[English] 日本語
Yorodumi
- PDB-9fbl: STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT (CK2ALPHA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fbl
TitleSTRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT (CK2ALPHA, CSNK2A1 gene product) IN COMPLEX WITH THE CYCLIC PEPTIDOMIMETIC COMPOUND FMP35 DISCOVERED BY HIGH-THROUGHPUT SCREENING
Components
  • Casein kinase II subunit alpha
  • Cyclic peptidomimetic compound FMP35
KeywordsTRANSFERASE / HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT ALPHA / CSNK2A1 GENE PRODUCT / INHIBITION OF CK2ALPHA/CK2BETA SUBUNIT INTERACTION
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / kinase activity / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
NICOTINIC ACID / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWerner, C. / Niefind, K. / Eimermacher, S. / Pietsch, M. / Lindenblatt, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: To Be Published
Title: Structure of human protein kinase CK2 catalytic subunit (CK2alpha) in complex with the cyclic peptidomimetic compound FMP35 discovered by high-throughput screening
Authors: Werner, C. / Niefind, K. / Eimermacher, S. / Pietsch, M. / Lindenblatt, D.
#1: Journal: Anal Biochem / Year: 2015
Title: Development of a high-throughput screening-compatible assay to identify inhibitors of the CK2alpha/CK2beta interaction.
Authors: Hochscherf, J. / Lindenblatt, D. / Steinkrueger, M. / Yoo, E. / Ulucan, O. / Herzig, S. / Issinger, O.G. / Helms, V. / Goetz, C. / Neundorf, I. / Niefind, K. / Pietsch, M.
#2: Journal: ACS Chem Biol / Year: 2013
Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2beta-competitive ligand.
Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
C: Casein kinase II subunit alpha
L: Cyclic peptidomimetic compound FMP35
N: Cyclic peptidomimetic compound FMP35
P: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,89923
Polymers127,2586
Non-polymers1,64117
Water3,495194
1
A: Casein kinase II subunit alpha
L: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1199
Polymers42,4192
Non-polymers6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
N: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8316
Polymers42,4192
Non-polymers4114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase II subunit alpha
P: Cyclic peptidomimetic compound FMP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9508
Polymers42,4192
Non-polymers5306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.952, 206.560, 76.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-513-

HOH

21B-581-

HOH

31B-582-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 159 or resid 161 through 227 or resid 229 through 331))
d_2ens_1(chain "B" and (resid 3 through 159 or resid 161 through 227 or resid 229 through 331))
d_3ens_1(chain "C" and (resid 3 through 159 or resid 161 through 227 or resid 229 through 331))
d_1ens_2chain "L"
d_2ens_2chain "N"
d_3ens_2chain "P"
d_1ens_3chain "M"
d_2ens_3chain "O"
d_3ens_3chain "Q"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYPROPROAA3 - 15917 - 173
d_12ens_1ASNASNPHEPHEAA161 - 227175 - 241
d_13ens_1LYSLYSGLNGLNAA229 - 331243 - 345
d_21ens_1GLYGLYPROPROBB3 - 15917 - 173
d_22ens_1ASNASNPHEPHEBB161 - 227175 - 241
d_23ens_1LYSLYSGLNGLNBB229 - 331243 - 345
d_31ens_1GLYGLYPROPROCC3 - 15917 - 173
d_32ens_1ASNASNPHEPHECC161 - 227175 - 241
d_33ens_1LYSLYSGLNGLNCC229 - 331243 - 345
d_11ens_2A1ICCA1ICCVALVALLD1 - 51 - 5
d_21ens_2A1ICCA1ICCVALVALNE1 - 51 - 5
d_31ens_2A1ICCA1ICCVALVALPF1 - 51 - 5
d_11ens_3NIONIONIONIOAG401
d_21ens_3NIONIONIONIOBN401
d_31ens_3NIONIONIONIOCR401

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999994957629, 0.00166421252426, -0.00270464648522), (0.00142848388343, 0.9963854298, 0.0849354738346), (0.00283622102995, 0.0849311820145, -0.996382782956)39.3452149422, -35.7043722711, 7.90771726888
2given(-0.999345327888, 0.0230930402251, -0.0278500829688), (0.025535550143, 0.995541849782, -0.0907984637055), (0.0256291105406, -0.0914501876736, -0.995479789783)36.7647797181, 33.8110367774, 5.82845565329
3given(-0.997448777249, -0.0441496222113, 0.056095878847), (-0.0316719657316, 0.977932414836, 0.206506848796), (-0.0639751776216, 0.204203337073, -0.976835796732)36.8172366622, -39.3644597843, 8.30731244756
4given(-0.993912838111, 0.0952207370921, -0.0554101206089), (0.102409790127, 0.983961671252, -0.146053635327), (0.0406141000678, -0.150839122027, -0.987723672968)36.6916425895, 33.3841013371, 5.88496885284
5given(-0.981784061772, -0.149891297462, 0.116758961097), (-0.152121686456, 0.988307261181, -0.0103802700207), (-0.113837816919, -0.0279527537342, -0.993106034116)37.0711859947, -27.9030052714, 13.2168947369
6given(-0.954960434858, 0.273923797068, -0.114089093498), (0.287887473976, 0.948453244742, -0.132503754159), (0.0719122394527, -0.159380663627, -0.984594553041)34.348980578, 28.6498700815, 5.0718464971

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABCLNP

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide Cyclic peptidomimetic compound FMP35


Mass: 733.876 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 211 molecules

#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H5NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP35 in DMSO and incubated for ...Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP35 in DMSO and incubated for 30 min. reservoir: 1.5 mol/l lithium sulphate, 100 mM sodium HEPES buffer pH 7.5. crystallization drop: 200 nanoliter protein solution plus 100 nanoliter reservoir.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.176→72.931 Å / Num. obs: 39662 / % possible obs: 60.2 % / Redundancy: 17.6 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.479 / Rpim(I) all: 0.116 / Rrim(I) all: 0.493 / Rsym value: 0.479 / Net I/σ(I): 8.1
Reflection shellResolution: 2.176→2.403 Å / Redundancy: 17.7 % / Rmerge(I) obs: 8.397 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1983 / CC1/2: 0.502 / Rpim(I) all: 1.999 / Rrim(I) all: 8.637 / Rsym value: 8.397 / % possible all: 11.9

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→72.93 Å / SU ML: 0.3109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1186 2.99 %
Rwork0.2087 38434 -
obs0.2104 39620 60.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.79 Å2
Refinement stepCycle: LAST / Resolution: 2.18→72.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8366 0 246 194 8806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168871
X-RAY DIFFRACTIONf_angle_d0.447612013
X-RAY DIFFRACTIONf_chiral_restr0.04211227
X-RAY DIFFRACTIONf_plane_restr0.00341536
X-RAY DIFFRACTIONf_dihedral_angle_d10.74483332
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.89469610891
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.899319047678
ens_2d_2DLX-RAY DIFFRACTIONTorsion NCS0.937830782811
ens_2d_3DLX-RAY DIFFRACTIONTorsion NCS0.829497394494
ens_3d_2ENX-RAY DIFFRACTIONTorsion NCS1.04899751215
ens_3d_3ENX-RAY DIFFRACTIONTorsion NCS1.04918739775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.280.327390.3076314X-RAY DIFFRACTION3.98
2.28-2.40.3123440.31921475X-RAY DIFFRACTION18.71
2.4-2.550.3879890.312906X-RAY DIFFRACTION36.73
2.55-2.740.39431380.29354254X-RAY DIFFRACTION53.8
2.74-3.020.33611810.2766070X-RAY DIFFRACTION76.43
3.02-3.450.27082150.22897165X-RAY DIFFRACTION89.63
3.45-4.350.25212510.1777909X-RAY DIFFRACTION98.01
4.35-72.930.2282590.18198341X-RAY DIFFRACTION99.84
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)
10.58714674563-0.2136619738270.4195806931030.0797932676563-0.08146516603291.57320162764-0.1942400879680.291093303720.220083271331-0.0478727431301-0.0925218312589-0.266163373734-0.2501796689760.846736041364-0.07095913949880.234323977772-0.1527858602490.1152222673620.4465310932430.06393552142110.53273806673538.544072013725.57485197510.9750860345
20.0266180056173-0.1843347794430.02110817486071.337201117220.1736107132030.4882320705540.06118808315220.267892346505-0.2002971221510.6987677214840.36423714999-0.5886707896790.0489212256676-0.3574853290050.1138669228440.4127966878460.0341828332994-0.07125233216870.6829613892080.01328296332610.72610371865636.129417135110.9132065137.1641085487
30.450872440084-0.007435828100060.2595777662040.843772894738-0.6699007167970.672021967964-0.00917930796604-0.3006996627970.1173849059320.5790441457230.00518422180353-0.406471080177-0.0214361751273-0.00715927767753-0.0001561736868990.4506128973840.0587235376712-0.07670381607660.375680432465-0.1115564958920.58349961001737.917114378114.493749001133.8682050024
42.45056452408-0.1512872489850.2713781545990.9025596218630.1149793805250.052323261368-0.177721948615-0.594983006514-0.2918795736980.3093651260040.334652949417-0.238132322216-0.224353296587-0.4146947086110.09529300495030.3274956513310.1500867355220.04803078929750.343138651608-0.1066898233550.152676270321.317806426725.558358811531.0011396615
52.380586062670.05173507164751.111045155871.090328775770.5483788684172.36918103698-0.0551822474942-7.80580903988E-5-0.1659154924910.05086571351990.0697891378252-0.0230945101793-0.0713700561586-0.01529064166770.0001492358611850.1832057130120.01865377067580.04064212366480.102785355661-0.02068024507340.30664684696419.503013039218.008081508314.6363456529
60.463794404081-0.5713135912820.07624198547321.51440901695-0.3619762324741.621137441350.0626811252063-0.2091396887920.147400043996-0.0173975078637-0.206668988961-0.0954610354952-0.558394804793-0.380308910781-0.00559297188560.3135537547090.03324855455560.02736240135750.269563900888-0.1302236895020.32326294185512.736065114532.280079379318.0395056224
73.801186692370.3550913836730.388801545030.5657168162150.4689423998050.673535625458-0.101016735005-0.5186546073370.0164220047661-0.00363154046276-0.09046667412920.1839084332850.136908175309-0.0809231565903-0.2658336919180.2304228984680.112204971404-0.00356486807424-0.00215569410163-0.1700056923070.4465018266641.17955137065-10.13111816890.108481001538
80.7432468562630.6566580915980.5467046693340.9206781315881.173833840552.33976477427-0.3998490718890.491253473038-0.0398621132557-0.4736220861660.2309816585160.3424342526040.5188925799410.307123711574-0.05089208074380.428570171477-0.0827628047047-0.1201381963150.335203624690.0735756619830.4237374085032.15200408178-19.4841108951-26.0329447693
92.089420518221.0044295131.247927907742.198757634091.09970923170.8826339671720.02849036357721.2867669114-0.340635353547-0.8619978858750.558092956584-0.4563684081690.02387004928620.4521203047690.3102871510540.597628921613-0.1237998201910.03120180861010.625597616268-0.05399818702130.30538131549518.3191604643-13.3123499277-25.8034150996
102.847218223130.2180941015610.2781169107291.79241071766-0.5239641734481.46062470524-0.05636065395740.258768652278-0.0281535561306-0.1779864611970.0440646992115-0.2339606770150.008603570578380.2855283271810.001374028345230.165133342356-0.0124951647723-0.0122043382742-0.00102627940331-0.03019666774720.36371705478821.3969564658-11.3807524579-6.74260891884
111.511135331980.01146180759270.6600956470770.7993801117940.07192675750962.210864077880.3219611939660.37537822057-0.04967395942310.00883014269603-0.06271225359050.2889843545480.0918932620338-0.03171172780990.1004899830270.2903008910650.144839574243-0.1160550235760.366777822367-0.1016341823890.0216136116435-1.2145291461147.7340995451-24.6638904085
123.480833065350.8214715922031.593205684780.4442582330050.4557457381020.7491370962850.1165824770290.599625011431-0.248450003895-0.552139703949-0.409707870691-0.586949015635-0.01340241350681.13888599479-0.1132103417280.5183438129230.1062965879180.1685299656740.9376036388540.1329472066470.49508628488315.174690168450.596880999-30.987067926
132.58851563497-0.2645388913811.821994377431.378084067540.1311390751882.46418815875-0.03552034474980.4566948765010.06641711663350.0383412766385-0.119792565164-0.216231324188-0.2687741666050.774038161183-0.02063680484460.297311180469-0.0687252880180.0248256400270.4154936246210.0009047941924830.11362934336818.839737737855.6242605437-12.4545888013
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 24 )AA2 - 241 - 23
22chain 'A' and (resid 25 through 58 )AA25 - 5824 - 57
33chain 'A' and (resid 59 through 108 )AA59 - 10858 - 107
44chain 'A' and (resid 109 through 149 )AA109 - 149108 - 148
55chain 'A' and (resid 150 through 280 )AA150 - 280149 - 279
66chain 'A' and (resid 281 through 331 )AA281 - 331280 - 330
77chain 'B' and (resid 1 through 24 )BD1 - 241 - 24
88chain 'B' and (resid 25 through 108 )BD25 - 10825 - 108
99chain 'B' and (resid 109 through 129 )BD109 - 129109 - 129
1010chain 'B' and (resid 130 through 331 )BD130 - 331130 - 331
1111chain 'C' and (resid 3 through 108 )CG3 - 1081 - 106
1212chain 'C' and (resid 109 through 129 )CG109 - 129107 - 127
1313chain 'C' and (resid 130 through 331 )CG130 - 331128 - 329

+
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