[English] 日本語
Yorodumi
- PDB-4wnp: Structure of ULK1 bound to a potent inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wnp
TitleStructure of ULK1 bound to a potent inhibitor
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / autophagy / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


omegasome membrane / regulation of protein lipidation / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / nucleophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs ...omegasome membrane / regulation of protein lipidation / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / nucleophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / reticulophagy / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / response to starvation / autophagosome membrane / cellular response to nutrient levels / autophagosome assembly / autophagosome / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / Regulation of TNFR1 signaling / macroautophagy / peptidyl-threonine phosphorylation / protein localization / recycling endosome / small GTPase binding / autophagy / neuron projection development / GTPase binding / peptidyl-serine phosphorylation / mitochondrial outer membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / negative regulation of cell population proliferation / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / endoplasmic reticulum membrane / signal transduction / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, Ulk1/Ulk2 / : / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Serine/threonine-protein kinase, Ulk1/Ulk2 / : / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3RJ / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLazarus, M.B. / Novotny, C.J. / Shokat, K.M.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Structure of the Human Autophagy Initiating Kinase ULK1 in Complex with Potent Inhibitors.
Authors: Lazarus, M.B. / Novotny, C.J. / Shokat, K.M.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name / _struct_keywords.text
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK1
B: Serine/threonine-protein kinase ULK1
C: Serine/threonine-protein kinase ULK1
D: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,05110
Polymers129,2814
Non-polymers1,7706
Water4,378243
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9014
Polymers32,3201
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7172
Polymers32,3201
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7172
Polymers32,3201
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7172
Polymers32,3201
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.410, 113.800, 100.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein
Serine/threonine-protein kinase ULK1 / Autophagy-related protein 1 homolog / hATG1 / Unc-51-like kinase 1


Mass: 32320.262 Da / Num. of mol.: 4 / Fragment: UNP residues 1-283 / Mutation: E37A K38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Escherichia coli (E. coli)
References: UniProt: O75385, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-3RJ / N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine


Mass: 396.448 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H20N8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.55 M sodium malonate pH 7.0, 0.35 M sodium malonate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 1.88→46.02 Å / Num. obs: 94168 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.042 / Net I/σ(I): 10.4 / Num. measured all: 396367
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.88-1.984.30.801258064136150.5760.448100
5.95-46.024.10.03125.81317531830.9990.01699.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→46.018 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 4721 5.02 %Random Selection
Rwork0.1922 89404 --
obs0.1939 94125 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.46 Å2 / Biso mean: 43.4051 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 1.88→46.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8723 0 228 243 9194
Biso mean--39.18 35.78 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089188
X-RAY DIFFRACTIONf_angle_d1.04812406
X-RAY DIFFRACTIONf_chiral_restr0.0441345
X-RAY DIFFRACTIONf_plane_restr0.0041582
X-RAY DIFFRACTIONf_dihedral_angle_d15.8063476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.90140.34291630.291829783141100
1.9014-1.92370.31711630.278529243087100
1.9237-1.94720.30361640.272629263090100
1.9472-1.97180.33161520.258429893141100
1.9718-1.99780.27551230.251429723095100
1.9978-2.02520.28621650.249329383103100
2.0252-2.05410.28031660.23229373103100
2.0541-2.08480.27581570.231629393096100
2.0848-2.11730.24041270.213430023129100
2.1173-2.1520.25071510.215429303081100
2.152-2.18910.23531480.207430003148100
2.1891-2.2290.2681550.210929493104100
2.229-2.27180.24971570.211829523109100
2.2718-2.31820.22441720.206429303102100
2.3182-2.36860.2561630.203329693132100
2.3686-2.42370.24541460.207129603106100
2.4237-2.48430.2671360.204129903126100
2.4843-2.55150.25591550.193829683123100
2.5515-2.62650.24281500.20630013151100
2.6265-2.71130.2421670.207230013168100
2.7113-2.80820.24861680.211429373105100
2.8082-2.92060.25271470.202230103157100
2.9206-3.05350.22531500.187929763126100
3.0535-3.21450.23311930.187429633156100
3.2145-3.41580.23211550.194129893144100
3.4158-3.67940.21231610.183430273188100
3.6794-4.04950.20461780.163330053183100
4.0495-4.6350.18131580.14833002316099
4.635-5.83780.17011640.16493072323699
5.8378-46.03150.19411670.17883168333598
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)
12.0259-0.89130.77944.52711.62172.0343-0.0775-0.05850.32230.28360.06050.4874-0.5832-0.01240.03210.3840.00680.01830.29240.03610.298592.456850.126511.4297
22.94231.29172.73519.11322.29297.41730.0077-0.06070.17710.4552-0.01170.6244-0.0163-0.3037-0.00410.22310.01360.09230.21520.01820.204296.029347.55311.0579
31.6565-0.2085-0.44867.67242.45135.64870.0319-0.09140.3414-0.244-0.04180.0419-0.32960.08620.03580.1686-0.0074-0.00240.19810.01190.1662109.411550.99628.3347
40.3414-0.68320.61244.5533-3.65374.0291-0.0007-0.03720.09260.0611-0.07930.0307-0.06540.08840.08520.2211-0.00180.02920.16620.010.1432102.281246.322410.2201
52.97480.3452-2.98212.0213-0.77393.0828-0.0234-0.3756-0.30821.1960.1814-0.40660.06140.2418-0.16360.30960.0096-0.00170.23150.01760.1514107.226232.528330.5619
61.40891.0663-0.8864.0237-2.34112.6372-0.0223-0.0083-0.139-0.1281-0.1702-0.19740.31740.24540.23490.24070.02230.02820.16480.01750.1276115.644335.597815.012
73.4528-0.6741-4.20860.9811-0.99219.0114-0.6212-0.1837-0.94110.1568-0.0817-0.41261.22610.34110.54530.8864-0.03440.14920.4813-0.02430.507898.928224.441717.0481
84.89854.5615-1.38979.8541-7.83858.3177-0.05860.0649-0.3323-0.0304-0.0461-0.12320.515-0.06050.09430.17330.02010.08370.14230.00690.153109.000636.764512.9823
90.45060.57450.02694.3219-1.8552.4240.0155-0.00590.00150.2372-0.1075-0.1424-0.10810.25270.05730.14470.02040.00040.21520.04330.1498124.375246.070117.9185
107.20771.65864.96772.8777-0.11154.08960.7547-0.53510.38821.8523-0.74310.6127-0.3246-0.742-0.05810.47660.02030.12060.3204-0.04210.2592120.782540.478532.8828
118.64-1.85220.35899.48532.05678.9888-0.0343-0.40540.47461.18730.0322-0.4147-1.01960.55790.12460.5692-0.0722-0.04180.35760.01880.2706128.153449.65732.6388
120.85970.26070.44145.5193-0.91235.29510.01530.1433-0.0047-0.2886-0.038-0.31420.32770.4654-0.01540.22470.11460.04260.27020.06570.2462127.869631.383421.5747
130.14290.35780.3771.25820.5631.4046-0.07780.2612-0.0421-0.12460.1385-0.6065-0.19170.41090.01950.4723-0.00210.06030.77170.41311.6523162.130349.6554-7.8444
141.345-0.7853-0.10570.91120.62750.74050.13780.4430.2948-0.516-0.2795-0.7772-0.07920.469-0.01810.48990.18940.36380.78190.52381.1587154.298249.3871-12.386
150.5861.1246-0.58327.0881-1.41182.37850.18670.3980.6250.0811-0.07940.0118-0.2784-0.0877-0.13990.26210.09280.11920.36920.14470.5393142.724944.4359-3.6088
160.17651.0507-0.09336.2899-0.26681.3890.10520.20780.3255-0.16920.0979-0.2845-0.26030.0137-0.13720.38570.04110.10870.47540.37121.0626151.980653.9981-3.5726
171.1233-0.2485-0.16750.07460.0590.05110.0110.297-0.0079-0.2822-0.2386-0.27810.10940.01450.05170.48380.35240.32540.62410.24660.6281150.445237.5918-14.2132
180.740.9493-1.02121.9331-0.14423.30260.16750.21130.1732-0.16290.1046-0.2532-0.20770.1987-0.18641.0080.66350.21251.18530.06080.5831143.130426.6391-25.3846
191.7546-0.4791-0.64280.30470.41880.87310.25520.5188-0.0574-0.4853-0.4218-0.34730.4720.15570.17470.41190.20470.18970.40160.10730.3075138.412934.8486-10.8974
200.6904-0.0140.79221.4647-0.10561.1203-0.4407-0.0485-0.0903-0.45810.2663-0.69380.13660.39740.11380.81350.17620.14290.8935-0.27490.9663154.714223.9757-14.8857
210.9291-0.42950.0381.0979-0.37721.16780.35690.5190.0383-0.5748-0.3409-0.21720.14880.0777-0.06220.42510.17940.09350.47760.0920.2915131.003742.298-16.1088
221.00860.52510.16913.2934-0.20153.63790.00050.27210.2619-0.69080.1205-0.0193-0.68160.2061-0.02421.06960.282-0.01031.22840.10650.4162125.134643.9705-31.4363
230.30240.822-0.19482.2871-1.05244.9080.28520.1725-0.1414-1.2535-0.0492-0.14590.64820.1336-0.15060.93450.2225-0.13780.9054-0.25010.5213126.614624.6309-25.8498
242.0322-0.5192-1.67087.86590.20529.11480.1170.1469-0.1137-0.1425-0.490.49050.9303-0.40180.29750.50090.0631-0.01080.4558-0.0790.3504124.565930.5594-14.1015
252.78540.7224-0.81174.94830.6425.874-0.14760.1972-0.2302-0.83630.3335-0.43580.30860.5618-0.11050.74270.090.1610.58030.05530.498985.00947.5254-34.6663
262.0736-0.92710.62976.2354-1.02627.137-0.01390.49330.3695-0.67110.4065-0.8252-0.20360.6037-0.120.4195-0.0050.2610.42230.05470.605487.865710.7235-29.4009
271.2891-0.014-0.35147.739-0.15954.04560.3419-0.00780.24260.04650.2676-0.36980.17690.1231-0.46260.40790.05180.08740.25040.01850.480184.58595.4467-16.5844
280.4640.32340.36030.4040.02860.55620.25350.06130.3184-0.21890.204-0.0357-0.13890.06480.12620.36130.07120.3530.23360.01460.510985.872412.2545-22.6959
290.6911-0.208-0.75661.86031.01831.40170.0867-0.17570.0652-0.0287-0.0325-0.1814-0.17680.2165-0.14590.6766-0.2730.63670.4099-0.130.7731103.619129.1687-14.7662
300.0523-0.0580.0510.7383-0.11930.05640.31450.06460.49550.18350.13740.1086-0.596-0.0209-0.15750.46880.03820.64120.2505-0.09650.636388.809720.6443-9.4326
312.15041.51010.61011.59280.79651.92240.13450.20640.55360.8034-0.260.01220.5415-0.54990.08811.24970.29380.54420.73160.29171.045892.643633.3721-27.7564
321.22670.74530.16192.6209-1.77772.05510.46230.06860.4796-0.15120.0809-0.0709-0.63040.1627-0.23950.313-0.00750.23380.1993-00.444986.498912.0257-5.8667
330.86521.7568-0.64884.1672-1.80351.16060.4312-0.44720.15310.0943-0.0589-0.316-0.48680.9296-0.19420.4841-0.19220.21580.5047-0.21260.46598.916915.1735-2.4182
342.8293-1.2621.48526.6882.85.8057-0.57060.14230.0482-0.81420.5005-0.97630.4610.93910.11610.6046-0.13350.17341.0739-0.11780.5772109.13277.2573-1.8227
350.4349-0.0101-0.24012.06480.12010.14160.1459-0.54610.00980.42690.0705-0.335-0.21190.4702-0.06930.6902-0.31690.09250.7772-0.17030.5293106.742922.43943.2059
360.87350.00010.50011.3235-0.9191.22770.1528-0.31480.17210.7201-0.1680.5257-0.2809-0.19210.12490.7903-0.31640.41730.5796-0.31060.795293.638424.55183.7002
373.49771.6251-0.89966.2025-0.33743.81570.1364-0.443-0.20711.1126-0.13590.33281.205-0.3508-0.0090.862-0.1567-0.01830.37280.00970.3425167.63216.685635.1277
382.68580.2824-0.11494.28092.4365.1410.1618-0.432-0.13851.0216-0.04360.21230.2164-0.2838-0.09680.5277-0.07540.02870.29510.02590.2281165.50239.357930.1591
391.55930.6663-0.03238.323-0.84264.80050.12940.0426-0.1212-0.13880.14740.15740.4709-0.0592-0.24170.2009-0.0088-0.01650.2016-0.02470.1736168.40176.615417.1179
402.3327-0.96270.16412.0707-3.24926.0490.109-0.2015-0.34980.4717-0.03470.10980.1417-0.2621-0.11080.2943-0.07820.00370.26550.0060.2494172.65383.55124.7286
414.205-1.1181.81571.2746-0.7473.2695-0.0551-0.2849-0.10.52680.19810.2351-0.0727-0.7458-0.02750.40440.02890.13460.3973-0.01730.2508159.85419.409723.9821
421.6056-0.08890.45184.9914-0.81682.64670.165-0.30030.32550.3429-0.12220.6271-0.4982-0.7886-0.17320.44620.16230.20220.5141-0.15650.4191149.413628.331716.9823
431.0465-0.6142-0.3265.10391.41173.55740.0906-0.13570.2820.0362-0.04770.2557-0.305-0.2058-0.15920.14430.00670.07290.2083-0.02730.1952163.878120.103710.8472
441.07440.381-0.06252.8962.8993.09030.4276-0.4083-0.32191.3537-0.11711.0689-0.3251-0.728-0.24950.9490.01440.33060.94120.00050.7518160.488932.100227.8864
450.7646-0.86760.17863.52961.06232.06130.16260.0629-0.0255-0.0617-0.10670.2761-0.1162-0.3037-0.03220.13540.00320.06510.19310.00550.182159.794712.59574.4995
462.6428-1.15821.31295.44325.21977.45540.9434-0.17290.2541.3755-0.57791.36010.5461-1.7572-0.38950.4869-0.02910.18010.60350.04740.5813144.209416.78486.4227
470.76551.2487-0.82096.9497-2.92195.55630.1644-0.0956-0.0923-0.332-0.00281.15090.4437-0.6558-0.18530.3015-0.0387-0.03310.6137-0.05540.6375144.50549.479-2.2424
482.1590.03890.1815.194-0.04683.92930.07770.12110.1421-0.3928-0.0623-0.2059-0.3166-0.10420.03120.28040.11150.06010.26970.05070.2663155.972626.5755-0.5548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 8:24)A8 - 24
2X-RAY DIFFRACTION2(chain A and resid 25:49)A25 - 49
3X-RAY DIFFRACTION3(chain A and resid 50:75)A50 - 75
4X-RAY DIFFRACTION4(chain A and resid 76:103)A76 - 103
5X-RAY DIFFRACTION5(chain A and resid 104:108)A104 - 108
6X-RAY DIFFRACTION6(chain A and resid 109:147)A109 - 147
7X-RAY DIFFRACTION7(chain A and resid 148:157)A148 - 157
8X-RAY DIFFRACTION8(chain A and resid 158:166)A158 - 166
9X-RAY DIFFRACTION9(chain A and resid 167:217)A167 - 217
10X-RAY DIFFRACTION10(chain A and resid 218:223)A218 - 223
11X-RAY DIFFRACTION11(chain A and resid 224:237)A224 - 237
12X-RAY DIFFRACTION12(chain A and resid 238:280)A238 - 280
13X-RAY DIFFRACTION13(chain B and resid 8:19)B8 - 19
14X-RAY DIFFRACTION14(chain B and resid 20:59)B20 - 59
15X-RAY DIFFRACTION15(chain B and resid 60:77)B60 - 77
16X-RAY DIFFRACTION16(chain B and resid 78:89)B78 - 89
17X-RAY DIFFRACTION17(chain B and resid 90:103)B90 - 103
18X-RAY DIFFRACTION18(chain B and resid 104:112)B104 - 112
19X-RAY DIFFRACTION19(chain B and resid 113:150)B113 - 150
20X-RAY DIFFRACTION20(chain B and resid 151:157)B151 - 157
21X-RAY DIFFRACTION21(chain B and resid 158:220)B158 - 220
22X-RAY DIFFRACTION22(chain B and resid 221:237)B221 - 237
23X-RAY DIFFRACTION23(chain B and resid 238:251)B238 - 251
24X-RAY DIFFRACTION24(chain B and resid 252:280)B252 - 280
25X-RAY DIFFRACTION25(chain C and resid 8:20)C8 - 20
26X-RAY DIFFRACTION26(chain C and resid 21:48)C21 - 48
27X-RAY DIFFRACTION27(chain C and resid 49:73)C49 - 73
28X-RAY DIFFRACTION28(chain C and resid 74:103)C74 - 103
29X-RAY DIFFRACTION29(chain C and resid 104:113)C104 - 113
30X-RAY DIFFRACTION30(chain C and resid 114:147)C114 - 147
31X-RAY DIFFRACTION31(chain C and resid 148:156)C148 - 156
32X-RAY DIFFRACTION32(chain C and resid 157:182)C157 - 182
33X-RAY DIFFRACTION33(chain C and resid 183:221)C183 - 221
34X-RAY DIFFRACTION34(chain C and resid 222:231)C222 - 231
35X-RAY DIFFRACTION35(chain C and resid 232:251)C232 - 251
36X-RAY DIFFRACTION36(chain C and resid 252:279)C252 - 280
37X-RAY DIFFRACTION37(chain D and resid 8:21)D8 - 21
38X-RAY DIFFRACTION38(chain D and resid 22:49)D22 - 49
39X-RAY DIFFRACTION39(chain D and resid 50:76)D50 - 76
40X-RAY DIFFRACTION40(chain D and resid 77:91)D77 - 91
41X-RAY DIFFRACTION41(chain D and resid 92:103)D92 - 103
42X-RAY DIFFRACTION42(chain D and resid 104:113)D104 - 113
43X-RAY DIFFRACTION43(chain D and resid 114:147)D114 - 147
44X-RAY DIFFRACTION44(chain D and resid 148:158)D148 - 158
45X-RAY DIFFRACTION45(chain D and resid 159:217)D159 - 217
46X-RAY DIFFRACTION46(chain D and resid 218:223)D218 - 223
47X-RAY DIFFRACTION47(chain D and resid 224:239)D224 - 239
48X-RAY DIFFRACTION48(chain D and resid 240:280)D240 - 280

+
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