[English] 日本語
Yorodumi
- PDB-5sb5: Tubulin-todalam-9-complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5sb5
TitleTubulin-todalam-9-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 / 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 / microtubule-based process / regulation of microtubule polymerization or depolymerization / 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 / cytoplasm / cytosol
Similarity search - Function
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. ...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. / 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 / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Chem-4CJ / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.31 Å
AuthorsMuehlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
Funding support Italy, Switzerland, 3items
OrganizationGrant numberCountry
NEON/Regione LombardiaID239047 Italy
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action.
Authors: Muhlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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)264,87422
Polymers261,6316
Non-polymers3,24216
Water13,403744
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.810, 157.711, 180.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 , 8 types, 760 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.: 4 / 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-4CJ / N-{4-[2-(3-fluoroanilino)-1,3-thiazol-4-yl]phenyl}acetamide


Mass: 327.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14FN3OS / Feature type: SUBJECT OF INVESTIGATION
#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.: 744 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2% PEG 4K, 4% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.31→49.55 Å / Num. obs: 131912 / % possible obs: 99.9 % / Redundancy: 13.716 % / Biso Wilson estimate: 41.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.197 / Χ2: 0.792 / Net I/σ(I): 11.45 / Num. measured all: 1809337 / Scaling rejects: 112
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.3714.0191.8581.45134593965396010.5831.92799.5
2.37-2.4314.2571.5711.76134548943794370.6721.629100
2.43-2.514.2241.2682.21130509917691750.761.315100
2.5-2.5814.11.0842.6125149887688760.8091.124100
2.58-2.6613.9450.8933.19120635865286510.8660.927100
2.66-2.7613.790.7553.73115479837883740.8920.783100
2.76-2.8613.2930.5914.68107169806280620.9270.615100
2.86-2.9812.7750.4695.7799746780978080.950.489100
2.98-3.1114.0390.3498.11104676745674560.9770.362100
3.11-3.2613.6380.27410.0297691716371630.9840.285100
3.26-3.4412.8240.20612.4787104679267920.990.215100
3.44-3.6514.2270.15417.2192090647364730.9950.16100
3.65-3.914.1840.11921.6186153607460740.9970.124100
3.9-4.2113.9690.09625.479525569356930.9970.099100
4.21-4.6113.6320.0829.3271443524152410.9980.083100
4.61-5.1612.8780.07429.7560899472947290.9980.078100
5.16-5.9613.1230.08527.2655706424542450.9980.088100
5.96-7.2912.8550.08127.7646316360336030.9980.084100
7.29-10.3213.9310.05639.5939314282228220.9990.058100
10.32-49.5512.5790.04942.4120592165816370.9980.05198.7

-
Processing

Software
NameVersionClassificationNB
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 2.31→49.55 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 6596 5 %
Rwork0.1882 125303 -
obs0.1898 131899 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.97 Å2 / Biso mean: 55.0259 Å2 / Biso min: 22.26 Å2
Refinement stepCycle: final / Resolution: 2.31→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17299 0 195 744 18238
Biso mean--47.42 48.62 -
Num. residues----2187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.330.31812150.29954095431099
2.33-2.360.3262170.296941174334100
2.36-2.390.34312170.278841334350100
2.39-2.420.31582170.264941084325100
2.42-2.450.27422180.259541544372100
2.45-2.480.27792180.237341434361100
2.48-2.520.3042180.241941434361100
2.52-2.560.25832200.234641654385100
2.56-2.60.26632160.217141164332100
2.6-2.640.252190.223541634382100
2.64-2.690.26252180.223541414359100
2.69-2.730.2792170.217541234340100
2.73-2.790.25662190.218741594378100
2.79-2.840.25482190.222141564375100
2.84-2.910.27642190.23541644383100
2.91-2.970.25492190.229841534372100
2.97-3.050.27652180.209441504368100
3.05-3.130.20332190.195841634382100
3.13-3.220.2612200.194141764396100
3.22-3.330.20752190.191641634382100
3.33-3.450.23152200.190441774397100
3.45-3.580.22822210.185142044425100
3.58-3.750.2232210.176142004421100
3.75-3.940.20172200.161241734393100
3.94-4.190.19012210.154542114432100
4.19-4.510.17362230.147842214444100
4.51-4.970.1732220.139942254447100
4.97-5.690.18322240.166842494473100
5.69-7.160.23262260.184242934519100
7.16-49.550.15482360.164544654701100
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)
11.4236-0.2651-0.18623.07210.13071.69970.0650.04930.2437-0.45180.1514-0.2845-0.94190.2576-0.23430.7262-0.11540.14120.4175-0.12390.426228.953397.507153.8325
21.14160.40960.35972.67391.15642.4735-0.08060.13870.0912-0.60140.3183-0.3384-0.61720.4592-0.24390.4578-0.14760.12860.4811-0.18020.446834.859783.305648.7651
30.94590.2959-0.99482.99570.24591.2238-0.0322-0.009-0.11490.37530.2593-0.10570.25220.1971-0.14670.37570.0141-0.02030.4218-0.14270.396929.797973.837558.7969
41.9071-0.51750.31163.05470.79693.37610.131-0.0287-0.09110.2575-0.04860.0761-0.07580.0438-0.04330.32740.00690.06550.2832-0.07290.316321.444684.338564.7419
51.01070.5823-0.14861.79111.02443.96180.1183-0.047-0.02310.4306-0.21250.8591-0.0951-0.69140.01060.4714-0.00480.13380.4617-0.12690.53929.243684.67271.5784
60.579-0.03180.18542.99561.57732.59080.0129-0.11330.00030.65420.06280.06290.22530.1231-0.09060.3893-0.01690.05870.3615-0.06950.351323.067476.840769.8869
72.8056-1.0522-1.27422.0468-0.4153.03560.02890.02750.3472-0.03770.07440.3257-0.5474-0.1934-0.02770.36830.04150.04580.3399-0.04090.442716.193165.198722.2075
82.392-0.6756-0.92332.69860.11892.28550.3420.16270.4575-0.3521-0.18720.0413-0.9309-0.1837-0.15970.57290.08130.02920.3253-0.01340.47616.285572.410618.0273
91.3081-0.1685-0.25762.40460.81352.7730.08310.2680.1363-0.30270.1037-0.2445-0.57470.3377-0.18380.3745-0.03970.05980.4949-0.0460.363129.182756.448114.5687
101.0934-0.1555-0.22012.4911.19572.9163-0.0066-0.13520.04720.0238-0.10290.1266-0.0347-0.19280.01530.21280.00020.02730.321-0.09980.327517.526853.361326.5064
111.0545-0.20211.59840.89670.12842.8858-0.0554-0.20140.07790.29830.00760.1549-0.6330.00040.03610.50090.01560.10370.4634-0.14840.531419.301768.419638.4904
121.9306-0.63680.31111.9887-0.25472.7718-0.0884-0.2883-0.13040.0371-0.0570.4893-0.0799-0.80360.18970.34610.0126-0.01570.4939-0.21660.42485.511458.860138.5363
131.9536-0.90640.52661.5732-0.24282.3129-0.2506-0.25760.07410.478-0.12610.2944-0.0036-0.98430.22410.43830.06210.07220.6637-0.20190.47795.240659.678244.8717
141.1093-0.21150.29870.75151.16682.1323-0.0449-0.160.17790.3848-0.19260.22690.1823-0.37860.21630.2855-0.04530.08160.3818-0.07740.355612.134752.255539.2083
151.0136-0.4950.68522.72311.14183.1648-0.0151-0.1253-0.1590.58940.0843-0.19390.56570.5237-0.06570.3295-0.0021-0.02310.3299-0.01030.319925.829537.894930.4825
161.0776-0.24810.09422.76490.19741.7053-0.03640.12750.0921-0.28130.0817-0.0325-0.14740.1672-0.03720.2547-0.06490.03620.3412-0.0290.291620.19933.0904-11.9966
170.836-0.40250.46611.26540.80482.27370.04690.00480.03080.0332-0.14710.22240.0687-0.32740.11950.2134-0.04320.03530.3278-0.02060.3283.87328.93060.4114
181.8964-0.33890.7562.11880.70212.1771-0.0813-0.18850.1796-0.091-0.12080.31080.0355-0.46440.10990.1968-0.04270.05460.2919-0.08410.33280.881434.99628.8402
190.7758-0.6402-0.49422.04081.36371.8544-0.0520.0599-0.01990.30250.125-0.08430.36430.1706-0.14090.2896-0.0007-0.00180.2872-0.03530.332920.083413.4742.7189
202.8851-0.45040.73962.66170.26822.3899-0.25240.44480.1904-0.45430.29270.1845-0.0214-0.1924-0.03720.512-0.08130.01930.6511-0.00650.327615.253412.1453-41.273
211.8262-0.8224-0.61232.27250.06731.3573-0.14760.78910.1799-0.66050.2177-0.3860.090.3032-0.15160.6964-0.10930.17710.8563-0.21570.406828.57011.9115-46.2781
221.9124-0.0426-0.42281.2844-0.17982.0811-0.17570.3217-0.2065-0.32820.1775-0.11550.3433-0.0128-0.06410.5655-0.04010.05850.5411-0.18820.425520.8437-5.3458-34.2024
231.7702-0.74030.09552.23520.60722.92450.08610.1971-0.0422-0.3426-0.11960.18390.2025-0.32930.01910.3692-0.03990.0090.4507-0.08950.31610.50022.7496-25.1346
241.7749-0.4809-0.36911.27620.45052.2638-0.17520.2445-0.2040.00880.08150.15280.2928-0.2930.04570.3962-0.10410.03060.3811-0.10340.33028.4562-3.0703-20.9766
252.0141-0.2557-0.28941.97990.05311.814-0.20650.075-0.72530.06730.0596-0.10430.68910.4316-0.05170.67670.05250.06450.474-0.21310.593230.3018-17.2267-24.5039
262.3892-0.6717-0.1861.55030.61610.6925-0.1578-0.16680.09990.73410.308-0.60250.20350.588-0.20770.9637-0.0290.01190.6169-0.17170.504427.604392.716682.0196
270.1882-0.4738-0.5870.32370.36020.6820.0229-0.0294-0.03340.20150.3936-0.51880.30390.5208-0.51790.39430.06670.03530.6866-0.22610.604943.085827.95544.137
282.31450.1692-2.30121.29870.14392.3379-0.41780.3192-0.5127-0.32130.0437-0.19510.9953-0.25580.26280.7993-0.08270.13290.4456-0.08160.54547.605456.478174.2349
292.75350.02880.14480.50960.06721.9542-0.0136-0.4743-0.23160.4039-0.6058-0.92580.08441.7610.62050.80530.1333-0.10391.52360.39950.933318.885858.6027105.3875
301.4170.3996-1.37210.9666-0.07161.4814-0.488-0.227-0.6346-0.00420.0097-0.15831.11150.01790.06470.99050.11790.2350.4660.17340.7669-0.428251.22399.4008
311.62940.70282.01172.2379-1.14394.5667-0.39890.1921-0.8209-0.4004-0.2949-1.03580.71240.73250.44591.83720.25970.490.59450.23621.47214.151238.0593101.6473
322.1581-0.0271-1.7950.43240.55122.653-0.39820.0642-0.46910.01980.23680.08230.6686-0.11080.1340.7775-0.00360.12450.39140.04780.5403-2.774356.961893.083
332.3842-0.4422-0.51180.5784-1.25014.2348-0.08010.6561-0.1914-0.08690.20480.31-0.0222-1.0504-0.18860.5396-0.09890.0590.7695-0.06510.6314-7.655461.985478.3482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )A1 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 160 )A72 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 197 )A161 - 197
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 273 )A198 - 273
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )A274 - 311
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 438 )A312 - 438
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 27 )B1 - 27
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 88 )B28 - 88
9X-RAY DIFFRACTION9chain 'B' and (resid 89 through 127 )B89 - 127
10X-RAY DIFFRACTION10chain 'B' and (resid 128 through 238 )B128 - 238
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 259 )B239 - 259
12X-RAY DIFFRACTION12chain 'B' and (resid 260 through 296 )B260 - 296
13X-RAY DIFFRACTION13chain 'B' and (resid 297 through 338 )B297 - 338
14X-RAY DIFFRACTION14chain 'B' and (resid 339 through 401 )B339 - 401
15X-RAY DIFFRACTION15chain 'B' and (resid 402 through 437 )B402 - 437
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 197 )C1 - 197
17X-RAY DIFFRACTION17chain 'C' and (resid 198 through 311 )C198 - 311
18X-RAY DIFFRACTION18chain 'C' and (resid 312 through 372 )C312 - 372
19X-RAY DIFFRACTION19chain 'C' and (resid 373 through 440 )C373 - 440
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 59 )D1 - 59
21X-RAY DIFFRACTION21chain 'D' and (resid 60 through 127 )D60 - 127
22X-RAY DIFFRACTION22chain 'D' and (resid 128 through 238 )D128 - 238
23X-RAY DIFFRACTION23chain 'D' and (resid 239 through 295 )D239 - 295
24X-RAY DIFFRACTION24chain 'D' and (resid 296 through 399 )D296 - 399
25X-RAY DIFFRACTION25chain 'D' and (resid 400 through 441 )D400 - 441
26X-RAY DIFFRACTION26chain 'E' and (resid 6 through 46 )E6 - 46
27X-RAY DIFFRACTION27chain 'E' and (resid 47 through 143 )E47 - 143
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 83 )F1 - 83
29X-RAY DIFFRACTION29chain 'F' and (resid 84 through 184 )F84 - 184
30X-RAY DIFFRACTION30chain 'F' and (resid 185 through 236 )F185 - 236
31X-RAY DIFFRACTION31chain 'F' and (resid 237 through 257 )F237 - 257
32X-RAY DIFFRACTION32chain 'F' and (resid 258 through 353 )F258 - 353
33X-RAY DIFFRACTION33chain 'F' and (resid 354 through 380 )F354 - 380

+
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