[English] 日本語
Yorodumi
- PDB-3tt0: Co-structure of Fibroblast Growth Factor Receptor 1 kinase domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tt0
TitleCo-structure of Fibroblast Growth Factor Receptor 1 kinase domain with 3-(2,6-dichloro-3,5-dimethoxy-phenyl)-1-{6-[4-(4-ethyl-piperazin-1-yl)-phenylamino]-pyrimidin-4-yl}-1-methyl-urea (BGJ398)
ComponentsBasic fibroblast growth factor receptor 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase domain / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / response to sodium phosphate / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / cellular response to fibroblast growth factor stimulus / outer ear morphogenesis / middle ear morphogenesis / skeletal system morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / positive regulation of endothelial cell chemotaxis / ureteric bud development / midbrain development / inner ear morphogenesis / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / regulation of cell differentiation / phosphatidylinositol-mediated signaling / PI3K Cascade / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / : / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / stem cell proliferation / Signal transduction by L1 / skeletal system development / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / positive regulation of MAP kinase activity / neuron migration / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / neuron projection development / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / in utero embryonic development / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / 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-07J / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBussiere, D.E. / Murray, J.M. / Shu, W.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Discovery of 3-(2,6-dichloro-3,5-dimethoxy-phenyl)-1-{6-[4-(4-ethyl-piperazin-1-yl)-phenylamino]-pyrimidin-4-yl}-1-methyl-urea (NVP-BGJ398), a potent and selective inhibitor of the fibroblast ...Title: Discovery of 3-(2,6-dichloro-3,5-dimethoxy-phenyl)-1-{6-[4-(4-ethyl-piperazin-1-yl)-phenylamino]-pyrimidin-4-yl}-1-methyl-urea (NVP-BGJ398), a potent and selective inhibitor of the fibroblast growth factor receptor family of receptor tyrosine kinase.
Authors: Guagnano, V. / Furet, P. / Spanka, C. / Bordas, V. / Le Douget, M. / Stamm, C. / Brueggen, J. / Jensen, M.R. / Schnell, C. / Schmid, H. / Wartmann, M. / Berghausen, J. / Drueckes, P. / ...Authors: Guagnano, V. / Furet, P. / Spanka, C. / Bordas, V. / Le Douget, M. / Stamm, C. / Brueggen, J. / Jensen, M.R. / Schnell, C. / Schmid, H. / Wartmann, M. / Berghausen, J. / Drueckes, P. / Zimmerlin, A. / Bussiere, D. / Murray, J. / Graus Porta, D.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Basic fibroblast growth factor receptor 1
B: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,37811
Polymers88,5962
Non-polymers1,7819
Water7,440413
1
A: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1475
Polymers44,2981
Non-polymers8494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic fibroblast growth factor receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2316
Polymers44,2981
Non-polymers9335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.110, 50.600, 66.900
Angle α, β, γ (deg.)90.00, 107.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21A-371-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain B and not (resid 461:466 or resid 470 or...
211(chain A and not (resid 461:466 or resid 470 or...

-
Components

#1: Protein Basic fibroblast growth factor receptor 1 / FGFR-1 / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 / Proto-oncogene c-Fgr


Mass: 44298.145 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 456-769 / Mutation: C584S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, FGFBR, FLG, FLT2 / Cell line (production host): TN5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P11362, receptor protein-tyrosine kinase
#2: Chemical ChemComp-07J / 3-(2,6-dichloro-3,5-dimethoxyphenyl)-1-(6-{[4-(4-ethylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)-1-methylurea / BGJ398


Mass: 560.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H31Cl2N7O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALLIZED FROM RESERVOIR CONTAINING 18-28% (V:V) PEG-MME 5000, 0.2 M AMSO4, AND 0.1 M SODIUM CACODYLATE , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. all: 16744 / Num. obs: 16610 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2382 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25.86 Å / SU ML: 0.42 / σ(F): 0 / σ(I): 0 / Phase error: 25.48 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 976 5.89 %5.89% of data was selected for cross-validation set
Rwork0.2041 ---
all0.2074 16751 --
obs0.2074 16572 98.93 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.348 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8038 Å2-0 Å2-6.4821 Å2
2--9.7907 Å2-0 Å2
3----10.9727 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 114 413 5036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074740
X-RAY DIFFRACTIONf_angle_d1.1276430
X-RAY DIFFRACTIONf_dihedral_angle_d15.5551769
X-RAY DIFFRACTIONf_chiral_restr0.069699
X-RAY DIFFRACTIONf_plane_restr0.004841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1227X-RAY DIFFRACTIONPOSITIONAL
12A1227X-RAY DIFFRACTIONPOSITIONAL0.124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8001-2.94750.36021540.29472177217799
2.9475-3.13190.30111380.2552198219899
3.1319-3.37320.30961250.21672239223999
3.3732-3.71180.26021320.19262202220299
3.7118-4.24690.22341510.1792225222599
4.2469-5.34290.20441350.165922602260100
5.3429-25.86140.25061410.20482295229598
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)
10.4306-0.4577-0.11260.21470.10.2646-0.19181.2327-1.347-0.0130.7195-0.50.8144-0.104700.38630.06980.00910.46680.00670.5401-5.00596.043119.1065
20.00470.0142-0.0004-0.00820.00770.00670.21750.04280.52640.1732-0.03-0.3469-0.35580.0974-00.4737-0.23340.01770.92860.01140.4425-3.383820.64527.6649
30.42870.04290.16140.23990.0240.4071-0.11390.0485-0.2071-0.41440.47580.31070.54510.582600.43330.03470.0530.4622-0.02390.3991-5.63674.661510.8487
40.59080.5173-0.71551.43080.27851.2625-0.27990.2079-0.27630.30310.18610.1489-0.06960.156500.2894-0.01750.01270.150.04590.0884-16.932213.800712.2146
50.4659-0.62610.02711.83060.35850.99210.0715-0.05380.11150.0875-0.01680.3119-0.0084-0.088900.2287-0.0747-0.00150.29460.04490.2236-22.990818.87465.5247
6-0.03390.01770.0221-0.04210.1072-0.0547-0.0767-0.1262-0.03570.31290.15060.41680.2635-1.1739-00.638-0.0060.00010.7542-0.0090.5915-16.25391.0636-3.6352
70.125-0.3075-0.10970.31430.10780.1671-0.23620.3943-0.2039-0.01850.2175-0.09310.2901-0.3879-00.233-0.02890.04490.17290.03450.2873-22.432512.4507-7.6971
80.24640.04810.0441-0.0033-0.18930.14250.00430.7249-0.4697-0.4654-0.17190.2593-0.1619-0.2846-00.3264-0.10040.00440.64430.00670.3712-31.741410.5727-13.0043
90.0222-0.0649-0.11080.0194-0.08440.06430.18880.30860.6887-0.42640.57910.4204-1.0636-0.019500.16830.1361-0.04420.33350.32450.3022-25.078422.8081-12.7577
100.0257-0.030.1840.18480.07850.04310.2121-0.07320.8861-0.04170.00540.1993-1.1115-0.104600.3992-0.02790.07190.31610.15890.4035-23.662231.8108-1.6893
110.1029-0.585-0.25870.4883-0.44390.3860.26710.1563-0.6947-0.5879-0.07490.146-0.3508-0.6267-00.4719-0.0343-0.0610.45260.00270.5091-36.91933.147242.1747
12-0.00840.0068-0.0031-0.00650.0095-0.0010.07840.116-0.1467-0.29090.1171-0.1460.01990.1475-01.2427-0.1521-0.00780.480.0080.8042-30.718650.236642.0301
130.5084-0.09690.1810.44470.02280.278-0.0876-0.0063-0.0461-0.6972-0.1199-0.00190.7689-0.2821-00.1685-0.0557-0.00580.6093-0.07880.3048-39.120928.98335.706
140.240.5431-0.3360.69010.06780.6665-0.4129-0.47540.01440.27870.38320.2023-0.2944-0.6407-00.3382-0.0148-0.00420.2323-0.02220.2333-43.67840.808432.3636
150.89730.57180.08050.559-0.26280.87240.0301-0.04890.09470.20480.1137-0.0118-0.0479-0.319700.2916-0.0251-0.02220.22930.00990.3641-45.285544.055321.2703
160.00110.0190.00640.0541-0.00160.0015-0.07750.1022-0.35020.0526-0.06260.18290.2279-0.0147-0.00010.9099-0.06660.03960.56250.22830.7616-41.089330.815925.1842
170.38320.36410.23060.1473-0.01950.354-0.3351-0.0573-0.72430.42340.26620.45720.8757-0.2851-00.3541-0.0220.05610.2081-0.00970.4719-52.479634.673813.4786
180.15670.01870.02920.0249-0.10610.11710.24060.2411-0.6445-0.0576-0.15230.85530.151-0.2301-00.4535-0.04290.0440.43540.05510.6244-62.324634.3728.2739
190.18370.03130.12260.03440.0120.1166-0.10691.23390.3874-1.42330.34060.17490.09080.276900.31010.0318-0.02390.41560.06170.3525-51.121641.45074.168
200.14540.32160.10070.181-0.15320.0683-0.01030.20280.8983-0.8396-0.0201-0.4211-0.95930.2314-00.4643-0.0279-0.00980.44630.10480.3887-43.792551.26629.6067
21-0.00170.02810.00410.0617-0.00730.01360.0271-0.13230.3450.05890.24811.4518-0.0849-0.4248-00.3908-0.38690.05291.02780.10680.1049-47.823838.308733.5864
220.0012-0.00080.00240.01410.05550.0276-0.236-0.2742-0.38170.7530.05551.6090.2041-1.1126-0-0.3226-0.8872-2.362-0.791-1.4987-1.5818-17.33079.249212.6158
232.4275-4.3262-4.66367.71038.31198.96050.00290.0629-0.0342-0.0474-0.0007-0.01440.0939-0.00770.0081.21310.19930.2390.9850.13381.2814-28.84455.4118-0.9748
242.00021.99959.18062.0003-8.4794.37130.0023-0.06140.02140.0004-0.0335-0.25470.03410.1090.01671.1945-0.07450.49491.1791-0.09781.1548-36.1089.61971.2377
252.00041.99991.99999.08849.98882.00020.02670.1614-0.0051-0.0705-0.01540.12520.048-0.1088-0.00081.32580.05530.64281.2901-0.31331.6467-38.529255.057820.7507
262.0005-2.8525-0.1592.00051.30112.00030.00280.43720.0156-0.00330.0013-1.06180.568-0.9288-0.00161.53170.3802-0.26231.6601-0.21311.9678-40.087727.8515-7.357
272.00042.00062.00012.00071.99982.0002-0.8192-0.2051-1.4160.3404-0.07480.60490.54210.25050.90311.0134-0.05070.46380.48330.09311.3745-54.450355.608229.3447
281.99982.0003-1.97032.00011.99962.0005-0.1075-0.2846-0.1335-0.0454-0.46910.5813-0.0183-0.57580.59261.07-0.26590.0220.65060.39970.6958-33.192345.266617.2723
292.00091.99991.99912.00061.99962.00050.5022-1.0666-0.89861.1706-0.3851-0.3352.18990.7854-0.09850.67380.07840.11330.78290.00440.8591-65.627442.181620.1683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 461:498 )A461 - 498
2X-RAY DIFFRACTION2( CHAIN A AND RESID 499:507 )A499 - 507
3X-RAY DIFFRACTION3( CHAIN A AND RESID 508:537 )A508 - 537
4X-RAY DIFFRACTION4( CHAIN A AND RESID 538:581 )A538 - 581
5X-RAY DIFFRACTION5( CHAIN A AND RESID 582:641 )A582 - 641
6X-RAY DIFFRACTION6( CHAIN A AND RESID 642:661 )A642 - 661
7X-RAY DIFFRACTION7( CHAIN A AND RESID 662:701 )A662 - 701
8X-RAY DIFFRACTION8( CHAIN A AND RESID 702:725 )A702 - 725
9X-RAY DIFFRACTION9( CHAIN A AND RESID 726:745 )A726 - 745
10X-RAY DIFFRACTION10( CHAIN A AND RESID 746:765 )A746 - 765
11X-RAY DIFFRACTION11( CHAIN B AND RESID 461:498 )B461 - 498
12X-RAY DIFFRACTION12( CHAIN B AND RESID 499:507 )B499 - 507
13X-RAY DIFFRACTION13( CHAIN B AND RESID 508:537 )B508 - 537
14X-RAY DIFFRACTION14( CHAIN B AND RESID 538:577 )B538 - 577
15X-RAY DIFFRACTION15( CHAIN B AND RESID 594:641 )B594 - 641
16X-RAY DIFFRACTION16( CHAIN B AND RESID 642:645 )B642 - 645
17X-RAY DIFFRACTION17( CHAIN B AND RESID 663:701 )B663 - 701
18X-RAY DIFFRACTION18( CHAIN B AND RESID 702:725 )B702 - 725
19X-RAY DIFFRACTION19( CHAIN B AND RESID 726:745 )B726 - 745
20X-RAY DIFFRACTION20( CHAIN B AND RESID 746:763 )B746 - 763
21X-RAY DIFFRACTION23( CHAIN A AND RESID 790:790 )A790
22X-RAY DIFFRACTION24( CHAIN A AND RESID 2:2 )A2
23X-RAY DIFFRACTION25( CHAIN B AND RESID 3:3 )B3
24X-RAY DIFFRACTION26( CHAIN A AND RESID 4:4 )A4
25X-RAY DIFFRACTION27( CHAIN B AND RESID 790:790 )B790
26X-RAY DIFFRACTION28( CHAIN B AND RESID 2:2 )B2
27X-RAY DIFFRACTION29( CHAIN B AND RESID 791:791 )B791

+
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://pdbjlvh1.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