[English] 日本語
Yorodumi
- PDB-3tcp: Crystal structure of the catalytic domain of the proto-oncogene t... -

+
Open data


ID or keywords:

Loading...

-
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 / phagocytosis / positive regulation of 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 / phagocytosis / positive regulation of phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell migration / cell-cell signaling / retina development in camera-type eye / nervous system development / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface receptor signaling pathway / 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 ...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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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