[English] 日本語
Yorodumi
- PDB-4yr8: Crystal structure of JNK in complex with a regulator protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yr8
TitleCrystal structure of JNK in complex with a regulator protein
Components
  • Dual specificity protein phosphatase 16
  • Mitogen-activated protein kinase 8
KeywordsTRANSFERASE/HYDROLASE / kinase domain / catalytic domain / TRANSFERASE-HYDROLASE complex
Function / homology
Function and homology information


protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / MAP kinase tyrosine/serine/threonine phosphatase activity / Suppression of autophagy / protein carrier chaperone ...protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / MAP kinase tyrosine/serine/threonine phosphatase activity / Suppression of autophagy / protein carrier chaperone / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria / WNT5:FZD7-mediated leishmania damping / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / positive regulation of cyclase activity / mitogen-activated protein kinase binding / histone deacetylase regulator activity / dephosphorylation / mitogen-activated protein kinase p38 binding / NRAGE signals death through JNK / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of NLRP3 inflammasome complex assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / phosphatase activity / positive regulation of protein metabolic process / phosphoprotein phosphatase activity / JUN kinase activity / mitogen-activated protein kinase / regulation of macroautophagy / negative regulation of MAPK cascade / response to UV / response to mechanical stimulus / stress-activated MAPK cascade / energy homeostasis / JNK cascade / protein serine/threonine kinase binding / negative regulation of protein binding / peptidyl-threonine phosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to reactive oxygen species / FCERI mediated MAPK activation / regulation of circadian rhythm / histone deacetylase binding / cellular response to mechanical stimulus / Negative regulation of MAPK pathway / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptidyl-serine phosphorylation / regulation of protein localization / cellular response to lipopolysaccharide / cellular response to oxidative stress / cytoplasmic vesicle / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / protein phosphorylation / positive regulation of apoptotic process / axon / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / negative regulation of apoptotic process / enzyme binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Mitogen-activated protein (MAP) kinase, JNK / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. ...Mitogen-activated protein (MAP) kinase phosphatase / Mitogen-activated protein (MAP) kinase, JNK / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase 8 / Dual specificity protein phosphatase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, X. / Wang, J. / Wu, J.W. / Wang, Z.X.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology2013CB530600 China
Ministry of Science and Technology2011CB910800 China
National Natural Science Foundation of China31270848 China
National Natural Science Foundation of China31130062 China
CitationJournal: Nat Commun / Year: 2016
Title: A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation.
Authors: Liu, X. / Zhang, C.S. / Lu, C. / Lin, S.C. / Wu, J.W. / Wang, Z.X.
History
DepositionMar 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Mitogen-activated protein kinase 8
G: Dual specificity protein phosphatase 16
A: Mitogen-activated protein kinase 8
B: Dual specificity protein phosphatase 16
C: Mitogen-activated protein kinase 8
D: Dual specificity protein phosphatase 16
F: Mitogen-activated protein kinase 8
H: Dual specificity protein phosphatase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,13912
Polymers246,9978
Non-polymers1424
Water6,413356
1
E: Mitogen-activated protein kinase 8
G: Dual specificity protein phosphatase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7853
Polymers61,7492
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-18 kcal/mol
Surface area21640 Å2
MethodPISA
2
A: Mitogen-activated protein kinase 8
B: Dual specificity protein phosphatase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7853
Polymers61,7492
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-18 kcal/mol
Surface area21620 Å2
MethodPISA
3
C: Mitogen-activated protein kinase 8
D: Dual specificity protein phosphatase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7853
Polymers61,7492
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-19 kcal/mol
Surface area21790 Å2
MethodPISA
4
F: Mitogen-activated protein kinase 8
H: Dual specificity protein phosphatase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7853
Polymers61,7492
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-19 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.151, 74.850, 134.810
Angle α, β, γ (deg.)76.94, 84.32, 67.44
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Mitogen-activated protein kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase ...MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 42830.461 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / Plasmid: PET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45983, mitogen-activated protein kinase
#2: Protein
Dual specificity protein phosphatase 16 / Mitogen-activated protein kinase phosphatase 7 / MKP-7


Mass: 18918.904 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 156-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP16, KIAA1700, MKP7 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BY84, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF THE CHAINS A,C,E,F WAS BASED ON ISOFORM 4 OF DATABASE P45983

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, pH 7.0, 14% PEG 3350, 0.2M MgCl2, 6% 1,6-Hexanediol, 0.005M EDTA

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 78865 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.04 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

-
Processing

SoftwareName: PHENIX / Version: 1.8.4_1496 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UKH, 1ZZW

1ukh

1zzw


Resolution: 2.4→38.02 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 3405 5.09 %
Rwork0.217 --
obs0.218 66889 83.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14615 0 4 356 14975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514948
X-RAY DIFFRACTIONf_angle_d1.56420185
X-RAY DIFFRACTIONf_dihedral_angle_d16.725675
X-RAY DIFFRACTIONf_chiral_restr0.1162240
X-RAY DIFFRACTIONf_plane_restr0.0082566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4012-2.43550.311890.2151181X-RAY DIFFRACTION6
2.4355-2.47190.269220.2223399X-RAY DIFFRACTION13
2.4719-2.51050.2844440.2699932X-RAY DIFFRACTION29
2.5105-2.55170.2774660.26961563X-RAY DIFFRACTION49
2.5517-2.59570.31841310.29172262X-RAY DIFFRACTION72
2.5957-2.64280.2951410.28362508X-RAY DIFFRACTION80
2.6428-2.69370.28161250.2712746X-RAY DIFFRACTION87
2.6937-2.74860.2931410.2692881X-RAY DIFFRACTION91
2.7486-2.80840.31151640.2833049X-RAY DIFFRACTION96
2.8084-2.87370.25661600.26893144X-RAY DIFFRACTION98
2.8737-2.94550.31781730.27453105X-RAY DIFFRACTION99
2.9455-3.02510.26441530.25783167X-RAY DIFFRACTION100
3.0251-3.11410.2751730.25533138X-RAY DIFFRACTION100
3.1141-3.21460.28031810.24083163X-RAY DIFFRACTION100
3.2146-3.32940.27591610.23543102X-RAY DIFFRACTION100
3.3294-3.46260.25041590.22453185X-RAY DIFFRACTION100
3.4626-3.62010.22011780.19783139X-RAY DIFFRACTION100
3.6201-3.81080.20991850.18883114X-RAY DIFFRACTION99
3.8108-4.04930.211710.18353117X-RAY DIFFRACTION99
4.0493-4.36150.19951530.17563170X-RAY DIFFRACTION99
4.3615-4.79970.19021850.16863108X-RAY DIFFRACTION99
4.7997-5.49240.2251950.18733099X-RAY DIFFRACTION100
5.4924-6.91310.23671630.21493182X-RAY DIFFRACTION100
6.9131-38.02170.19671720.18943030X-RAY DIFFRACTION96
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)
16.02024.7003-1.95534.063-0.26075.0492-0.2063-0.1546-0.0976-0.0745-0.0123-0.71750.10410.18630.14930.35780.2148-0.00780.37410.00950.332-23.253452.264590.1022
22.84271.48791.01552.05910.61252.3177-0.20930.12610.0942-0.27070.1294-0.20810.2350.13110.03910.4650.1681-0.02930.3269-0.03540.3421-34.499750.295282.8564
30.88010.39731.38954.65620.43232.2236-0.07610.22910.3805-0.5590.1429-0.6471-0.14630.1541-0.1790.42420.1672-0.06840.3056-0.04570.3595-28.741950.101782.5422
41.07580.1576-0.14971.34320.74990.8804-0.2796-0.15370.0679-0.19380.0490.032-0.16370.07830.07860.38120.3213-0.07760.37960.03090.218-53.380945.067385.6406
51.35841.26070.63562.37041.26550.7803-0.23580.3160.0079-0.28510.3415-0.5453-0.14770.28190.05370.48510.1205-0.00920.3405-0.02040.254-48.2732.181776.5068
61.48570.57880.20461.45860.36370.6162-0.22620.02580.0794-0.16240.06730.2476-0.1761-0.17220.06950.40250.1896-0.05060.29460.00610.1439-58.901332.948580.7786
74.86040.08610.91712.1470.0612.7181-0.2133-0.0897-0.16110.359-0.0923-1.0493-0.08451.66510.2270.38050.0361-0.02911.00530.15540.6016-24.099614.232585.364
83.7822-0.90751.36952.4623-0.19381.9474-0.11930.4209-0.2431-0.2356-0.2146-0.97180.2321.73430.1180.35060.16190.09661.09620.08370.5166-27.13511.186472.7788
93.91752.2047-0.10082.6051-0.96611.939-0.07740.0858-0.4738-0.05870.0393-0.18850.35320.7060.07030.29070.11120.02510.3681-0.04580.2933-35.800610.717977.7333
103.9747-0.55961.3135.2948-0.35775.1807-0.0916-0.2688-0.7030.31280.13070.0170.38710.27430.10190.22490.09450.01450.2570.06020.2497-41.882310.100784.0837
114.5236-0.34340.2796.5676-0.55064.9154-0.00890.5915-0.8026-0.6511-0.0260.09150.60380.410.07620.33570.0590.00220.3194-0.06760.2299-45.15018.5171.4721
122.9025-1.3388-0.59281.88510.22030.56610.0198-0.24-0.16140.14290.0949-0.14450.08790.1288-0.0060.2701-0.2195-0.00220.24420.03770.2604-51.9174-13.526840.2827
131.6406-0.8482-0.17261.91310.41260.946-0.0985-0.2674-0.07020.20450.08370.18250.1427-0.137-0.04550.2836-0.18950.06070.270.010.1798-69.51471.884645.109
143.56070.61920.29032.4524-1.28163.7661-0.15510.45030.208-0.34570.1671-0.75390.24871.51020.14770.3033-0.04380.04560.7524-0.010.376-37.183621.949440.0633
154.94410.6617-0.11761.30610.02561.5255-0.0878-0.1589-0.17090.0204-0.2392-0.9398-0.02421.53990.15980.3015-0.0105-0.0190.95070.04950.3709-33.670320.218451.8282
163.36250.4479-0.04422.69950.11382.8852-0.08620.04960.47650.27410.0475-0.3404-0.40440.79770.03140.2341-0.1143-0.0520.3256-0.03790.2558-45.971525.352850.3241
173.76640.3855-0.27574.955-0.57455.762-0.00560.40740.7183-0.43810.17710.2534-0.4382-0.0377-0.02120.1318-0.0516-0.01440.1980.06640.1839-55.189724.876440.5988
185.10140.75820.69837.7851-0.56896.65090.0118-0.520.85660.67810.06930.3837-0.7174-0.3199-0.03710.24280.00140.0320.2352-0.06020.243-58.258526.491453.2133
191.9266-0.5017-0.78311.58140.5293.83180.31460.5554-0.3815-0.3396-0.17480.070.62770.28360.06140.60050.0239-0.11410.4858-0.00240.4236-42.811827.05813.943
202.36920.1184-0.64071.7532-0.00592.08570.08410.176-0.0039-0.1979-0.05820.12550.0262-0.0154-0.03140.3238-0.1453-0.07670.15920.07140.2803-58.100637.9722.6825
215.9732-0.5487-1.84518.3273-1.33054.19780.4111.7201-0.614-0.41790.1491-0.0641.38990.3444-0.28810.71360.0998-0.26271.1693-0.00640.4827-49.048332.5078-10.3079
225.74812.03410.79826.02462.11563.51110.03640.103-0.5746-0.10180.19980.17580.9332-0.0909-0.20790.7013-0.1956-0.03410.2809-0.05890.286-71.97222.351319.1525
233.5078-0.04571.01333.9991.91454.68090.01230.6772-0.7924-0.60580.3758-0.52171.20970.6532-0.3921.18090.09130.0130.5799-0.22360.4575-64.7458-1.52129.0596
242.15020.73320.93412.95050.68563.0241-0.24030.6427-0.0302-1.15760.23690.69550.7172-0.1793-0.04690.8471-0.3179-0.16920.50960.04880.3682-76.998.13079.9298
256.07-1.2530.05646.25280.15775.4967-0.139-0.38020.10560.49590.23320.82640.4499-0.3548-0.03080.4355-0.15560.06320.2555-0.0380.247-74.829614.023626.5046
263.1078-0.01691.19375.43040.25424.8383-0.33440.19760.3816-0.53210.10490.9353-0.0479-0.51760.10570.413-0.1677-0.12360.32930.05830.3517-77.629119.929318.3365
273.12340.70821.04661.2451-0.18752.69730.3332-0.52310.45330.3788-0.3185-0.0447-0.41480.29210.04160.55230.04790.04410.4194-0.05120.3361-32.22095.9334116.8767
280.7110.4383-0.00440.92890.26030.58890.2718-0.0921-0.02270.242-0.1190.04010.1343-0.0090.07810.40940.36690.00490.20210.02450.2681-43.7124-3.5081104.8284
294.5419-1.0397-0.23272.29831.28346.55540.0303-0.0250.36450.14070.14660.0309-1.3727-0.0136-0.03970.79390.175-0.00060.3438-0.01040.1051-58.70832.6856105.8307
301.51950.99290.18090.71270.12690.02280.1646-0.61240.45730.19690.0944-0.0204-0.42010.431-0.23491.1231-0.0066-0.110.5503-0.20340.3692-51.7636.5734115.8968
311.6371-0.4372-1.21982.00870.44132.795-0.1139-0.51750.17540.75540.21020.2404-0.5896-0.093-0.04371.12040.43730.25540.5739-0.06190.2471-63.89827.9808117.2488
322.44491.23772.68292.43031.24594.12710.2067-0.08360.09210.0427-0.13860.4307-0.0769-0.2616-0.1390.4880.2420.0480.3849-0.00990.2496-62.077722.8227108.9192
336.26751.1967-0.3966.2726-0.34065.1924-0.20390.51250.0227-0.57440.14530.6262-0.2993-0.3690.04170.51810.1351-0.06630.28590.01110.1974-62.040421.376998.4282
344.4388-0.2053-0.76095.2585-0.02614.5805-0.3034-0.1821-0.41530.31720.17030.89810.0796-0.50430.15010.42020.20710.09740.31690.05610.316-64.716915.0261106.4843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'E' AND (RESID 7 THROUGH 23 )
2X-RAY DIFFRACTION2CHAIN 'E' AND (RESID 24 THROUGH 92 )
3X-RAY DIFFRACTION3CHAIN 'E' AND (RESID 93 THROUGH 114 )
4X-RAY DIFFRACTION4CHAIN 'E' AND (RESID 115 THROUGH 167 )
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 168 THROUGH 203 )
6X-RAY DIFFRACTION6CHAIN 'E' AND (RESID 204 THROUGH 362 )
7X-RAY DIFFRACTION7CHAIN 'G' AND (RESID 158 THROUGH 183 )
8X-RAY DIFFRACTION8CHAIN 'G' AND (RESID 184 THROUGH 243 )
9X-RAY DIFFRACTION9CHAIN 'G' AND (RESID 244 THROUGH 262 )
10X-RAY DIFFRACTION10CHAIN 'G' AND (RESID 263 THROUGH 284 )
11X-RAY DIFFRACTION11CHAIN 'G' AND (RESID 285 THROUGH 298 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 8 THROUGH 167 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 168 THROUGH 362 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 158 THROUGH 190 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 191 THROUGH 208 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 209 THROUGH 262 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 263 THROUGH 284 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 285 THROUGH 298 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 10 THROUGH 167 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 168 THROUGH 330 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 331 THROUGH 362 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 158 THROUGH 169 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 170 THROUGH 182 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 183 THROUGH 263 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 264 THROUGH 277 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 278 THROUGH 299 )
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 10 THROUGH 220 )
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 221 THROUGH 362 )
29X-RAY DIFFRACTION29CHAIN 'H' AND (RESID 158 THROUGH 169 )
30X-RAY DIFFRACTION30CHAIN 'H' AND (RESID 170 THROUGH 182 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 183 THROUGH 243 )
32X-RAY DIFFRACTION32CHAIN 'H' AND (RESID 244 THROUGH 262 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 263 THROUGH 277 )
34X-RAY DIFFRACTION34CHAIN 'H' AND (RESID 278 THROUGH 300 )

+
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