[English] 日本語
Yorodumi
- PDB-7au5: Tubulin-noscapine-analogue-14e complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7au5
TitleTubulin-noscapine-analogue-14e 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / Chem-RYK / 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: 2.2 Å
AuthorsYong, C. / Devine, S.M. / Abel, A.-C. / Muthiah, D. / Gao, X. / Callaghan, R. / Capuano, B. / Steinmetz, M.O. / Prota, A.E. / Scammels, P.J.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
H2020 Marie Curie Actions of the European Commission860070 TUBINTRAINEuropean Union
CitationJournal: Chemmedchem / Year: 2021
Title: 1,3-Benzodioxole-Modified Noscapine Analogues: Synthesis, Antiproliferative Activity, and Tubulin-Bound Structure.
Authors: Yong, C. / Devine, S.M. / Abel, A.C. / Tomlins, S.D. / Muthiah, D. / Gao, X. / Callaghan, R. / Steinmetz, M.O. / Prota, A.E. / Capuano, B. / Scammells, P.J.
History
DepositionNov 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 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)265,20425
Polymers261,6316
Non-polymers3,57319
Water12,160675
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22710 Å2
ΔGint-156 kcal/mol
Surface area81290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.642, 157.838, 180.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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 , 10 types, 694 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-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-RYK / (5~{R})-5-[(1~{S})-4,5-dimethoxy-1,3-dihydro-2-benzofuran-1-yl]-~{N}-ethyl-4-methoxy-7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinoline-6-carboxamide


Mass: 456.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N2O7 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#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


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 4 % PEG 4K, 7 % glycerol, 30 mM MgCl2, 30 mM CaCl2, 5 mM L-tyrosine and 100 mM MES/Imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.2→47.88 Å / Num. obs: 149600 / % possible obs: 98.64 % / Redundancy: 13.2 % / Biso Wilson estimate: 51.82 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0789 / Rrim(I) all: 0.08206 / Net I/σ(I): 24.5
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 10.8 % / Rmerge(I) obs: 2.003 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 14004 / CC1/2: 0.417 / Rrim(I) all: 2.103 / % possible all: 93.26

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
REFMAC5.8.0258refinement
XDSJan 31, 2020data processing
PHENIXphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 2.2→47.88 Å / SU ML: 0.2599 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 7480 5 %
Rwork0.1776 142120 -
obs0.1793 149600 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17404 0 217 675 18296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002218328
X-RAY DIFFRACTIONf_angle_d0.511624902
X-RAY DIFFRACTIONf_chiral_restr0.04062699
X-RAY DIFFRACTIONf_plane_restr0.00283247
X-RAY DIFFRACTIONf_dihedral_angle_d13.13636828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.33662290.32034353X-RAY DIFFRACTION91.24
2.22-2.250.33142330.29674418X-RAY DIFFRACTION93.85
2.25-2.280.3072360.28634483X-RAY DIFFRACTION93.54
2.28-2.310.31192370.27684508X-RAY DIFFRACTION95.57
2.31-2.340.28952420.26294592X-RAY DIFFRACTION96.18
2.34-2.370.30132440.24564650X-RAY DIFFRACTION97.63
2.37-2.40.25572480.2294716X-RAY DIFFRACTION99.3
2.4-2.440.28512480.21644711X-RAY DIFFRACTION98.77
2.44-2.480.25052500.20344741X-RAY DIFFRACTION99.86
2.48-2.520.24872480.20834718X-RAY DIFFRACTION99.04
2.52-2.560.25432500.1984743X-RAY DIFFRACTION99.09
2.56-2.610.23442510.19154763X-RAY DIFFRACTION99.7
2.61-2.660.24752480.20064711X-RAY DIFFRACTION99.4
2.66-2.710.24352490.20324745X-RAY DIFFRACTION99.26
2.71-2.770.25012510.20594768X-RAY DIFFRACTION99.35
2.77-2.840.24382500.20424747X-RAY DIFFRACTION99.42
2.84-2.910.25582520.20254782X-RAY DIFFRACTION99.56
2.91-2.980.2452490.20614743X-RAY DIFFRACTION99.78
2.98-3.070.23262520.19144787X-RAY DIFFRACTION99.66
3.07-3.170.23412510.18954767X-RAY DIFFRACTION99.5
3.17-3.290.23282530.19364798X-RAY DIFFRACTION99.7
3.29-3.420.22342520.19154792X-RAY DIFFRACTION99.76
3.42-3.570.21142530.18024804X-RAY DIFFRACTION99.84
3.57-3.760.18362530.16484805X-RAY DIFFRACTION99.76
3.76-40.18532540.15094841X-RAY DIFFRACTION99.92
4-4.30.1812550.14384844X-RAY DIFFRACTION99.88
4.3-4.740.16152560.1324861X-RAY DIFFRACTION99.92
4.74-5.420.18572570.14684882X-RAY DIFFRACTION99.96
5.42-6.830.20392590.17974925X-RAY DIFFRACTION99.98
6.83-47.880.20042700.175122X-RAY DIFFRACTION99.63
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)
11.139911648020.0502331741330.0279676103994.238594722731.296772299972.68065558571-0.04006605938330.1469206460180.120573281673-0.4202517437580.375504236212-0.394936291263-0.6725685351310.5042426983256.05993982602E-50.636951325174-0.1341990424180.1294051228290.644625163159-0.1893610816960.54983935016631.632689506386.43067990652.4423971189
21.64630566627-0.03813359545880.05614104453943.498957942310.8954043895614.208134860010.171348626366-0.0322902434386-0.001264164153480.244533138313-0.102898902390.236216588194-0.172759303639-0.0884312969677-0.0001012685609550.5425820920450.01702424986820.0837925073950.462162167795-0.1230486466050.52794910826117.743535902384.37740063867.0414287026
30.5581148985680.1583274064920.1362154129443.030728691441.856120102182.962306768660.024185687235-0.162513719959-0.001462460470510.7255131826980.146478953989-0.007473863495130.2389415347240.2248893623550.0002036497547750.564402094581-0.004645668164220.05860693320830.544178892583-0.118344545430.54912678393422.90409335376.950766677869.8630892645
41.59949924394-0.601167187366-0.4076868320080.702360797882-0.6278450737771.357299039170.07807449070570.1646381235930.848211658001-0.1267549008980.03577840057290.0114281615526-0.955142833299-0.1520895885681.14914531972E-60.7331746518840.06186599227670.06298941000040.541516689626-0.06744321201580.83127795518215.007065993472.224823750422.171673081
50.324192305467-0.160519053295-0.1749132812250.151246190984-0.09673849137090.5121990061580.2892443476440.4358338413570.444169139733-1.28529475673-0.20619255295-0.0343264340527-0.950287739352-0.268555368425-0.0001083722901810.7809047301280.1110370081310.03289973822970.621805395354-0.0232792898490.71461276790617.819866934964.680214902812.6001537567
61.56109726532-0.441724460726-0.1526682301171.695217360671.07780649792.776678090910.08300047453620.1066639579030.325716260566-0.2195158680330.089453626298-0.221189587153-0.4387096091840.248581793526-3.80868044745E-50.411792124066-0.02951826420990.0810868284640.518311935868-0.1333817595030.58476194721826.323245017656.409989631520.9989306103
70.0856507843927-0.411933584692-0.1184000927041.78699250450.1419209770671.600500977220.107917556218-0.329402305934-0.0964757013110.474571984778-0.1689749689470.09496937623830.317078793113-0.251653785879-0.000851375024150.3534243219510.008550564563430.05571279603890.519877003309-0.1594191550470.53715954597316.234944145647.833960005228.8452134729
80.332126607346-0.148217293988-0.9697602450181.253720258750.2306555929522.517592142540.06286039480690.005179925838810.2831973543030.112194678809-0.1702707890640.30487143718-0.169601696959-0.415588183839-0.0004823157556020.3691973642820.01983625381850.03462298488540.48964149343-0.1921413530010.56420428563412.812731165859.160031800533.0351366008
90.0939166275792-0.08352411614310.1243953613890.241468099784-0.1695310267790.2038187684620.366074912352-0.12944407-0.747045173027-0.7607850147560.03893666826541.340731967380.0132653756435-1.773494512320.008743233752210.7027833214180.148531790246-0.1700303424441.15629191134-0.2444707022410.815734652099-5.5148175392962.603790855236.1637835412
101.756454102540.275467433483-0.06187033155790.8816788727560.7606284563391.56856296954-0.132221061288-0.3536022177090.08036894702120.369264362718-0.1126612644770.367661591461-0.0339795662288-0.9177224060910.0001454048303710.6134258530810.06073243902140.07153098535940.836777758606-0.2485907072870.6893679522596.3164239008360.937512876644.7346244552
110.270076967058-0.08366073809740.250082653410.163238589890.2577038187740.713683928446-0.112438920677-0.150480758696-0.1789905526020.397502934225-0.04517440173580.6760266967790.479021033186-0.0981319653697-0.0001473055739510.529464074472-0.009771118309360.07986618541890.567774346857-0.1117968486310.53338538386315.305914093142.193253966134.1189759694
120.5600007438860.295220951780.1475508011431.49904191396-0.01496003687950.579564091506-0.0339966915124-0.166538119352-0.1722112706870.8557163427740.0718662845632-0.2826398218510.6210100582890.5741129079280.002549704779610.6190433565480.0472615136392-0.05007895264080.577963355176-0.07101825230870.53847850612525.584542985938.024326161930.8540020888
131.71967958055-0.5341024775810.1667940953023.566170840650.1785458566262.0692420573-0.02762273631970.1995712724290.120061905992-0.3609365689030.0948665009869-0.035499047505-0.1677386597630.1769950380491.24578369224E-50.357321150828-0.07678218871130.04873990420650.463750688374-0.04193479204080.39839250112720.306986037833.1018270528-11.8751919387
141.25590202388-0.3766436086220.01349547410182.131556586131.233976027881.96181690060.0008693870861510.003444719148430.09061188621740.0954712576708-0.09095315004930.1753024101520.117058182986-0.24569775018-0.0003485615539280.33442569313-0.07628850070150.05034269902040.414220275913-0.03650972050380.4500776494987.5916627466425.99984659543.17361080413
152.210758663550.06045932590650.8522548138451.26352122481-0.6453467510611.33423955614-0.14338688660.8776688050810.190547095857-0.7732519380080.1545619064590.157122642367-0.0676216804067-0.3574424882120.001118805728170.944263015071-0.07293921981910.05479040310131.08018279735-0.07429338674240.53406194079317.24941403149.77137993885-44.065584219
162.14354084139-0.275798135824-0.7856932653171.854519629140.03147838879562.8534030997-0.186001558740.723296711449-0.260177142801-0.5420642962410.287194313703-0.3178863895990.2799702247850.0955982800921-0.002759166712630.829123712812-0.05326447688290.1018980749640.841975076584-0.2784791502720.578416868424.3211957705-3.91622119468-36.7696422579
170.4283276599430.4825892419830.1157794818040.5403910193950.0850760785130.666732755073-0.05625245631860.399042924477-0.122251570805-0.1182652198290.247352942078-0.04215397984520.00323292153919-0.04065214920323.36171352755E-50.625816060356-0.02185261866890.05642060539420.668318602232-0.1490697798110.52392192994718.57236559076.5444139484-23.0217535643
182.17955403245-0.281102124832-0.04560019137261.678625518010.3317087859562.63479845692-0.154077515680.455525074711-0.259891055862-0.1956999791870.08486669550420.2756976386090.334400386475-0.5839834747790.0009326237135790.702414093136-0.1300181704130.02425077487260.738875876469-0.1585015418940.5999705600597.0894001534-3.37484783843-22.4643966629
191.361356863560.1538765080880.7041861713430.86765860159-0.4902220372040.746330580598-0.2251718857180.240608504041-0.827192455670.3287093756010.0218958958766-0.1812826443830.9502545872290.286580942215-0.03928850697131.036706741430.08662079272930.1074941469450.677982770476-0.303663077570.94891604880430.4613859823-16.7360368177-24.5377721452
201.196170125320.4268547881060.3925281414050.5109031281010.4315587828250.363459665804-0.0994813214188-0.172533515110.2319148695730.5960282153440.173513847716-0.4233565741830.2193419622240.6877644024343.10776434786E-51.167127239350.004938859738340.02754550666850.818489196095-0.1111811088780.73226103913528.651224065392.065798108181.1072115754
210.462601738274-0.193940720548-0.3950893002870.2662325787460.009561852473810.346892924786-0.105589353-0.121504279259-0.03259982914150.5059205637410.364593144941-0.3100938647450.6248035282640.6674072244860.00250113297250.5844748502340.08460041408760.06382492887490.910901769724-0.2553264054030.84586327031242.799748102327.85535089163.91273999961
221.359580259850.208021285042-1.331789264140.706900507843-0.1245691567891.30772280582-0.3454256713950.380304737001-0.657290377097-0.1111982322690.121364278266-0.3063099794761.19884549453-0.3152676157089.40271765102E-51.21237692074-0.1586765793620.1412088570950.778538786537-0.1757939801210.8273491195176.1053827157154.848260598169.8612187639
230.6039912497890.6093798151480.09938345649040.5683838938260.08136559554740.04420226818480.133037732841-0.4230937164490.0347977641740.348537217967-0.117882068673-0.606001856028-0.552397441520.9288186914735.50425117318E-51.027484844090.0303446600603-0.1770383850011.241009583960.1008596235941.0071257916616.059031605164.5188578888102.474623803
240.2255487425360.2675987834670.006651007853170.2799749773450.0146760782175-0.003018086442050.097960148893-0.7680758688970.1734391922680.595039807798-0.0840934284149-0.6685030093760.1067037670440.7581116270892.22846642594E-51.386862241790.308458354312-0.228011557811.824564716910.3920130423751.3867214105619.468503646652.9094049366108.700629146
251.295194878730.476991898666-1.537926669731.005761609540.3679182384792.59587339788-0.516480078663-0.31751730465-0.9392548419790.246486061381-0.00479409233622-0.3048708590591.468493915760.619068561043-0.02298806828751.469050512360.1886891527120.2165299614760.7860560380380.2764756100871.16456473180.49439755359347.7829724154100.960815568
261.110492743760.131063615586-0.9264883567550.3630086654780.239499603691.07279161424-0.191057368278-0.263485504496-0.3229733654830.06130693203320.276674387717-0.1171826617050.4981166689840.299789765825-0.0001117630463120.9920657000050.0765869840910.1019018317330.6550998828070.06255611015160.7064988542860.27831847220761.980505239592.9890089279
270.44862730662-0.0767976900046-0.09617730584170.11323512994-0.03441065314420.276469336229-0.1053462154890.62573015139-0.2269503474110.2289835724340.09968400336620.725029885711.14012303559-1.34717447382-0.004078307875150.970473026029-0.2481185910080.05239925584110.922313684469-0.04499631713250.990650678729-7.882034825856.528730737379.8031773951
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 197 )AA1 - 1971 - 203
22chain 'A' and (resid 198 through 311 )AA198 - 311204 - 323
33chain 'A' and (resid 312 through 438 )AA312 - 438324 - 457
44chain 'B' and (resid 1 through 60 )BF1 - 601 - 64
55chain 'B' and (resid 61 through 88 )BF61 - 8865 - 92
66chain 'B' and (resid 89 through 180 )BF89 - 18093 - 187
77chain 'B' and (resid 181 through 215 )BF181 - 215188 - 223
88chain 'B' and (resid 216 through 273 )BF216 - 273224 - 279
99chain 'B' and (resid 274 through 295 )BF274 - 295280 - 299
1010chain 'B' and (resid 296 through 373 )BF296 - 373300 - 371
1111chain 'B' and (resid 374 through 401 )BF374 - 401372 - 399
1212chain 'B' and (resid 402 through 438 )BF402 - 438400 - 436
1313chain 'C' and (resid 1 through 199 )CN1 - 1991 - 205
1414chain 'C' and (resid 200 through 440 )CN200 - 440206 - 450
1515chain 'D' and (resid 1 through 88 )DS1 - 881 - 86
1616chain 'D' and (resid 89 through 238 )DS89 - 23887 - 237
1717chain 'D' and (resid 239 through 268 )DS239 - 268238 - 269
1818chain 'D' and (resid 269 through 400 )DS269 - 400270 - 389
1919chain 'D' and (resid 401 through 441 )DS401 - 441390 - 430
2020chain 'E' and (resid 6 through 46 )EV6 - 461 - 28
2121chain 'E' and (resid 47 through 142 )EV47 - 14229 - 127
2222chain 'F' and (resid 1 through 66 )FW1 - 661 - 66
2323chain 'F' and (resid 67 through 139 )FW67 - 13967 - 118
2424chain 'F' and (resid 140 through 176 )FW140 - 176119 - 152
2525chain 'F' and (resid 177 through 275 )FW177 - 275153 - 252
2626chain 'F' and (resid 276 through 339 )FW276 - 339253 - 318
2727chain 'F' and (resid 340 through 380 )FW340 - 380319 - 351

+
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