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- PDB-3tcp: Crystal structure of the catalytic domain of the proto-oncogene t... -

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Basic information

Entry
Database: PDB / ID: 3tcp
TitleCrystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC569
ComponentsTyrosine-protein kinase Mer
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / tyrosine kinase / acute lymphoblastic leukemia / rational structure-based drug design / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / positive regulation of phagocytosis / phagocytosis ...negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / positive regulation of phagocytosis / phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / retina development in camera-type eye / cell-cell signaling / nervous system development / spermatogenesis / cell surface receptor signaling pathway / receptor complex / protein phosphorylation / extracellular space / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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-CKJ / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLiu, J. / Yang, C. / Simpson, C. / DeRyckere, D. / Van Deusen, A. / Miley, M. / Kireev, D.B. / Norris-Drouin, J. / Sather, S. / Hunter, D. ...Liu, J. / Yang, C. / Simpson, C. / DeRyckere, D. / Van Deusen, A. / Miley, M. / Kireev, D.B. / Norris-Drouin, J. / Sather, S. / Hunter, D. / Patel, H.S. / Janzen, W.P. / Machius, M. / Johnson, G. / Earp, H.S. / Graham, D.K. / Frye, S. / Wang, X.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: Discovery of Novel Small Molecule Mer Kinase Inhibitors for the Treatment of Pediatric Acute Lymphoblastic Leukemia.
Authors: Liu, J. / Yang, C. / Simpson, C. / Deryckere, D. / Van Deusen, A. / Miley, M.J. / Kireev, D. / Norris-Drouin, J. / Sather, S. / Hunter, D. / Korboukh, V.K. / Patel, H.S. / Janzen, W.P. / ...Authors: Liu, J. / Yang, C. / Simpson, C. / Deryckere, D. / Van Deusen, A. / Miley, M.J. / Kireev, D. / Norris-Drouin, J. / Sather, S. / Hunter, D. / Korboukh, V.K. / Patel, H.S. / Janzen, W.P. / Machius, M. / Johnson, G.L. / Earp, H.S. / Graham, D.K. / Frye, S.V. / Wang, X.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 1.2Sep 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase Mer
B: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,79810
Polymers71,7792
Non-polymers1,0208
Water64936
1
A: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4025
Polymers35,8891
Non-polymers5124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3975
Polymers35,8891
Non-polymers5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.158, 91.142, 68.356
Angle α, β, γ (deg.)90.00, 100.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase Mer / Proto-oncogene c-Mer / Receptor tyrosine kinase MerTK


Mass: 35889.434 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 570-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MERTK, MER / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3)pLysS
References: UniProt: Q12866, receptor protein-tyrosine kinase
#2: Chemical ChemComp-CKJ / 1-[(trans-4-aminocyclohexyl)methyl]-N-butyl-3-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-6-amine


Mass: 396.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29FN6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 288 K / pH: 8.5
Details: Protein: 32.5 mg/mL in 20 mM Tris pH 8.0, 500mM sodium chloride, 2mM beta-mercaptoethanol; incubated with inhibitor (2.5 mM final concentration) overnight; Mixed 1:1 with crystallization ...Details: Protein: 32.5 mg/mL in 20 mM Tris pH 8.0, 500mM sodium chloride, 2mM beta-mercaptoethanol; incubated with inhibitor (2.5 mM final concentration) overnight; Mixed 1:1 with crystallization solution (27-33% (v/v) Peg400, 200 mM magnesium chloride, 100 mM Tris pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.06205
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06205 Å / Relative weight: 1
ReflectionResolution: 2.69→29.02 Å / Num. obs: 16603 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.7
Reflection shellResolution: 2.69→2.72 Å / Redundancy: 2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 1.5 / % possible all: 59.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRB
Resolution: 2.69→29.02 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.87 / SU B: 35.667 / SU ML: 0.355 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 840 5.1 %RANDOM
Rwork0.225 ---
obs0.228 15728 95.9 %-
all-16603 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.62 Å2
Baniso -1Baniso -2Baniso -3
1-7.16 Å2-0 Å2-0.95 Å2
2---4.01 Å20 Å2
3----3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.69→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 64 36 4159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9995682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9835498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37123.799179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4961527
X-RAY DIFFRACTIONr_chiral_restr0.0670.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2351.52529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.44924089
X-RAY DIFFRACTIONr_scbond_it0.70831676
X-RAY DIFFRACTIONr_scangle_it1.1564.51593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 50 -
Rwork0.254 931 -
obs--78.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.9026-1.76223.01757.73740.412.07230.0323-0.23520.1099-0.0240.0771-0.53690.21370.2704-0.10940.38660.0689-0.05620.5081-0.05690.228913.0256-28.463820.3326
213.32243.48255.501914.79826.53811.5282-0.0991-0.574-0.6433-0.0625-0.0207-0.41580.68970.21070.11990.13670.01330.01060.21910.04250.10127.2084-31.260218.6273
32.7848-0.469-6.81716.298-2.30146.26350.8881-0.2990.4618-0.1387-0.42520.2556-1.03960.5239-0.46290.9214-0.0330.11921.05380.07860.683721.7544-18.979433.7127
415.89831.3928-0.71764.7855-5.05794.69440.1113-1.0347-0.42990.4824-0.3401-0.2287-0.5040.29780.22880.2088-0.02790.12430.5399-0.08230.58769.0857-25.758935.3906
520.2997-1.7868-7.17897.55831.55272.59410.0281-0.0361-2.0180.1034-0.6560.1258-0.0650.10860.62790.2511-0.00560.07430.4425-0.07630.23454.9379-27.030627.3728
61.721-4.1990.95029.5254-2.97252.4269-0.05060.0120.13870.1453-0.0947-0.3275-0.07890.31320.14530.1839-0.04880.04040.16960.01240.17810.6549-17.141517.9192
71.97170.3127-0.53842.9322-0.18454.7401-0.11610.36890.2347-0.46740.15260.3054-0.0979-0.5807-0.03650.1751-0.0351-0.00030.20030.04230.2057-12.4312-12.239821.6471
85.977-1.1341-0.81850.9611-1.151811.6623-0.0576-0.34640.09710.24260.0323-0.170.39160.36460.02520.18450.0216-0.00020.0530.00990.1638-1.5414-17.22229.7223
91.04232.90493.305415.81936.880910.47340.1437-0.0389-0.09690.5009-0.0918-1.34560.370.2221-0.05190.0734-0.00130.02510.28610.02090.20951.4667-8.757731.1189
105.4661-0.76968.849519.559-6.603310.1350.31540.6639-0.15010.517-0.5879-1.82830.33971.04810.27240.65520.03420.1990.6713-0.11670.60557.4771-4.992641.9546
113.3769-0.91122.42212.48832.84546.4505-0.24310.1239-0.02860.14840.15410.0998-0.07480.36680.0890.1893-0.017-0.020.08730.01320.1433-5.2807-5.832931.6656
123.8438-1.0615-0.16966.19772.51616.58220.0641-0.10090.73610.53990.0533-0.4923-0.75250.336-0.11740.2597-0.03410.02970.11290.03690.25470.71716.344130.1294
135.21640.87462.78968.5186-3.73175.3763-0.3527-0.08390.40090.13250.41240.5013-0.0137-0.7359-0.05970.11990.0141-0.00950.2440.02820.1328-12.99680.814332.0656
142.6713-1.1478-2.08461.0867-0.94474.9893-0.2076-0.1291-0.00020.20320.19510.02670.0192-0.21410.01250.3347-0.00160.11090.11310.0220.1053-11.9357-9.531939.6259
1539.32752.857124.949914.3338-4.468515.57990.8815-0.7038-0.1923-0.1052-0.59020.94290.5627-0.4678-0.29130.3476-0.1698-0.01410.7042-0.07180.499-25.1418-12.57226.4918
17-3.189217.6304-9.819728.3001-23.6449.4620.60190.3021-0.61851.484-1.0003-0.3965-1.45760.31090.39831.00130.33380.1041.8034-0.3030.451819.049535.75965.7392
189.3973-5.03412.95962.8213-0.62487.82780.0329-0.66110.00070.11850.3682-0.29890.24890.5697-0.40110.2681-0.0669-0.07630.33780.01260.381311.527627.987522.7079
195.5598-0.88681.44496.0609-2.79176.12590.0710.03330.5367-0.56750.29530.0403-0.53910.2606-0.36630.2273-0.08820.02280.21240.01460.17446.61834.480518.4242
2027.65673.92196.275511.90139.66855.5065-0.03010.508-0.85470.30230.659-0.85720.21260.5903-0.62890.5657-0.025-0.08680.69590.28670.349810.339927.03564.954
2129.078718.02241.735918.59265.56063.0264-1.0338-0.27931.5991-0.15620.86361.4430.06590.79660.17020.1896-0.01630.03180.3453-0.05130.26983.390326.99256.9877
2241.4794-0.357729.44090.772-0.387220.0953-1.50250.81341.76760.37380.1783-0.5306-1.11290.5721.32420.3258-0.0037-0.16390.65870.00250.512122.350230.268819.2677
230.73541.60640.92726.5664-0.96092.78120.04250.059-0.00650.06350.11790.18020.07230.1437-0.16040.08850.01740.07680.2187-0.03190.09431.34619.202217.2335
245.44162.48187.359212.436-3.149913.82930.1875-0.73150.66951.0341-0.44851.32880.0732-1.12650.2610.55270.03170.23430.49780.13880.3243-14.481710.094317.0875
257.31537.1154-6.88778.8424-9.707113.44720.01240.88520.44670.13050.59060.58450.0596-0.798-0.60290.1644-0.0438-0.00420.20810.01890.0625-5.707217.43032.4302
2627.336426.4843-5.359623.0631-6.45041.0234-0.08590.1099-0.12540.02-0.2369-0.4228-0.16740.29520.32280.5709-0.1320.01110.53990.16030.30667.386422.1479-4.2637
270.5436-1.63962.25720.4063-0.921727.22980.1311-0.30911.0657-0.03510.3421-1.1080.15681.4216-0.47320.0595-0.0889-0.03030.2451-0.38671.2515.19614.38917.6629
283.0786-2.552-3.55357.99223.45085.1931-0.1817-0.13260.22530.76950.1595-0.86870.10950.4290.02220.1204-0.0546-0.10870.24730.02010.2264.7911.8586.3467
290.37270.09361.10496.3654-1.29223.8532-0.04330.11210.0107-0.2499-0.2289-0.56920.20810.32440.27220.1878-0.0540.05070.11070.0240.1562.62865.58023.0857
3012.6305-0.83263.64572.9385-1.2157.0048-0.0159-0.1469-1.0091-0.00520.137-0.07640.32550.2952-0.12110.232-0.02460.07940.05080.00970.24151.0932-5.01632.7762
311.74660.944-0.34823.82670.48694.9295-0.03640.453-0.1373-0.39420.0330.23970.2382-0.41580.00340.1591-0.0529-0.03480.1896-0.01070.1177-5.64188.6828-5.7767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A577 - 603
2X-RAY DIFFRACTION2A604 - 621
3X-RAY DIFFRACTION3A622 - 631
4X-RAY DIFFRACTION4A632 - 644
5X-RAY DIFFRACTION5A645 - 665
6X-RAY DIFFRACTION6A666 - 686
7X-RAY DIFFRACTION7A687 - 713
8X-RAY DIFFRACTION8A714 - 735
9X-RAY DIFFRACTION9A736 - 771
10X-RAY DIFFRACTION10A772 - 778
11X-RAY DIFFRACTION11A779 - 795
12X-RAY DIFFRACTION12A796 - 817
13X-RAY DIFFRACTION13A818 - 838
14X-RAY DIFFRACTION14A839 - 857
15X-RAY DIFFRACTION15A858 - 863
16X-RAY DIFFRACTION17B576 - 581
17X-RAY DIFFRACTION18B582 - 605
18X-RAY DIFFRACTION19B606 - 620
19X-RAY DIFFRACTION20B621 - 647
20X-RAY DIFFRACTION21B648 - 652
21X-RAY DIFFRACTION22B653 - 665
22X-RAY DIFFRACTION23B666 - 686
23X-RAY DIFFRACTION24B687 - 698
24X-RAY DIFFRACTION25B699 - 713
25X-RAY DIFFRACTION26B714 - 719
26X-RAY DIFFRACTION27B720 - 731
27X-RAY DIFFRACTION28B732 - 773
28X-RAY DIFFRACTION29B774 - 803
29X-RAY DIFFRACTION30B804 - 827
30X-RAY DIFFRACTION31B828 - 861

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