[English] 日本語
Yorodumi
- PDB-4md7: Crystal Structure of full-length symmetric CK2 holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4md7
TitleCrystal Structure of full-length symmetric CK2 holoenzyme
Components
  • Casein kinase II subunit alpha
  • Casein kinase II subunit beta
KeywordsTRANSFERASE / protein serine/threonine kinase
Function / homology
Function and homology information


regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of chromosome separation / protein kinase regulator activity / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes ...regulation of DNA binding / adiponectin-activated signaling pathway / positive regulation of activin receptor signaling pathway / endothelial tube morphogenesis / negative regulation of viral life cycle / regulation of chromosome separation / protein kinase regulator activity / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / 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 signal transduction by p53 class mediator / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / peptidyl-threonine phosphorylation / 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 / Hsp90 protein binding / PML body / Regulation of PTEN stability and activity / Wnt signaling pathway / fibrillar center / 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 / protein-containing complex assembly / secretory granule lumen / protein-macromolecule adaptor activity / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / Neutrophil degranulation / chromatin binding / chromatin / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / Casein Kinase 2, subunit alpha / N-terminal domain of TfIIb / Single Sheet / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Casein kinase II subunit beta / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsLolli, G. / Ranchio, A. / Battistutta, R.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Active Form of the Protein Kinase CK2 alpha 2 beta 2 Holoenzyme Is a Strong Complex with Symmetric Architecture.
Authors: Lolli, G. / Ranchio, A. / Battistutta, R.
History
DepositionAug 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Sep 20, 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_ncs_dom_lim / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Casein kinase II subunit beta
B: Casein kinase II subunit beta
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
E: Casein kinase II subunit alpha
F: Casein kinase II subunit alpha
G: Casein kinase II subunit alpha
H: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,53412
Polymers281,2728
Non-polymers2624
Water00
1
A: Casein kinase II subunit beta
B: Casein kinase II subunit beta
E: Casein kinase II subunit alpha
F: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7676
Polymers140,6364
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-66 kcal/mol
Surface area47850 Å2
MethodPISA
2
C: Casein kinase II subunit beta
D: Casein kinase II subunit beta
G: Casein kinase II subunit alpha
H: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7676
Polymers140,6364
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-65 kcal/mol
Surface area47770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.316, 57.958, 186.188
Angle α, β, γ (deg.)90.000, 102.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TRPTRPPROPROAA9 - 589 - 58
211TRPTRPPROPROBB9 - 589 - 58
311TRPTRPPROPROCC9 - 589 - 58
411TRPTRPPROPRODD9 - 589 - 58
121ASNASNHISHISAA67 - 19367 - 193
221ASNASNHISHISBB67 - 19367 - 193
321ASNASNHISHISCC67 - 19367 - 193
421ASNASNHISHISDD67 - 19367 - 193
112PROPROARGARGEE4 - 474 - 47
212PROPROARGARGFF4 - 474 - 47
312PROPROARGARGGG4 - 474 - 47
412PROPROARGARGHH4 - 474 - 47
122TYRTYRASPASPEE50 - 10350 - 103
222TYRTYRASPASPFF50 - 10350 - 103
322TYRTYRASPASPGG50 - 10350 - 103
422TYRTYRASPASPHH50 - 10350 - 103
132ARGARGVALVALEE107 - 116107 - 116
232ARGARGVALVALFF107 - 116107 - 116
332ARGARGVALVALGG107 - 116107 - 116
432ARGARGVALVALHH107 - 116107 - 116
142LEULEULEULEUEE128 - 265128 - 265
242LEULEULEULEUFF128 - 265128 - 265
342LEULEULEULEUGG128 - 265128 - 265
442LEULEULEULEUHH128 - 265128 - 265
152LEULEUASPASPEE273 - 330273 - 330
252LEULEUASPASPFF273 - 330273 - 330
352LEULEUASPASPGG273 - 330273 - 330
452LEULEUASPASPHH273 - 330273 - 330

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Casein kinase II subunit beta / CK2 subunit beta / CK II beta / Phosvitin / Protein G5a


Mass: 24969.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2B, CK2N, G5A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P67870
#2: Protein
Casein kinase II subunit alpha / CK2 subunit alpha / CK II alpha


Mass: 45348.652 Da / Num. of mol.: 4 / Mutation: T344E/T360E/S362E/S370E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P68400, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2010
RadiationMonochromator: horizontally diffracting Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.1→181.832 Å / Num. all: 52811 / Num. obs: 52811 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rsym value: 0.162 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.275.20.6431.24050777750.64398.7
3.27-3.475.20.4031.93825373060.40398.5
3.47-3.715.30.25433601568530.25498.5
3.71-45.30.1814.23358663970.18198.3
4-4.385.30.1266.13138459250.12698.4
4.38-4.95.30.0997.62801253200.09998.2
4.9-5.665.30.1017.52491446820.10197.7
5.66-6.935.30.0987.62091639340.09897.2
6.93-9.85.30.06410.71621230370.06496.1
9.8-48.8725.30.0512842115820.0591.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4DGL AND 4KWP

4dgl

4kwp


Resolution: 3.1→181.832 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.841 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.2124 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8495 / SU B: 40.124 / SU ML: 0.327 / SU R Cruickshank DPI: 0.1012 / SU Rfree: 0.1058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 2675 5.1 %RANDOM
Rwork0.2332 ---
obs0.2347 52686 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.59 Å2 / Biso mean: 56.7009 Å2 / Biso min: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--10.58 Å2-0 Å2-3.22 Å2
2--3.23 Å20 Å2
3---7.35 Å2
Refinement stepCycle: LAST / Resolution: 3.1→181.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17617 0 4 0 17621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0218109
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.94624507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.73552100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99523.402976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.282153104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.17215140
X-RAY DIFFRACTIONr_chiral_restr0.0790.22513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114120
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A746MEDIUM POSITIONAL0.080.5
12B746MEDIUM POSITIONAL0.070.5
13C746MEDIUM POSITIONAL0.050.5
14D746MEDIUM POSITIONAL0.060.5
11A708TIGHT THERMAL5.510.5
12B708TIGHT THERMAL4.630.5
13C708TIGHT THERMAL4.920.5
14D708TIGHT THERMAL7.390.5
11A746MEDIUM THERMAL5.892
12B746MEDIUM THERMAL4.762
13C746MEDIUM THERMAL5.082
14D746MEDIUM THERMAL7.812
21E1363MEDIUM POSITIONAL0.040.5
22F1363MEDIUM POSITIONAL0.040.5
23G1363MEDIUM POSITIONAL0.030.5
24H1363MEDIUM POSITIONAL0.030.5
21E1216TIGHT THERMAL5.70.5
22F1216TIGHT THERMAL3.270.5
23G1216TIGHT THERMAL4.220.5
24H1216TIGHT THERMAL7.920.5
21E1363MEDIUM THERMAL6.172
22F1363MEDIUM THERMAL3.92
23G1363MEDIUM THERMAL4.682
24H1363MEDIUM THERMAL8.242
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 188 -
Rwork0.318 3647 -
all-3835 -
obs--95.71 %
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)
14.0419-1.68970.88772.03651.57273.68060.13110.4229-0.1541-0.1403-0.013-0.25230.06170.4024-0.11810.04870.01950.10710.0793-0.00580.310764.2289-3.98050.9223
22.2561-1.6576-1.60961.81582.981113.0411-0.04060.4432-0.6432-0.185-0.16180.48040.73470.53360.20240.35170.0023-0.01040.157-0.11880.383261.9296-9.87670.3283
314.6964-3.89624.67534.0720.36872.3387-0.04971.04521.2798-0.8755-0.3517-0.3502-0.48870.28640.40140.26210.0152-0.01280.10170.15050.250948.40518.0668.2454
44.06510.9021-0.37861.27740.02180.8996-0.0315-0.0189-0.07820.1004-0.03130.05730.0575-0.11740.06280.0133-0.00810.01310.02040.0130.128937.3276-0.75717.3457
53.33660.233-3.07121.06090.69015.24030.0148-0.70740.33690.2306-0.0733-0.4379-0.41170.65240.05850.4541-0.1339-0.24880.9123-0.10990.695244.36473.361890.3784
63.76891.08711.66123.5116-1.27291.69950.3325-0.94970.96611.3106-0.75310.3235-0.4925-0.19990.42060.66-0.20760.08431.167-0.30140.579842.06599.103190.6985
74.5273-0.7412-1.22032.3908-0.46262.4090.1046-0.592-0.02640.0799-0.06430.0011-0.07850.366-0.04030.17770.0232-0.10250.4476-0.04540.213726.1473-2.350778.8354
83.3399-1.53890.64132.4448-3.07225.14910.69070.66720.6599-0.6861-0.47660.00660.15150.552-0.2140.7631-0.0106-0.10910.6382-0.03710.5396-0.66056.504364.7545
94.5969-1.63090.85291.0806-0.98654.36930.08550.72090.1426-0.22830.23960.1757-0.1259-0.4418-0.3250.1827-0.169-0.09870.62860.11660.53983.8847-2.8644-1.1262
102.2176-3.68862.77047.0317-2.383411.66160.26640.49380.1074-0.6537-0.3362-0.0481-0.19430.95890.06980.1002-0.0839-0.09120.61970.14480.54836.82321.7834-1.1894
115.79090.3050.39270.35270.29780.57040.01580.409-0.2838-0.02230.04820.03160.1705-0.0638-0.0640.1151-0.0675-0.03920.07090.01870.272724.1691-5.982813.762
125.2264-9.884.430223.7409-8.18217.43210.01510.21820.79230.7407-0.5949-0.1393-0.8913-0.54140.57990.41880.03330.19030.31940.07480.517147.357811.01127.3362
135.21310.51950.28092.4574-0.04641.70930.0365-0.35-0.12550.28750.17320.42050.2748-0.1523-0.20970.35410.04230.09580.67650.04670.5428-15.87853.742892.0708
142.3904-1.6119-3.48948.7434-7.926819.1397-0.3687-0.2578-0.31330.1176-0.21530.22780.84020.51310.5840.241-0.0975-0.01260.94620.1190.6595-13.3171-1.78593.1548
153.80370.11810.42690.934-0.17982.14310.0045-0.41610.42290.10430.11830.0629-0.1047-0.0919-0.12280.17390.0824-0.00440.3258-0.03660.40611.81097.173478.5541
167.085610.3278-0.328215.8902-0.35330.4073-0.4220.4349-0.76350.16430.7482-0.88120.4498-0.0289-0.32620.92130.1717-0.07760.6754-0.04170.481327.6594-10.018863.5562
176.21081.78680.15211.4268-0.08080.0840.0416-0.3961-0.42240.0452-0.0789-0.18430.10060.04370.03730.20310.0783-0.00870.09760.06720.217472.999-0.741331.8595
183.12121.8182-0.30772.39390.59241.42270.1402-0.29890.0113-0.0742-0.1870.1438-0.0781-0.13040.04670.0936-0.0171-0.08650.13630.10910.220475.34198.364834.1703
192.72620.5272-0.02361.2011-0.26094.66340.05960.2405-0.1445-0.0829-0.0074-0.1119-0.0099-0.0858-0.05220.02480.0054-0.06290.02760.01580.315889.729316.696121.6604
202.91680.25990.04633.05960.29713.59930.2076-0.29020.07980.1273-0.0301-0.282-0.38040.2215-0.17760.0685-0.0482-0.02190.05730.0220.269391.750123.145930.3484
214.48940.9736-2.2651.69090.58431.9644-0.7713-0.1055-0.87111.06510.07450.44631.34670.12310.69691.32650.04110.30940.44030.13581.1285-47.234-0.266959.7013
222.9906-0.51680.77230.1739-0.41012.66540.03980.0259-0.19250.12510.0615-0.0625-0.04780.1323-0.10140.3720.134-0.11770.40660.0150.5849-20.40083.28461.262
232.29420.2158-0.8724.4898-0.49853.82050.2454-0.6153-0.01380.4294-0.1821-0.0070.00920.3479-0.06340.0877-0.0769-0.07910.32370.01170.2961-36.224916.387362.1341
243.17320.14510.16494.087-0.24064.16410.2422-0.36070.21810.48280.01530.4031-0.3606-0.2782-0.25750.1423-0.00020.02450.2859-0.03750.3952-45.367925.057460.57
253.85481.551-0.75792.2669-0.02780.21750.0491-0.10231.05-0.2270.06060.6167-0.07580.0749-0.10970.1591-0.01820.02960.24620.00430.7465-13.81644.572828.8156
264.36791.643-1.4072.659-0.21952.90530.0304-0.1862-0.02880.0601-0.02450.01320.2569-0.0162-0.00590.0922-0.05860.05190.0961-0.0350.4585-1.2913-2.813829.8136
274.12181.05730.16663.40650.43691.99140.12150.17940.1076-0.0345-0.01750.06310.14750.1749-0.1040.02750.01670.05370.0398-0.01210.3582-18.0366-14.280427.3813
283.198-0.26750.13943.4901-0.1152.52430.2106-0.1113-0.24940.0721-0.130.14270.3276-0.2482-0.08060.0881-0.08470.03110.096-0.02250.4376-24.732-22.487731.0272
291.46630.7739-0.47740.81830.51541.6296-0.0320.08470.15520.14220.13220.01440.1830.3721-0.10020.705-0.0814-0.04281.3020.0860.826773.1482.275554.4218
303.5754-0.3376-0.65210.4397-0.42563.54860.0857-0.1670.0752-0.0538-0.0697-0.06170.06750.4502-0.0160.42830.0509-0.01860.5287-0.02370.339647.5526-2.332859.2702
313.57580.62631.05313.5285-0.33586.6464-0.015-0.4141-0.03780.0755-0.2111-0.06970.16520.6040.2260.29450.21180.05870.72380.0410.30760.3549-10.880657.4662
321.4783-0.6192-0.38031.7031-1.20081.4309-0.0879-0.3401-0.0329-0.1112-0.1377-0.26340.27640.5390.22550.62030.2420.03331.09390.12050.584871.0041-20.843763.7385
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 59
2X-RAY DIFFRACTION2A63 - 89
3X-RAY DIFFRACTION3A90 - 111
4X-RAY DIFFRACTION4A112 - 207
5X-RAY DIFFRACTION5C6 - 58
6X-RAY DIFFRACTION6C64 - 89
7X-RAY DIFFRACTION7C90 - 179
8X-RAY DIFFRACTION8C180 - 207
9X-RAY DIFFRACTION9B7 - 59
10X-RAY DIFFRACTION10B66 - 89
11X-RAY DIFFRACTION11B90 - 189
12X-RAY DIFFRACTION12B190 - 207
13X-RAY DIFFRACTION13D7 - 59
14X-RAY DIFFRACTION14D66 - 87
15X-RAY DIFFRACTION15D88 - 180
16X-RAY DIFFRACTION16D190 - 207
17X-RAY DIFFRACTION17E2 - 74
18X-RAY DIFFRACTION18E75 - 188
19X-RAY DIFFRACTION19E189 - 260
20X-RAY DIFFRACTION20E261 - 333
21X-RAY DIFFRACTION21G2 - 24
22X-RAY DIFFRACTION22G25 - 129
23X-RAY DIFFRACTION23G130 - 249
24X-RAY DIFFRACTION24G250 - 333
25X-RAY DIFFRACTION25F2 - 44
26X-RAY DIFFRACTION26F45 - 129
27X-RAY DIFFRACTION27F130 - 260
28X-RAY DIFFRACTION28F261 - 333
29X-RAY DIFFRACTION29H4 - 24
30X-RAY DIFFRACTION30H25 - 131
31X-RAY DIFFRACTION31H132 - 197
32X-RAY DIFFRACTION32H198 - 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://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