3867
120.898-1.8635-0.86851.7514-2.10071.3908-0.4034-0.05280.2694-0.10680.00110.468-0.30090.195-01.13590.1009-0.39591.2412-0.14482.278-72.026193.7818-20.8774
132.8030.9792-0.4460.2494-0.74382.0749-0.34490.21950.17870.4219-0.00910.3660.0935-0.150.00011.31280.09060.01891.4444-0.46652.155-88.185175.0276-0.8781
142.9718-1.07350.18970.2255-0.57671.1055-0.3085-0.36750.04930.07640.18650.41260.0956-0.04280.00011.70650.01140.28011.6651-0.11531.7254-76.923954.257220.9081
152.03351.8226-0.5080.3132-0.774.02890.0384-0.32490.3379-1.0975-0.12020.7825-0.70170.1943-02.14590.3629-0.4411.1428-0.00751.625940.0582115.270924.3707
160.8216-0.0981.20190.06941.14491.38380.32680.30850.1043-0.08-0.73720.3499-0.259-0.0792-0.00011.36830.237-0.35511.2705-0.30431.955217.2563100.076940.6201
170.85081.41350.81712.47950.13851.7929-0.2150.1002-0.06810.2101-0.52610.71690.2887-0.0063-0.00011.03-0.11620.36951.2414-0.37251.760720.768278.248263.6996
180.88231.75381.92222.55361.98090.65070.0414-0.10910.11740.5224-0.53440.17160.80290.028-01.74650.00590.49981.29210.17761.309647.626366.523476.0977
190.4162-0.50460.55694.49481.45122.25720.0255-0.0538-0.23720.63610.2460.04020.38620.32440.00010.99430.03050.08011.49430.12061.225277.76173.53568.678
202.785-0.8882-1.39033.59392.61445.1227-0.2240.0375-0.44390.02870.5994-0.5802-0.03720.3920.00021.3871-0.24360.17211.48220.19860.926288.378594.2346.7629
212.95670.0092-2.03781.64121.22631.76150.08280.31540.0933-0.5260.38260.1009-0.41750.2336-0.00042.2922-0.0082-0.00731.14450.06950.933671.7882112.815727.2104
222.6249-0.08370.41142.53270.9070.5876-0.4013-0.24220.08671.14320.00350.27180.74510.183902.6696-0.15810.42871.14190.03741.2082-55.806719.06081.1496
231.25020.2627-2.35384.26511.44832.5143-0.07030.0923-0.010.61540.0161-0.09490.70420.345401.96950.3668-0.14131.1986-0.00871.0832-25.720825.9807-6.2389
242.792-0.4642-1.41292.43412.50163.4302-0.63820.33620.20680.56890.79640.03390.13060.38240.00010.7910.1187-0.27671.16040.0290.777-14.902346.667-28.1023
252.25880.6373-1.13021.33562.7811.6903-0.4985-0.7270.0844-0.95350.07980.0776-0.38170.16780.00020.9928-0.1475-0.29650.83430.35011.1867-31.513765.2539-47.7361
260.7441-0.6042-0.20841.4191.10653.04240.49530.17160.3547-0.2306-0.50010.7219-0.78290.25890.00011.31360.0462-0.49181.31240.02311.6192-63.2467.7047-50.4828
27-0.5416-0.15870.3962-0.07711.73232.3146-0.225-0.206-0.3743-0.0134-0.56390.7163-0.2134-0.1517-0.00011.0197-0.05270.01921.3073-0.41081.8915-86.002452.5457-34.5718
282.57521.11491.02641.81391.64730.8733-0.3672-0.08950.14381.0126-0.29210.63060.7552-0.45150.00011.8063-0.24440.52741.6309-0.20381.8911-82.799730.7838-11.3952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:244 )A13 - 244
2X-RAY DIFFRACTION2( CHAIN B AND RESID 13:244 )B13 - 244
3X-RAY DIFFRACTION3( CHAIN C AND RESID 13:244 )C13 - 244
4X-RAY DIFFRACTION4( CHAIN D AND RESID 13:244 )D13 - 244
5X-RAY DIFFRACTION5( CHAIN E AND RESID 13:244 )E13 - 244
6X-RAY DIFFRACTION6( CHAIN F AND RESID 13:244 )F13 - 244
7X-RAY DIFFRACTION7( CHAIN G AND RESID 13:244 )G13 - 244
8X-RAY DIFFRACTION8( CHAIN H AND RESID 13:244 )H13 - 244
9X-RAY DIFFRACTION9( CHAIN I AND RESID 13:244 )I13 - 244
10X-RAY DIFFRACTION10( CHAIN J AND RESID 13:244 )J13 - 244
11X-RAY DIFFRACTION11( CHAIN K AND RESID 13:244 )K13 - 244
12X-RAY DIFFRACTION12( CHAIN L AND RESID 13:244 )L13 - 244
13X-RAY DIFFRACTION13( CHAIN M AND RESID 13:244 )M13 - 244
14X-RAY DIFFRACTION14( CHAIN N AND RESID 13:244 )N13 - 244
15X-RAY DIFFRACTION15( CHAIN a AND RESID 7:208 )a7 - 208
16X-RAY DIFFRACTION16( CHAIN b AND RESID 7:208 )b7 - 208
17X-RAY DIFFRACTION17( CHAIN c AND RESID 7:208 )c7 - 208
18X-RAY DIFFRACTION18( CHAIN d AND RESID 7:208 )d7 - 208
19X-RAY DIFFRACTION19( CHAIN e AND RESID 7:208 )e7 - 208
20X-RAY DIFFRACTION20( CHAIN f AND RESID 7:208 )f7 - 208
21X-RAY DIFFRACTION21( CHAIN g AND RESID 7:208 )g7 - 208
22X-RAY DIFFRACTION22( CHAIN h AND RESID 7:208 )h7 - 208
23X-RAY DIFFRACTION23( CHAIN i AND RESID 7:208 )i7 - 208
24X-RAY DIFFRACTION24( CHAIN j AND RESID 7:208 )j7 - 208
25X-RAY DIFFRACTION25( CHAIN k AND RESID 7:208 )k7 - 208
26X-RAY DIFFRACTION26( CHAIN l AND RESID 7:208 )l7 - 208
27X-RAY DIFFRACTION27( CHAIN m AND RESID 7:208 )m7 - 208
28X-RAY DIFFRACTION28( CHAIN n AND RESID 7:208 )n7 - 208

+
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