[English] 日本語
Yorodumi
- PDB-4tuy: Tubulin-Rhizoxin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tuy
TitleTubulin-Rhizoxin complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / CYTOSKELETON / TUBULIN FOLD / RHIZOXIN
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / ATP-grasp fold, A domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Dna Ligase; domain 1 / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-36L / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsProta, A.E. / Bargsten, K. / Diaz, J.F. / Marsh, M. / Cuevas, C. / Liniger, M. / Neuhaus, C. / Andreu, J.M. / Altmann, K.H. / Steinmetz, M.O.
Funding support Switzerland, Spain, 5items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
Ministero de Economia y CompetitividadBIO2010-16351 Spain
Ministero de Economia y CompetitividadBFU2011-23416 Spain
Comunidad Autonoma de MadridS201/BMD-2457 Spain
Comunidad Autonoma de MadridS2010/BMD-2353 Spain
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A new tubulin-binding site and pharmacophore for microtubule-destabilizing anticancer drugs.
Authors: Prota, A.E. / Bargsten, K. / Diaz, J.F. / Marsh, M. / Cuevas, C. / Liniger, M. / Neuhaus, C. / Andreu, J.M. / Altmann, K.H. / Steinmetz, M.O.
History
DepositionJun 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 20, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,07620
Polymers261,6316
Non-polymers3,44514
Water21,4201189
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22400 Å2
ΔGint-141 kcal/mol
Surface area79720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.310, 156.920, 181.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain / Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: STATHMIN-LIKE DOMAIN, Residues 49-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein Tubulin-Tyrosine Ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 1203 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-36L / (1R,2R,3E,5R,7R,8S,10S,13E,16R)-8-hydroxy-10-[(2S,3R,4E,6E,8E)-3-methoxy-4,8-dimethyl-9-(2-methyl-1,3-oxazol-4-yl)nona-4,6,8-trien-2-yl]-2,7-dimethyl-6,11,19-trioxatricyclo[14.3.1.0~5,7~]icosa-3,13-diene-12,18-dione / Rhizoxin


Mass: 609.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H47NO8
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→68.4 Å / Num. obs: 173215 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 16.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 1.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4I4T

4i4t


Resolution: 2.1→62.7 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 8659 5 %
Rwork0.184 --
obs0.186 173178 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→62.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 214 1189 18659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218026
X-RAY DIFFRACTIONf_angle_d0.65824500
X-RAY DIFFRACTIONf_dihedral_angle_d12.5316744
X-RAY DIFFRACTIONf_chiral_restr0.0262689
X-RAY DIFFRACTIONf_plane_restr0.0033172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.34042870.3135448X-RAY DIFFRACTION100
2.1239-2.14890.29872830.29995381X-RAY DIFFRACTION100
2.1489-2.17510.31892890.29595496X-RAY DIFFRACTION100
2.1751-2.20260.29172830.28265383X-RAY DIFFRACTION100
2.2026-2.23160.31062870.27185459X-RAY DIFFRACTION100
2.2316-2.26220.29892850.26895415X-RAY DIFFRACTION100
2.2622-2.29450.27642860.25675424X-RAY DIFFRACTION100
2.2945-2.32870.2892870.25465460X-RAY DIFFRACTION100
2.3287-2.36510.31072850.24945408X-RAY DIFFRACTION100
2.3651-2.40390.28582870.24145464X-RAY DIFFRACTION100
2.4039-2.44530.27472890.22665478X-RAY DIFFRACTION100
2.4453-2.48980.23842870.21945452X-RAY DIFFRACTION100
2.4898-2.53770.27382850.21155423X-RAY DIFFRACTION100
2.5377-2.58950.22812860.20195435X-RAY DIFFRACTION100
2.5895-2.64580.24582880.2035469X-RAY DIFFRACTION100
2.6458-2.70740.25342870.2075445X-RAY DIFFRACTION100
2.7074-2.77510.26792870.20545461X-RAY DIFFRACTION100
2.7751-2.85010.24672880.19575475X-RAY DIFFRACTION100
2.8501-2.9340.23432880.19065466X-RAY DIFFRACTION100
2.934-3.02870.20842890.18235491X-RAY DIFFRACTION100
3.0287-3.13690.22112880.17625470X-RAY DIFFRACTION100
3.1369-3.26250.23362900.18435509X-RAY DIFFRACTION100
3.2625-3.4110.20632890.17835486X-RAY DIFFRACTION100
3.411-3.59080.19852900.16825514X-RAY DIFFRACTION100
3.5908-3.81570.17522890.15635497X-RAY DIFFRACTION100
3.8157-4.11030.18642910.14975521X-RAY DIFFRACTION100
4.1103-4.52380.16232930.13825576X-RAY DIFFRACTION100
4.5238-5.17820.17392930.13915556X-RAY DIFFRACTION100
5.1782-6.52280.19652970.17475652X-RAY DIFFRACTION100
6.5228-62.73020.19083060.16755805X-RAY DIFFRACTION99
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)
11.2116-0.1568-0.07973.01911.12182.10140.00050.1120.1792-0.43560.2899-0.3095-0.6680.4206-0.21750.5023-0.14040.11360.3943-0.12830.348131.680887.942351.895
20.999-0.337-0.10752.35611.13742.76270.03960.0355-0.00620.1876-0.00360.1558-0.155-0.0407-0.04540.3098-0.00090.04980.2512-0.0630.286319.205381.870265.8778
30.8089-0.25610.07763.5121.36141.94730.0003-0.08440.07660.4254-0.00570.1131-0.0926-0.01240.00070.4075-0.00240.07990.3369-0.05160.320518.743282.962373.4377
40.78340.056-0.13112.36871.70263.30570.0258-0.0204-0.1860.45650.358-0.37470.47640.7828-0.3730.32910.0833-0.06250.3407-0.12390.382732.641361.505860.5479
53.99220.0829-0.52150.66922.21287.76850.0048-0.30960.30790.2825-0.13650.1504-0.6870.10380.09371.38580.08920.10710.8491-0.08590.684124.260265.562784.7669
63.2721-0.8229-0.33743.13510.78952.92290.18110.2570.602-0.2458-0.09970.0608-0.7092-0.1651-0.06080.3940.03930.04270.3044-0.00310.413116.35469.959719.4068
71.9991-0.499-0.70713.17340.38761.80670.110.359-0.0148-0.30260.0588-0.2603-0.37250.3712-0.15260.3018-0.05940.02860.4861-0.07110.280429.072856.088614.5026
81.51990.7018-0.41182.93230.97152.21760.0312-0.1029-0.0639-0.02230.0586-0.201-0.09480.2275-0.07070.16810.0010.02760.3144-0.09610.291824.350852.921625.987
93.1786-1.10260.69510.6189-0.51480.4797-0.1678-0.4282-0.03440.0339-0.24410.65540.1388-0.82390.1630.2469-0.07230.05240.6722-0.29620.52845.28650.806428.0964
100.4317-0.5171-0.20491.46850.66021.73570.0068-0.0832-0.0091-0.0047-0.06970.2043-0.2792-0.35740.05510.28440.01370.02640.398-0.12280.405810.076961.731135.6185
112.1131-0.47110.70381.44050.25162.1295-0.1436-0.15950.03960.2343-0.10440.2331-0.0794-0.70170.19420.36070.03940.04720.553-0.1570.41116.510860.658844.7281
121.1554-1.068-0.20132.57172.07892.2764-0.0368-0.0461-0.11750.3154-0.04450.36590.4329-0.17140.10390.3155-0.03810.04280.3058-0.05140.30815.225541.970934.0359
130.5194-0.25690.15582.71571.99416.0755-0.0401-0.1256-0.12760.58480.0715-0.1150.67660.5925-0.02930.28350.0177-0.02740.2993-0.04550.31825.45738.02331.3487
140.9699-0.1594-0.04452.33150.15381.5363-0.03270.12670.1218-0.25790.0653-0.0841-0.10930.1022-0.02430.2173-0.04730.0320.2879-0.01760.242920.23732.6249-12.1009
150.8306-0.2509-0.08071.43390.82221.698-0.0090.00950.0630.0614-0.08960.11930.1004-0.19520.07630.1693-0.06060.02930.2389-0.02770.24717.690225.78083.1309
163.386-1.04160.60892.85040.2442.3629-0.05080.55310.1142-0.68020.03030.08320.0537-0.17360.03260.6525-0.09480.03220.6673-0.04620.324217.35789.3157-43.9826
170.8776-0.1153-0.21311.5560.50011.7415-0.08220.3841-0.1349-0.430.0737-0.16770.32780.0519-0.03350.5979-0.03430.0870.4973-0.14730.357320.9234-2.6494-33.5145
181.7544-0.5085-0.34371.21980.32691.8897-0.1510.2686-0.2067-0.12260.00910.20780.3561-0.19460.17930.4794-0.11210.03670.3813-0.10380.32728.7853-4.1757-21.2438
192.7314-0.8568-1.36181.64441.2942.0815-0.16470.0768-0.4459-0.0390.1234-0.27340.69430.3233-0.12070.80530.11030.1130.4287-0.15450.571230.131-16.7838-24.1616
201.6103-0.2331-0.12362.09330.20241.56390.0919-0.1240.05990.87690.2114-0.1357-0.00590.5867-0.27220.8162-0.0359-0.08170.5916-0.16050.515527.387792.164882.1177
210.16920.0552-0.15171.25811.47542.07-0.0384-0.0369-0.00150.42830.5389-0.56940.59970.7355-0.490.36940.09110.0250.6461-0.20160.567442.645129.0575.7594
221.72511.2233-0.97863.24230.21651.1155-0.51260.5277-0.5549-0.3740.1036-0.04711.1141-0.55190.21480.981-0.17860.16990.5199-0.14780.5576.252654.263769.873
230.9574-0.29770.10211.8877-0.64182.5878-0.182-0.9238-0.56740.6835-0.4175-0.94480.11151.56090.44280.77930.0574-0.1241.05270.30390.758614.845257.8816106.0501
242.17880.706-1.88311.3955-0.40431.681-0.4413-0.0571-0.67250.09720.1352-0.06550.879-0.0294-0.04070.8430.03370.1560.3430.05420.5688-1.188452.881793.8378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 1:180)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 181:311)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 312:401)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 402:436)
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 437:438)
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESSEQ 1:88)
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESSEQ 89:127)
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESSEQ 128:197)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 198:223)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESSEQ 224:295)
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESSEQ 296:373)
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESSEQ 374:401)
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESSEQ 402:438)
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESSEQ 1:197)
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESSEQ 198:440)
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESSEQ 1:88)
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESSEQ 89:295)
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESSEQ 296:401)
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESSEQ 402:441)
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESSEQ 6:46)
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESSEQ 47:140)
22X-RAY DIFFRACTION22CHAIN 'F' AND (RESSEQ 1:66)
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESSEQ 67:198)
24X-RAY DIFFRACTION24CHAIN 'F' AND (RESSEQ 199:362)

+
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