[English] 日本語
Yorodumi
- PDB-5m7g: Tubulin-MTD147 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m7g
TitleTubulin-MTD147 complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family ...Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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 / 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. / 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 / Dna Ligase; domain 1 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-FB7 / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.248 Å
AuthorsBohnacker, T. / Prota, A.E. / Steinmetz, M.O. / Wymann, M.P.
Funding support Switzerland, Spain, United Kingdom, 6items
OrganizationGrant numberCountry
Swiss Commission for Technology and Innovation (CTI)14032.1 ; 15811.2 ; 17241.1 Switzerland
Stiftung fuer Krebsbekaempfung341 Switzerland
Swiss National Science Foundation310030_153211 ; 316030_133860 ; 310030B_138659 ; 31003A_166608 Switzerland
Spanish Ministry of Economy and CompetitivenessBIO2013-42984-R Spain
Comunidad Autonoma de MadridS2010/BMD-2457 BIPEDD2 Spain
Medical Research Council (United Kingdom)U105184308 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Deconvolution of Buparlisib's mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention.
Authors: Bohnacker, T. / Prota, A.E. / Beaufils, F. / Burke, J.E. / Melone, A. / Inglis, A.J. / Rageot, D. / Sele, A.M. / Cmiljanovic, V. / Cmiljanovic, N. / Bargsten, K. / Aher, A. / Akhmanova, A. / ...Authors: Bohnacker, T. / Prota, A.E. / Beaufils, F. / Burke, J.E. / Melone, A. / Inglis, A.J. / Rageot, D. / Sele, A.M. / Cmiljanovic, V. / Cmiljanovic, N. / Bargsten, K. / Aher, A. / Akhmanova, A. / Diaz, J.F. / Fabbro, D. / Zvelebil, M. / Williams, R.L. / Steinmetz, M.O. / Wymann, M.P.
History
DepositionOct 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry

-
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)265,58926
Polymers261,6316
Non-polymers3,95820
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22860 Å2
ΔGint-177 kcal/mol
Surface area79560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.083, 156.864, 179.684
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


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / 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 (cattle) / Organ: Brain / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
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 , 9 types, 441 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.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-FB7 / 5-(2,6-dimorpholin-4-ylpyridin-4-yl)-4-(trifluoromethyl)pyridin-2-amine / MBT147


Mass: 409.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22F3N5O2
#10: 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
#11: 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
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 3% PEG 4000, 4-6% GLYCEROL, 30 MM MAGNESIUM CHLORIDE, 30 MM CALCIUM CHLORIDE, 100 MM MES/IMIDAZOLE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.248→46.723 Å / Num. obs: 138844 / % possible obs: 99.1 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.8
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.803 / Mean I/σ(I) obs: 1 / CC1/2: 0.335 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4I4T
Resolution: 2.248→46.723 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.74
RfactorNum. reflection% reflection
Rfree0.2168 6942 5 %
Rwork0.1723 --
obs0.1745 138844 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.248→46.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17116 0 243 421 17780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817731
X-RAY DIFFRACTIONf_angle_d0.9124036
X-RAY DIFFRACTIONf_dihedral_angle_d16.42310592
X-RAY DIFFRACTIONf_chiral_restr0.0522615
X-RAY DIFFRACTIONf_plane_restr0.0053099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2476-2.27310.35591990.34153782X-RAY DIFFRACTION86
2.2731-2.29990.35992310.30594378X-RAY DIFFRACTION100
2.2999-2.32790.33042290.29544358X-RAY DIFFRACTION99
2.3279-2.35740.32142290.28724351X-RAY DIFFRACTION99
2.3574-2.38840.30562300.27674362X-RAY DIFFRACTION99
2.3884-2.42110.28482270.26674321X-RAY DIFFRACTION99
2.4211-2.45570.31962320.26044403X-RAY DIFFRACTION100
2.4557-2.49230.30082280.26064339X-RAY DIFFRACTION99
2.4923-2.53130.31062330.24224419X-RAY DIFFRACTION99
2.5313-2.57280.24442280.22744342X-RAY DIFFRACTION99
2.5728-2.61710.292300.22774365X-RAY DIFFRACTION99
2.6171-2.66470.28642310.23074396X-RAY DIFFRACTION100
2.6647-2.7160.28682290.22424353X-RAY DIFFRACTION100
2.716-2.77140.25722330.20844417X-RAY DIFFRACTION99
2.7714-2.83170.24452300.19584367X-RAY DIFFRACTION99
2.8317-2.89750.26742330.18844423X-RAY DIFFRACTION100
2.8975-2.970.22132300.1844377X-RAY DIFFRACTION100
2.97-3.05030.23292330.17724428X-RAY DIFFRACTION100
3.0503-3.140.23372330.17754434X-RAY DIFFRACTION100
3.14-3.24130.2322310.18344389X-RAY DIFFRACTION100
3.2413-3.35710.22482340.17534436X-RAY DIFFRACTION100
3.3571-3.49150.23452320.1684414X-RAY DIFFRACTION100
3.4915-3.65040.22262330.16194433X-RAY DIFFRACTION100
3.6504-3.84270.1982360.154470X-RAY DIFFRACTION100
3.8427-4.08340.18272330.14114439X-RAY DIFFRACTION100
4.0834-4.39840.17222360.12964474X-RAY DIFFRACTION100
4.3984-4.84060.14952360.11864481X-RAY DIFFRACTION100
4.8406-5.54010.19542370.14434517X-RAY DIFFRACTION100
5.5401-6.97620.2032400.17014541X-RAY DIFFRACTION100
6.9762-46.73350.17822460.15284693X-RAY DIFFRACTION99
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)
11.5-0.4317-0.53724.65911.41373.07370.03390.070.2795-0.41360.2904-0.4694-0.72220.4414-0.28730.544-0.14560.10920.4936-0.16010.455931.494787.62951.7155
21.2694-0.3793-0.12883.36621.06183.17430.0883-0.01210.01430.3565-0.06980.325-0.1907-0.0954-0.02070.4511-0.00690.07990.3754-0.10360.45119.06981.711265.7864
31.075-0.89510.0255.77112.16252.9421-0.1143-0.24890.1120.97420.15910.1943-0.07090.0059-0.03870.5387-0.00940.15860.446-0.09060.459818.831982.559373.3761
42.2368-0.2385-0.81153.41012.75176.9367-0.0161-0.0442-0.19760.60110.3547-0.32070.39120.917-0.38290.45810.1096-0.06680.4256-0.13780.516332.84761.34260.546
56.0442-2.5622-1.31245.05631.52184.93590.23890.33850.6021-0.5244-0.23940.1599-0.935-0.33190.06340.4580.02630.00010.3750.00560.428615.934269.416219.2539
62.2406-0.6494-1.03887.32820.38882.92690.1530.44420.0964-0.4703-0.0958-0.3501-0.38850.2565-0.10320.3629-0.05860.04290.5965-0.06950.383129.034755.904114.5744
72.43432.21320.35447.52132.47094.0611-0.0127-0.16290.1316-0.00680.0762-0.1448-0.19630.1719-0.05430.23460.02490.03710.3832-0.12410.362224.483452.750626.1019
81.4825-1.23480.52951.9478-1.7942.2424-0.0584-0.5294-0.3477-0.0934-0.11670.55230.3226-1.23170.20190.4059-0.09360.09750.9093-0.32620.59745.435850.308228.2632
92.5574-1.22330.07012.24280.77923.288-0.0214-0.23740.15630.0365-0.12740.3372-0.2892-0.73970.10340.35790.00520.05750.5456-0.16590.491910.339661.49635.9341
103.9131-0.26191.08532.0557-1.5193.4769-0.3054-0.31660.11530.29630.18190.3715-0.2961-1.12230.1320.47440.04960.09770.7793-0.20010.5436.211659.860944.7689
111.6276-2.5643-2.83924.78465.87437.1495-0.1438-0.1842-0.00381.0082-0.1750.53210.8769-0.17260.34360.3317-0.09370.04240.4213-0.08620.396815.637741.457934.1338
122.3431-1.1956-1.42526.55035.18016.8258-0.0483-0.3685-0.22611.01610.2079-0.18811.1820.5276-0.19240.4082-0.0154-0.09260.42930.00280.416625.872537.52730.9066
131.3257-0.7832-0.16353.32910.21371.5657-0.0210.12790.1974-0.26770.1158-0.1613-0.23710.1303-0.09330.3005-0.08410.03570.3754-0.04450.32520.35332.721-12.0641
141.1266-0.46350.02491.70261.11161.7804-0.026-0.02180.05270.1152-0.06640.15960.0853-0.250.08890.2687-0.08120.04710.3189-0.04430.33048.035825.60753.069
156.1752-3.1683-1.00946.52231.42162.70240.20321.08040.164-0.8722-0.09350.0833-0.1308-0.2906-0.10910.6096-0.12420.05920.8012-0.02150.320717.42039.3913-44.3556
162.0488-0.1083-0.31931.74280.20942.6403-0.13680.4987-0.2283-0.36130.1937-0.21070.34140.0069-0.04630.5688-0.05540.07970.6315-0.21360.436221.3633-2.6856-33.9886
172.6032-0.1119-0.5891.7123-0.19423.6834-0.18590.4072-0.459-0.15720.21830.21440.3033-0.53620.00280.4575-0.10380.03730.4668-0.12970.44279.2569-4.2177-21.3502
184.6494-1.629-3.48643.44121.90095.4599-0.31780.0473-0.66050.2040.3059-0.43041.23690.7382-0.11660.7140.07550.0650.6039-0.29450.770530.6735-16.5463-24.2289
193.3709-2.45140.62936.98550.78840.5316-0.1375-0.2820.31131.57030.2328-0.5361-0.1530.3381-0.13981.1136-0.0982-0.00710.7064-0.25920.698627.406792.116181.8781
200.3932-0.2732-0.39680.12230.22340.7253-0.0739-0.0376-0.03740.2120.4748-0.43860.39160.6838-0.53890.46330.05380.03760.737-0.25180.691143.214127.67914.0333
213.92091.9104-1.06246.0210.89524.1875-0.60550.4392-0.9251-0.24780.121-0.13271.7447-0.27440.32631.0376-0.12710.25470.5479-0.14240.60486.267254.003869.7725
223.18290.222-0.14692.4386-0.6154.0884-0.2821-1.0294-0.86440.4089-0.3567-0.74350.54861.68590.58840.81590.26320.03021.22890.33540.815214.169856.904103.7718
233.16990.6481-2.24791.0533-0.3913.4007-0.5713-0.1415-0.86870.09620.1984-0.08131.277-0.05870.1360.95840.04340.18760.43470.08490.6896-2.22853.73792.8239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180)
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 311)
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 401)
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 436)
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 88)
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 127)
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 197)
8X-RAY DIFFRACTION8chain 'B' and (resid 198 through 223)
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 295)
10X-RAY DIFFRACTION10chain 'B' and (resid 296 through 373)
11X-RAY DIFFRACTION11chain 'B' and (resid 374 through 401)
12X-RAY DIFFRACTION12chain 'B' and (resid 402 through 438)
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 197)
14X-RAY DIFFRACTION14chain 'C' and (resid 198 through 440)
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 88)
16X-RAY DIFFRACTION16chain 'D' and (resid 89 through 295)
17X-RAY DIFFRACTION17chain 'D' and (resid 296 through 401)
18X-RAY DIFFRACTION18chain 'D' and (resid 402 through 441)
19X-RAY DIFFRACTION19chain 'E' and (resid 6 through 46)
20X-RAY DIFFRACTION20chain 'E' and (resid 47 through 143)
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 66)
22X-RAY DIFFRACTION22chain 'F' and (resid 67 through 198)
23X-RAY DIFFRACTION23chain 'F' and (resid 199 through 379)

+
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