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- PDB-6bs2: Tubulin-RB3_SLD-TTL in complex with heterocyclic pyrimidine compo... -

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Basic information

Entry
Database: PDB / ID: 6bs2
TitleTubulin-RB3_SLD-TTL in complex with heterocyclic pyrimidine compound 8b
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / Microtubule Inhibitor / Colchicine Cancer
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / 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 / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Dna Ligase; domain 1 / 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-E9Y / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKumar, G. / Wang, Y. / Li, W. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Heterocyclic-Fused Pyrimidines as Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy.
Authors: Banerjee, S. / Arnst, K.E. / Wang, Y. / Kumar, G. / Deng, S. / Yang, L. / Li, G.B. / Yang, J. / White, S.W. / Li, W. / Miller, D.D.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)265,12722
Polymers261,3056
Non-polymers3,82216
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.101, 157.602, 181.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 2 through 54 or (resid 55...
21(chain D and (resid 2 through 319 or (resid 320...
12chain A
22(chain C and (resid 1 through 95 or (resid 96...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGALAALA(chain B and (resid 2 through 54 or (resid 55...BB2 - 542 - 54
121THRTHRTHRTHR(chain B and (resid 2 through 54 or (resid 55...BB5555
131ARGARGALAALA(chain B and (resid 2 through 54 or (resid 55...BB2 - 4282 - 428
141ARGARGALAALA(chain B and (resid 2 through 54 or (resid 55...BB2 - 4282 - 428
151ARGARGALAALA(chain B and (resid 2 through 54 or (resid 55...BB2 - 4282 - 428
161ARGARGALAALA(chain B and (resid 2 through 54 or (resid 55...BB2 - 4282 - 428
211ARGARGGLYGLY(chain D and (resid 2 through 319 or (resid 320...DD2 - 3192 - 319
221ARGARGARGARG(chain D and (resid 2 through 319 or (resid 320...DD320320
231METMETASPASP(chain D and (resid 2 through 319 or (resid 320...DD1 - 4311 - 431
241METMETASPASP(chain D and (resid 2 through 319 or (resid 320...DD1 - 4311 - 431
251METMETASPASP(chain D and (resid 2 through 319 or (resid 320...DD1 - 4311 - 431
261METMETASPASP(chain D and (resid 2 through 319 or (resid 320...DD1 - 4311 - 431
112METMETVALVALchain AAA1 - 4371 - 437
212METMETGLYGLY(chain C and (resid 1 through 95 or (resid 96...CC1 - 951 - 95
222LYSLYSLYSLYS(chain C and (resid 1 through 95 or (resid 96...CC9696
232METMETVALVAL(chain C and (resid 1 through 95 or (resid 96...CC1 - 4401 - 440
242METMETVALVAL(chain C and (resid 1 through 95 or (resid 96...CC1 - 4401 - 440
252METMETVALVAL(chain C and (resid 1 through 95 or (resid 96...CC1 - 4401 - 440
262METMETVALVAL(chain C and (resid 1 through 95 or (resid 96...CC1 - 4401 - 440

NCS ensembles :
ID
1
2

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Components

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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) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#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

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Non-polymers , 8 types, 186 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-E9Y / 1-(3,6-dimethyl[1,2]oxazolo[5,4-d]pyrimidin-4-yl)-6-methoxy-1,2,3,4-tetrahydroquinoline


Mass: 310.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O2
#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.: 170 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% Glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 88135 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.65 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Χ2: 0.942 / Net I/σ(I): 4.7 / Num. measured all: 587933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.7160.94258110.6610.4161.0321.00299.9
2.71-2.786.50.81157950.7530.3430.8820.998100
2.78-2.856.80.68657940.8290.2840.7431.013100
2.85-2.946.80.5958060.8620.2430.6381.023100
2.94-3.036.70.45358150.9080.1890.4921.025100
3.03-3.146.30.35158160.9360.1510.3821.021100
3.14-3.276.90.28358490.9580.1160.3061.019100
3.27-3.4270.2258320.9740.0890.2370.996100
3.42-3.670.16458590.9830.0670.1770.991100
3.6-3.826.90.12758440.9880.0520.1380.955100
3.82-4.126.40.158940.990.0430.1090.936100
4.12-4.536.90.08458920.9920.0340.0910.926100
4.53-5.1970.07759170.9930.0310.0830.877100
5.19-6.536.40.07359980.9920.0310.0790.749100
6.53-506.40.05562130.9960.0240.060.60499.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→49.754 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2336 4222 4.93 %
Rwork0.1815 --
obs0.1841 85693 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.12 Å2 / Biso mean: 46.9287 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 2.65→49.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17210 0 253 170 17633
Biso mean--44.87 35.49 -
Num. residues----2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717833
X-RAY DIFFRACTIONf_angle_d1.01224185
X-RAY DIFFRACTIONf_chiral_restr0.0562626
X-RAY DIFFRACTIONf_plane_restr0.0073129
X-RAY DIFFRACTIONf_dihedral_angle_d18.55510673
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3881X-RAY DIFFRACTION13.33TORSIONAL
12D3881X-RAY DIFFRACTION13.33TORSIONAL
21A3971X-RAY DIFFRACTION13.33TORSIONAL
22C3971X-RAY DIFFRACTION13.33TORSIONAL
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 (%)
2.65-2.68010.4314860.30262013209972
2.6801-2.71160.2881130.26792245235881
2.7116-2.74470.31271280.25622394252288
2.7447-2.77940.35461390.24632575271493
2.7794-2.8160.27211310.22912691282297
2.816-2.85450.32751450.22312713285899
2.8545-2.89530.28721580.22392745290399
2.8953-2.93850.26031410.225727442885100
2.9385-2.98440.2951410.220527742915100
2.9844-3.03340.3041100.219927862896100
3.0334-3.08570.29171590.22627762935100
3.0857-3.14180.28071350.22727302865100
3.1418-3.20220.2571400.218827952935100
3.2022-3.26750.27041510.214927482899100
3.2675-3.33860.30491290.196127852914100
3.3386-3.41620.24851430.191727802923100
3.4162-3.50160.24021470.18228092956100
3.5016-3.59630.25891530.183427362889100
3.5963-3.70210.22251460.176627832929100
3.7021-3.82150.23131430.165127712914100
3.8215-3.95810.19851420.151227992941100
3.9581-4.11650.19191490.148927762925100
4.1165-4.30370.19961440.146327882932100
4.3037-4.53050.171530.132127792932100
4.5305-4.81410.18781390.13622796293599
4.8141-5.18540.17671470.14182810295799
5.1854-5.70660.21191400.1642811295199
5.7066-6.53080.25931650.18492803296899
6.5308-8.22210.21591610.17352836299799
8.2221-49.76260.19121440.18312880302495
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)
10.7838-0.07840.10542.55511.27182.28910.0373-0.0269-0.0419-0.06850.1634-0.09770.28960.2151-0.16390.28670.027-0.0330.2431-0.09630.264325.3978-83.1554-61.3397
21.10730.53660.27291.80121.07652.4380.04510.0242-0.20150.0077-0.08780.11470.2267-0.2168-0.00490.1645-0.0026-0.00020.2567-0.09710.2915.9813-57.3389-29.1706
30.8660.1837-0.01181.26340.49881.4299-0.036-0.0908-0.05490.1033-0.01890.08320.0358-0.06960.04470.17830.04750.00550.1636-0.02720.184413.1543-29.04013.7828
41.6977-0.05190.50231.61420.30362.2904-0.2373-0.61090.23920.43330.1894-0.012-0.2795-0.14960.01780.51930.118-0.05350.4704-0.20370.288218.34611.702731.6925
50.26760.28370.40481.85351.9632.5372-0.04390.0464-0.0202-0.44680.5441-0.5474-0.50750.6655-0.47730.2863-0.04040.00690.4477-0.15830.435739.8231-41.3219-20.4515
61.8548-0.39341.85812.0021-0.9363.4358-0.33610.25790.6544-0.19390.0806-0.1994-0.68820.34050.14190.633-0.0917-0.10130.26860.06410.52854.6272-55.6308-92.2751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:501)A1 - 501
2X-RAY DIFFRACTION2(chain B and resseq 2:501)B2 - 501
3X-RAY DIFFRACTION3(chain C and resseq 1:501)C1 - 501
4X-RAY DIFFRACTION4(chain D and resseq 1:431)D1 - 431
5X-RAY DIFFRACTION5(chain E and resseq 6:141)E6 - 141
6X-RAY DIFFRACTION6(chain F and resseq 1:380)F1 - 380

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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

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