[English] 日本語
Yorodumi
- PDB-6qtn: Tubulin-cyclostreptin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qtn
TitleTubulin-cyclostreptin complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine LigaseTubulin—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 / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / 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, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / 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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cyclostreptin / 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: 1.9 Å
AuthorsBalaguer, F.d.A. / Muehlethaler, T. / Estevez-Gallego, J. / Calvo, E. / Gimenez-Abian, J.F. / Risinger, A.L. / Sorensen, E.J. / Vanderwal, C.D. / Altmann, K.-H. / Mooberry, S.L. ...Balaguer, F.d.A. / Muehlethaler, T. / Estevez-Gallego, J. / Calvo, E. / Gimenez-Abian, J.F. / Risinger, A.L. / Sorensen, E.J. / Vanderwal, C.D. / Altmann, K.-H. / Mooberry, S.L. / Steinmetz, M.O. / Oliva, M.A. / Prota, A.E. / Diaz, J.F.
Funding support Spain, Switzerland, United States, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-75319-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-07900 Spain
Swiss National Science Foundation31003A_166608 Switzerland
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA121138 United States
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structure of the Cyclostreptin-Tubulin Adduct: Implications for Tubulin Activation by Taxane-Site Ligands.
Authors: Balaguer, F.A. / Muhlethaler, T. / Estevez-Gallego, J. / Calvo, E. / Gimenez-Abian, J.F. / Risinger, A.L. / Sorensen, E.J. / Vanderwal, C.D. / Altmann, K.H. / Mooberry, S.L. / Steinmetz, M.O. ...Authors: Balaguer, F.A. / Muhlethaler, T. / Estevez-Gallego, J. / Calvo, E. / Gimenez-Abian, J.F. / Risinger, A.L. / Sorensen, E.J. / Vanderwal, C.D. / Altmann, K.H. / Mooberry, S.L. / Steinmetz, M.O. / Oliva, M.A. / Prota, A.E. / Diaz, J.F.
History
DepositionFeb 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)265,67226
Polymers261,6316
Non-polymers4,04020
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23720 Å2
ΔGint-152 kcal/mol
Surface area80130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.585, 158.361, 179.946
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 / 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 , 10 types, 701 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-JHH / Cyclostreptin


Mass: 402.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34O5
#12: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#13: 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
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 6% glycerol, 3% PEG4000, 0.1 M Mes/0.1 M imidazole pH 6.7, 30 mM CaCl2, 30 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.7 Å / Num. obs: 234346 / % possible obs: 100 % / Redundancy: 26.8 % / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.025 / Rrim(I) all: 0.104 / Net I/σ(I): 22.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 27 % / Rmerge(I) obs: 4.485 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 17147 / CC1/2: 0.322 / Rpim(I) all: 0.843 / Rrim(I) all: 4.572 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT
Resolution: 1.9→49.655 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.29
RfactorNum. reflection% reflection
Rfree0.2133 11838 5.05 %
Rwork0.1866 --
obs0.188 234314 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17274 0 254 681 18209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418007
X-RAY DIFFRACTIONf_angle_d0.65224456
X-RAY DIFFRACTIONf_dihedral_angle_d15.49710787
X-RAY DIFFRACTIONf_chiral_restr0.0452662
X-RAY DIFFRACTIONf_plane_restr0.0043157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.40253920.38357284X-RAY DIFFRACTION100
1.9216-1.94420.41284270.39697354X-RAY DIFFRACTION100
1.9442-1.96790.3933620.37987347X-RAY DIFFRACTION100
1.9679-1.99280.32963830.33927341X-RAY DIFFRACTION100
1.9928-2.0190.34073750.30867403X-RAY DIFFRACTION100
2.019-2.04670.29643830.29667371X-RAY DIFFRACTION100
2.0467-2.07590.30323970.28587325X-RAY DIFFRACTION100
2.0759-2.10690.31053990.27537371X-RAY DIFFRACTION100
2.1069-2.13990.26473810.2537408X-RAY DIFFRACTION100
2.1399-2.17490.25233590.24077357X-RAY DIFFRACTION100
2.1749-2.21240.28683980.23957354X-RAY DIFFRACTION100
2.2124-2.25270.2614080.22887342X-RAY DIFFRACTION100
2.2527-2.2960.23584040.21487389X-RAY DIFFRACTION100
2.296-2.34290.25453860.2127386X-RAY DIFFRACTION100
2.3429-2.39380.22723840.20237393X-RAY DIFFRACTION100
2.3938-2.44950.22043970.19637365X-RAY DIFFRACTION100
2.4495-2.51070.2154150.19667383X-RAY DIFFRACTION100
2.5107-2.57860.22643990.19587368X-RAY DIFFRACTION100
2.5786-2.65450.2483980.20237409X-RAY DIFFRACTION100
2.6545-2.74020.24933940.20517402X-RAY DIFFRACTION100
2.7402-2.83810.26174130.20247404X-RAY DIFFRACTION100
2.8381-2.95170.23543870.20347424X-RAY DIFFRACTION100
2.9517-3.0860.23833920.19827450X-RAY DIFFRACTION100
3.086-3.24870.23923750.19237454X-RAY DIFFRACTION100
3.2487-3.45220.21023860.18787481X-RAY DIFFRACTION100
3.4522-3.71870.19774120.17167443X-RAY DIFFRACTION100
3.7187-4.09270.19554230.15157470X-RAY DIFFRACTION100
4.0927-4.68460.16364170.13857523X-RAY DIFFRACTION100
4.6846-5.90060.17484020.15527600X-RAY DIFFRACTION100
5.9006-49.67230.17383900.16847875X-RAY DIFFRACTION100
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)
10.86570.14070.04013.57121.46272.626-0.02520.17220.1053-0.44090.3489-0.4222-0.72360.4946-0.27110.5303-0.14640.10630.5241-0.19330.453931.638786.458952.8742
21.82230.19620.27733.32331.61613.99220.0625-0.08190.10520.4207-0.0860.298-0.2116-0.11290.01010.447-0.00320.10390.3523-0.13060.40816.835786.976970.5059
31.51620.3559-0.54974.18282.49464.56240.0867-0.1143-0.20830.86180.2217-0.30190.85820.3651-0.2430.460.1268-0.08920.4111-0.14860.454529.182262.407961.6733
41.9224-0.2633-0.02752.85591.22422.71470.00580.12060.3376-0.28540.0189-0.009-0.52550.0723-0.03430.3066-0.01610.01920.3372-0.09030.383121.399660.999321.2276
51.5275-0.26590.50191.39010.86233.0596-0.134-0.22590.06510.0916-0.15490.312-0.0835-0.82140.22550.34810.02940.04570.602-0.23280.52486.669159.918338.2838
60.7278-0.37070.65554.38162.8745.06540.0332-0.1193-0.15370.7985-0.0497-0.03060.76130.1106-0.03630.3494-0.012-0.0250.3282-0.05850.300222.787937.542230.8768
71.52980.0081-0.01672.27240.54442.0423-0.07460.2270.1406-0.31130.1423-0.0899-0.2430.1929-0.05640.2647-0.08630.03890.3511-0.05220.311820.045833.107-11.4955
81.2643-0.14410.48681.50541.09562.4609-0.0358-0.03460.11060.0085-0.18640.28430.0596-0.42650.18210.2112-0.05770.04950.3103-0.08430.35812.43131.38513.5679
91.8332-0.654-1.4283.26992.59154.32910.01860.0695-0.13880.3940.1323-0.1620.54730.2001-0.19380.35610.0488-0.02830.2826-0.0570.360122.293211.16952.0241
102.3711-0.27080.08062.46540.1842.2941-0.18880.6465-0.0931-0.63470.2769-0.31080.17690.129-0.08930.6708-0.12530.13480.7494-0.20950.402823.95513.0686-40.0235
111.40240.0882-0.31461.93660.71552.8442-0.1520.4-0.2275-0.24310.12780.20830.2746-0.54540.0210.4417-0.09610.00080.5374-0.14170.39537.6545-0.2159-24.8127
121.6515-1.422-2.03142.13681.47093.7146-0.3110.157-0.8779-0.0040.2164-0.47330.77890.68810.12630.8210.04550.08970.6094-0.31620.799628.7136-17.9512-26.8811
132.9818-2.19910.08168.5591-1.14022.096-0.44-0.42710.391.25820.4808-0.8137-0.21640.5573-0.12881.1668-0.10220.02550.5904-0.19140.519525.063995.368683.983
141.87343.60583.55726.24266.77947.09640.1751-0.43980.3550.3790.3897-0.47020.24480.6497-0.63870.43970.0025-0.00050.9672-0.42740.725643.480355.238834.6313
150.3352-1.6431-1.58768.33696.87417.1026-0.1416-0.2136-0.07410.45110.3631-0.43870.81460.8074-0.24830.46780.07390.14830.784-0.3160.754942.86776.2271-20.6206
163.34711.1946-1.64494.04280.47864.8434-0.44050.2793-0.6847-0.09630.0669-0.14661.0982-0.31030.31870.8626-0.07870.11550.5536-0.14830.57716.035855.170869.8355
172.76190.38590.31032.1099-0.63583.3375-0.1145-1.011-0.48950.5129-0.3875-0.76570.19241.59470.42350.81020.1564-0.11491.16020.21340.79614.407858.8458105.6912
182.10960.4897-1.57871.37690.07562.3769-0.40110.0238-0.75130.25390.2173-0.01630.9932-0.092-0.02730.92740.02650.12650.43910.06290.6696-2.316154.718793.053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 205)
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 381)
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 436)
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 205)
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 381)
6X-RAY DIFFRACTION6chain 'B' and (resid 382 through 436)
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 205)
8X-RAY DIFFRACTION8chain 'C' and (resid 206 through 381)
9X-RAY DIFFRACTION9chain 'C' and (resid 382 through 440)
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 205)
11X-RAY DIFFRACTION11chain 'D' and (resid 206 through 381)
12X-RAY DIFFRACTION12chain 'D' and (resid 382 through 436)
13X-RAY DIFFRACTION13chain 'E' and (resid 7 through 28)
14X-RAY DIFFRACTION14chain 'E' and (resid 45 through 89)
15X-RAY DIFFRACTION15chain 'E' and (resid 90 through 144)
16X-RAY DIFFRACTION16chain 'F' and (resid 1 through 66)
17X-RAY DIFFRACTION17chain 'F' and (resid 67 through 198)
18X-RAY DIFFRACTION18chain 'F' and (resid 199 through 384)

+
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