[English] 日本語
Yorodumi
- PDB-4ihj: Crystal structure of tubulin-stathmin-TTL-ADP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ihj
TitleCrystal structure of tubulin-stathmin-TTL-ADP complex
Components
  • Stathmin-4
  • TUBULIN TYROSINE LIGASE, TTL
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / LIGASE / GTPASE / MICROTUBULE / STATHMIN
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
ADENOSINE-5'-DIPHOSPHATE / 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 / Difference Fourier / Resolution: 2 Å
AuthorsProta, A.E. / Magiera, M.M. / Kuijpers, M. / Bargsten, K. / Frey, D. / Wieser, M. / Jaussi, R. / Hoogenraad, C.C. / Kammerer, R.A. / Janke, C. / Steinmetz, M.O.
CitationJournal: J.Cell Biol. / Year: 2013
Title: Structural basis of tubulin tyrosination by tubulin tyrosine ligase.
Authors: Prota, A.E. / Magiera, M.M. / Kuijpers, M. / Bargsten, K. / Frey, D. / Wieser, M. / Jaussi, R. / Hoogenraad, C.C. / Kammerer, R.A. / Janke, C. / Steinmetz, M.O.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / 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 / _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 / _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: 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, TTL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,51326
Polymers261,3056
Non-polymers3,20820
Water18,6091033
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.520, 157.310, 180.990
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: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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 (domestic 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 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: P63043
#4: Protein TUBULIN TYROSINE LIGASE, TTL


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Plasmid: PA23_007_ggTTL_KH6_2-378_NSKn1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1BQ43

-
Non-polymers , 9 types, 1053 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.: 7 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: 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
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#12: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1033 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsBRAIN TUBULIN PREPARATIONS CONTAIN THREE TUBULIN SUBPOPULATIONS: TYROSINATED (20-30%), DE- ...BRAIN TUBULIN PREPARATIONS CONTAIN THREE TUBULIN SUBPOPULATIONS: TYROSINATED (20-30%), DE-TYROSINATED (30-40%) AND DELTA-2 TUBULIN (ABOUT 40%) (LACKING THE CARBOXYTERMINAL GLUTAMYL-TYROSINE). TUBULIN-TYROSINE LIGASE BINDS ALL THREE VARIANTS, BUT ONLY CAN MODIFY DE-TYROSINATED TUBULIN. ALTHOUGH ALL SUBPOPULATIONS ARE PRESENT IN THE CRYSTAL, ONLY THE DE-TYROSINATED FORM WAS MODELED WITH A TERMINAL CARBOXYLATE TO DESCRIBE THE LIGASE REACTION. IN THE SEQRES RECORD FOR CHAIN A THE TERMINAL TYR WAS OMITTED TO MATCH THE MODELED VARIANT OF ALPHA-TUBULIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 4-10% PEG 4000, 4-6% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/Imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99995 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2011
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator, Sagittally - horizontally focussed
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2→72.137 Å / Num. all: 200646 / Num. obs: 198918 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.8 % / Biso Wilson estimate: 36.2 Å2 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 25.2 % / Mean I/σ(I) obs: 1.17 / Num. unique all: 13684 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
RemDAqdata collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: Difference Fourier
Starting model: PDB entry 4I4T

4i4t


Resolution: 2→72.1 Å / SU ML: 0.31 / σ(F): 2 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 10028 5.04 %RANDOM
Rwork0.1677 ---
obs0.1702 198893 99.13 %-
all-198918 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.273 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.2872 Å20 Å2-0 Å2
2--4.9205 Å2-0 Å2
3----0.3361 Å2
Refinement stepCycle: LAST / Resolution: 2→72.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17356 0 189 1033 18578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818119
X-RAY DIFFRACTIONf_angle_d1.1424607
X-RAY DIFFRACTIONf_dihedral_angle_d15.7176771
X-RAY DIFFRACTIONf_chiral_restr0.0632687
X-RAY DIFFRACTIONf_plane_restr0.0053191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0240.32472940.31155333X-RAY DIFFRACTION85
2.024-2.04780.32413530.28776215X-RAY DIFFRACTION99
2.0478-2.07280.31193250.27036268X-RAY DIFFRACTION100
2.0728-2.0990.32013520.27346219X-RAY DIFFRACTION99
2.099-2.12660.31753480.26256251X-RAY DIFFRACTION99
2.1266-2.15580.30053110.2456225X-RAY DIFFRACTION99
2.1558-2.18660.29083170.23036245X-RAY DIFFRACTION99
2.1866-2.21920.26123390.21976284X-RAY DIFFRACTION99
2.2192-2.25390.2913170.22516284X-RAY DIFFRACTION100
2.2539-2.29080.28663360.21526247X-RAY DIFFRACTION99
2.2908-2.33030.28263490.20776223X-RAY DIFFRACTION99
2.3303-2.37270.25373370.19336315X-RAY DIFFRACTION100
2.3727-2.41830.24713450.19196266X-RAY DIFFRACTION100
2.4183-2.46770.24523410.1796286X-RAY DIFFRACTION99
2.4677-2.52140.25383220.18116302X-RAY DIFFRACTION100
2.5214-2.580.24833380.17156290X-RAY DIFFRACTION100
2.58-2.64450.22113290.16046284X-RAY DIFFRACTION100
2.6445-2.71610.22993190.16966346X-RAY DIFFRACTION100
2.7161-2.7960.23243760.16886272X-RAY DIFFRACTION100
2.796-2.88620.22063190.15976366X-RAY DIFFRACTION100
2.8862-2.98940.23192930.16336354X-RAY DIFFRACTION100
2.9894-3.10910.21933400.15736362X-RAY DIFFRACTION100
3.1091-3.25060.21663090.16766378X-RAY DIFFRACTION100
3.2506-3.4220.23093580.176355X-RAY DIFFRACTION100
3.422-3.63630.22193470.16076380X-RAY DIFFRACTION100
3.6363-3.91710.17443400.14056376X-RAY DIFFRACTION100
3.9171-4.31120.17123220.12626452X-RAY DIFFRACTION100
4.3112-4.9350.14183510.10426449X-RAY DIFFRACTION100
4.935-6.2170.17513460.14276510X-RAY DIFFRACTION100
6.217-72.18430.22113550.19036728X-RAY DIFFRACTION100
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)
10.5101-0.0835-0.09241.58341.10651.30850.00350.06170.1199-0.32940.2287-0.2683-0.50.3-0.01640.4182-0.15870.12970.284-0.22820.218331.65987.93751.9643
20.9079-0.3028-0.15792.59481.27822.98730.0353-0.04360.00930.2395-0.01190.1123-0.0941-0.0432-0.02110.258-0.00830.04820.1777-0.0710.186819.014582.091965.8993
30.5794-0.2653-0.09252.58411.37581.57130.0285-0.11090.04440.3640.01080.13640.0037-0.03780.00210.32770.00610.07160.1529-0.08880.147218.738483.064473.4024
41.3406-0.7103-1.62513.06413.37125.1389-0.1348-0.1605-0.10770.69510.3529-0.23950.74980.822-0.29060.39840.147-0.08460.2961-0.15030.324132.61261.603360.6618
50.1661-0.0926-0.03030.05160.01690.00550.6976-0.22480.18790.1996-0.5256-0.3005-0.28850.4644-0.03131.55480.02550.43710.64540.15250.731715.920255.816286.6999
63.8693-1.5353-0.71135.99131.37292.87210.1340.26650.5636-0.5226-0.14980.1607-0.7958-0.29030.01730.30430.069-0.00220.2391-0.00210.213816.331569.819119.6074
72.4702-0.0183-1.53917.2315-1.07983.92430.1150.35710.0739-0.54820.0418-0.3689-0.41420.2359-0.15130.2039-0.00230.03710.3714-0.05750.154629.069256.020214.6375
81.98921.43720.24244.7821.90772.69580.0347-0.06430.117-0.08010.0229-0.0593-0.16240.1277-0.05790.1270.01240.03940.2173-0.10030.191524.324752.939226.1239
92.2694-0.57960.87870.324-0.14051.145-0.1724-0.2756-0.0323-0.0169-0.17520.37460.2349-0.64020.23030.2303-0.06620.07110.4798-0.26630.39775.390150.718128.3365
100.9353-0.6384-0.49921.01580.49121.274-0.02480.0160.09650.0006-0.13450.2099-0.1694-0.38730.11610.18820.01680.01090.2607-0.14370.281310.857161.485535.9041
112.3272-1.1790.35372.57730.41062.4061-0.214-0.19470.0870.3759-0.10670.37250.0079-0.76540.23130.2494-0.00790.06410.4177-0.1620.31056.526260.673744.8953
121.646-2.9973-2.44096.68935.59334.8287-0.1446-0.0926-0.12350.5487-0.0490.47510.5706-0.04480.2270.2094-0.05820.02880.2149-0.07590.172415.173142.048134.0991
131.6952-1.2002-1.22253.91314.18897.2517-0.1333-0.3087-0.00030.74920.1945-0.07260.75260.6876-0.03010.24260.0146-0.03070.2269-0.04940.212625.467137.93831.0252
141.1251-0.46120.03322.90670.18171.446-0.04780.14970.1052-0.29740.0925-0.0855-0.09770.1606-0.02530.1412-0.05850.01890.206-0.01760.134920.256632.9624-12.0932
151.1614-0.49260.13571.35990.60561.4622-0.0050.01830.02870.0799-0.05140.0920.1206-0.19240.05120.127-0.0510.02930.1492-0.01830.15887.579125.99753.0136
162.505-1.1479-0.08492.57960.7833.18030.08140.50930.0709-0.6448-0.0914-0.0099-0.1524-0.1070.00560.4366-0.0770.03810.4551-0.0820.073617.2319.6929-44.2927
170.6401-0.2454-0.05541.18480.60721.3486-0.04090.3376-0.1586-0.36990.0524-0.10680.2470.0245-0.04510.4389-0.06030.11790.3652-0.3010.165720.7432-2.2113-33.7118
181.4379-0.2283-0.20771.92740.87181.9173-0.13570.3122-0.2664-0.096-0.01270.18260.3507-0.16980.17220.4088-0.1070.03960.303-0.13310.20448.8398-3.8145-21.3748
191.887-0.5884-0.40341.8267-0.02060.3838-0.02940.0992-0.3589-0.02720.0449-0.19680.50350.28790.08680.57960.0820.07060.3122-0.21830.409230.1409-16.3148-24.4583
202.0574-1.4573-0.93283.07042.02772.6405-0.2299-0.2382-0.09930.77040.3029-0.15760.45490.5268-0.07250.5142-0.0123-0.03640.31-0.11590.241927.275792.438582.1073
210.3008-0.089-0.13611.12731.09121.6297-0.0918-0.0202-0.03770.11870.2916-0.3010.32940.5047-0.32790.16810.06140.06380.3981-0.23740.331842.591928.36324.7056
221.36471.30590.33573.8120.94242.3773-0.2160.2448-0.50350.05880.0636-0.15850.8806-0.2237-0.01630.6743-0.06690.15360.319-0.14230.34896.13854.514770.1511
231.4568-0.72380.8712.5608-1.16183.0364-0.1267-0.7654-0.27720.9063-0.3437-0.86110.12561.40650.5450.77340.086-0.11050.9440.26360.563215.007258.5899106.0349
241.47930.673-1.15751.2157-0.30791.7958-0.2557-0.1437-0.49970.2480.1342-0.04710.4027-0.0254-0.02620.66550.05760.15960.16680.08240.3598-1.795654.365394.0289
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 437:450)
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 2:88)
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 47:141)
22X-RAY DIFFRACTION22CHAIN F AND (RESSEQ 1:66)
23X-RAY DIFFRACTION23CHAIN F AND (RESSEQ 67:198)
24X-RAY DIFFRACTION24CHAIN F AND (RESSEQ 199:384)

+
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