[English] 日本語
Yorodumi
- PDB-8riw: T2R-TTL-1-L01 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8riw
TitleT2R-TTL-1-L01 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 / 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 / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase / 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 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / ATP binding / 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. ...: / 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 / 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: 2.57 Å
AuthorsProta, A.E.P. / Boiarska, Z. / Homer, J.A. / Steinmetz, M.O. / Moses, J.E.
Funding supportEuropean Union, Switzerland, United States, Australia, 4items
OrganizationGrant numberCountry
European Union (EU)860070 TubInTrainEuropean Union
Swiss National Science Foundation310030_192566 Switzerland
National Institutes of Health/National Cancer Institute (NIH/NCI)5P30CA045508 United States
Australian Research Council (ARC)FT170100156 Australia
Citation
Journal: Chem Sci / Year: 2024
Title: Modular synthesis of functional libraries by accelerated SuFEx click chemistry.
Authors: Homer, J.A. / Koelln, R.A. / Barrow, A.S. / Gialelis, T.L. / Boiarska, Z. / Steinohrt, N.S. / Lee, E.F. / Yang, W.H. / Johnson, R.M. / Chung, T. / Habowski, A.N. / Vishwakarma, D.S. / ...Authors: Homer, J.A. / Koelln, R.A. / Barrow, A.S. / Gialelis, T.L. / Boiarska, Z. / Steinohrt, N.S. / Lee, E.F. / Yang, W.H. / Johnson, R.M. / Chung, T. / Habowski, A.N. / Vishwakarma, D.S. / Bhunia, D. / Avanzi, C. / Moorhouse, A.D. / Jackson, M. / Tuveson, D.A. / Lyons, S.K. / Lukey, M.J. / Fairlie, W.D. / Haider, S.M. / Steinmetz, M.O. / Prota, A.E. / Moses, J.E.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
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)265,54327
Polymers261,5746
Non-polymers3,96921
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23280 Å2
ΔGint-132 kcal/mol
Surface area80490 Å2
Unit cell
Length a, b, c (Å)104.687, 156.104, 182.528
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) / 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) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16787.111 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: A0A8V0Z8P0

-
Non-polymers , 10 types, 163 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#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.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-A1H00 / (2-methyl-1~{H}-indol-5-yl) 3,4,5-trimethoxybenzenesulfonate


Mass: 377.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19NO6S / Feature type: SUBJECT OF INVESTIGATION
#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: 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.: 142 / 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: 56.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 4% PEG 4K, 9-10% glycerol, 30 mM MgCl2, 30 mM CaCl2, 5 mM 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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→47.99 Å / Num. obs: 181996 / % possible obs: 99.28 % / Redundancy: 7.3 % / Biso Wilson estimate: 81.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1033 / Rpim(I) all: 0.04086 / Rrim(I) all: 0.1112 / Net I/σ(I): 10.58
Reflection shellResolution: 2.57→2.6 Å / Redundancy: 7.3 % / Rmerge(I) obs: 3.169 / Mean I/σ(I) obs: 0.51 / Num. unique obs: 6020 / CC1/2: 0.175 / Rpim(I) all: 1.242 / Rrim(I) all: 3.406

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5058refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.57→47.99 Å / SU ML: 0.4634 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1788
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 9119 5.02 %
Rwork0.1887 172693 -
obs0.1907 181812 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.42 Å2
Refinement stepCycle: LAST / Resolution: 2.57→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17369 0 245 142 17756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001718017
X-RAY DIFFRACTIONf_angle_d0.449624422
X-RAY DIFFRACTIONf_chiral_restr0.03992651
X-RAY DIFFRACTIONf_plane_restr0.00333160
X-RAY DIFFRACTIONf_dihedral_angle_d12.28976638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.60.42992970.41255628X-RAY DIFFRACTION97.21
2.6-2.630.4113060.40265791X-RAY DIFFRACTION99.53
2.63-2.670.38612980.37845755X-RAY DIFFRACTION99.49
2.67-2.70.40963040.36215833X-RAY DIFFRACTION99.66
2.7-2.740.3752990.34055765X-RAY DIFFRACTION99.74
2.74-2.770.35043060.32085786X-RAY DIFFRACTION99.8
2.77-2.810.34193090.30865787X-RAY DIFFRACTION99.82
2.81-2.850.31833100.28515796X-RAY DIFFRACTION99.75
2.85-2.90.32453070.27795798X-RAY DIFFRACTION99.74
2.9-2.950.27353030.27785773X-RAY DIFFRACTION99.74
2.95-30.32043040.26835800X-RAY DIFFRACTION99.64
3-3.050.31993050.27975745X-RAY DIFFRACTION99.56
3.05-3.110.30343040.27875785X-RAY DIFFRACTION99.79
3.11-3.170.28363080.26375767X-RAY DIFFRACTION99.79
3.17-3.240.27983070.24365800X-RAY DIFFRACTION99.62
3.24-3.320.23593050.22125764X-RAY DIFFRACTION99.66
3.32-3.40.25393000.21485782X-RAY DIFFRACTION99.53
3.4-3.490.24523070.25782X-RAY DIFFRACTION99.43
3.49-3.60.24233040.19415660X-RAY DIFFRACTION97.96
3.6-3.710.21642880.1815457X-RAY DIFFRACTION94.55
3.71-3.840.2193040.18155796X-RAY DIFFRACTION99.48
3.84-40.21483070.16615760X-RAY DIFFRACTION99.59
4-4.180.20433110.16085786X-RAY DIFFRACTION99.77
4.18-4.40.19673040.15075790X-RAY DIFFRACTION99.97
4.4-4.680.17743080.14425822X-RAY DIFFRACTION99.98
4.68-5.040.19153060.1465803X-RAY DIFFRACTION99.98
5.04-5.540.2253080.16455784X-RAY DIFFRACTION99.82
5.54-6.340.21223080.18075752X-RAY DIFFRACTION99.74
6.34-7.990.20432890.17115566X-RAY DIFFRACTION95.65
7.99-47.990.19283030.14875780X-RAY DIFFRACTION99.59
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)
12.612878766520.0145761160493-1.150565122165.0774662932-0.8708491355852.83413893830.09933975406310.5237695045560.410327669323-0.696041896370.233318086459-0.288471392227-1.111445666830.264756342372-0.3736815792431.13118508785-0.1786626526820.2129541623340.906393851691-0.2176156253330.85043639769928.695737834796.047206816552.9964512202
21.55202488744-1.00635065739-0.009992452314623.4637520091.786802065453.89608963176-0.0840076309130.3513709463680.0868099271039-0.5084720484150.623832047685-0.717623293382-0.6436124083260.868121792436-0.4767608974950.724657370487-0.2155988787460.2171870177041.06516157772-0.3719151963820.93523966285835.783900921982.681322324749.7025811196
31.216269149890.696840720834-1.194930640878.180317616322.657401843973.117041279120.158104738130.212031228117-0.4753619534330.7027325566430.215111979484-0.7039452536140.5572692265290.817997718421-0.2606110475470.6502261170170.026074960266-0.06090634297590.940385511915-0.2910840623050.76858554028730.25390755673.742768181959.2012412553
43.33363451798-1.4862204960.4556973415044.625918214390.7493258144895.768375398260.034737332776-0.0317465738603-0.006890127092920.04524583017830.167808158899-0.0464092123717-0.4334444191570.0294769435055-0.1955465015570.6759355592880.06486980070920.1441859927440.738861815481-0.1205904395570.7137468761319.714369059185.311493308663.5314872984
51.626681503210.572180977829-0.2054399496294.168155109010.8238477051145.606258993440.0963421723026-0.309410597734-0.06045216530470.5498865853440.02102535659130.828321488898-0.210003715392-0.513569528835-0.06078135378550.8046409842420.002819865960980.09565870580760.751634790721-0.1428867153460.7189234824314.498864449483.582654243671.2815104814
60.9502565173350.6509070205531.342684080816.291362525461.572625655952.13179669859-0.0354718216773-0.1743545184380.248192700861.60659546271-0.0873403702131.145667419480.186912494897-0.2333007632740.08285665480711.154712530590.04355062413220.2964490451840.722720901483-0.1935613843050.77260022300517.264522386.509330674981.1699105735
71.11512887562-0.390960733655-0.7761632972975.139175269413.395656186214.3441745655-0.0148204353638-0.0415424920127-0.06349872254930.7692858503280.337580282786-0.03514571691010.3781396378940.483703197952-0.3506167406710.7294425114250.0216285911578-0.00550130605590.787008900105-0.1566731332480.7681224387722.681858155675.781228277666.5721984894
87.27678173959-0.787630510536-0.9811394560785.667955174755.638718124526.14276737628-0.199668868447-0.302887561575-0.9465954189581.73239952048-0.2144987428940.1964396934442.040388797810.6684346481010.2705465797661.139436776940.246056466736-0.1726802912991.08150417408-0.3332767884260.98715659819932.249008006263.078907730769.171640551
95.43014162941-1.34884643861-0.2809287199125.384354849760.9370313141513.472632500620.2172371222090.3444833057520.728576886156-0.651034052288-0.18933959180.0823374344394-0.729366382256-0.17844316714-0.0336953256690.7101995709280.06012924490080.03886531136890.6285439347970.06284209565260.67378899741216.923604057568.102998280217.5907753775
102.42253226621-0.883585369026-0.7277129350813.271631468541.489522960084.380920665810.05685978624320.001741003650870.282268071167-0.1985637309990.0258245538207-0.00926243426155-0.3243458773780.0511326806861-0.09556918980420.495530745980.02695068220850.03437312447660.587080542866-0.1150069525960.62846365522519.690011088956.035631739426.239874446
114.60505629034-1.940901451991.394146218463.55731496449-0.2594978115833.71503808881-0.105823725946-0.475740654238-0.06361459724540.254285130990.1008922253960.3376643061390.0566812281438-0.7059236489890.003937189817130.6453696651540.02487036688910.0743055328650.862773654319-0.235143368340.7217314169256.0158520008660.332072767142.2329659789
120.17431409197-0.964376903-0.6120297185064.711459504052.727839385793.58580646754-0.123586483228-0.204957232793-0.1399828193810.790545125170.09440733976340.02505683658210.8232733544110.340062661728-0.05167272856150.647984789775-0.0219260148917-0.01637261260760.780129582271-0.0680963686220.7070220051921.044064606339.798481629331.8454401907
134.46473866794-2.27631159451-0.09001820477335.457331423691.153318649492.39301519852-0.003909636776630.4766523966320.403958264141-0.624920895883-0.137032818190.285616682127-0.509324486678-0.08467048508320.1119586536830.735978989146-0.0839531817397-0.01324927131990.7402813950410.05919266409780.60523139941715.129002743538.4944755552-15.966251178
141.18323867576-1.04189886454-0.1290009075115.253064040091.558346277912.93036096365-0.06628660482930.3250718092010.0158421788779-0.2056693881480.170963833443-0.176838462115-0.08615354301640.30081035172-0.08288496131420.575505160077-0.07440670286040.0008344746705690.698749594616-0.0831101121060.68213994087724.487587841125.9296577123-7.57619226225
152.5480663376-0.690297287231.089292369512.033842970780.7611058888643.989815900510.146695156052-0.1064136925870.03773913440770.0102477172974-0.2946579074270.4929789315610.0666408115762-0.6949313041620.1209712107970.477904522328-0.0536218344080.05689399881410.632024672925-0.1103911453480.6380358087333.2272955952428.3828980890.600815192646
161.4922807566-0.391716054461-0.03110341303132.67475030391.26898858452.43417544926-0.192826144832-0.152471094118-0.08050775924940.3110682769420.1294998188670.2299098310050.252327296618-0.07939447122040.07687932302550.607414834857-0.1008031953850.03546332687510.619212816068-0.04589543353340.67843160335610.998393278323.0865462935.84212571273
175.14747416751-2.06857153838-0.3576404302023.528175386550.5870699290784.61201693722-0.2985954052441.159315690180.356865997426-0.55111093520.2369615187790.593303435304-0.154489462528-0.7859724529660.1105585820241.1797184477-0.323029102767-0.1610590382561.473972725480.04767584634060.78574447383415.495297945410.6398860693-41.664058843
183.090420494530.148254856978-0.2037596725282.13858449862-0.2076190904732.92284048996-0.5570289529220.986284975042-0.458441463124-1.006383287060.421016080988-0.2057464528150.3492805126070.07533108559990.09570077207651.25217073771-0.2570533188470.1411715773971.20510853043-0.4065131705480.81153761114726.7131366944-4.09917499636-37.8357539185
191.95563607390.156533678324-0.4120499550342.892365968060.3624762078082.62778531676-0.3087421742930.526614371953-0.240919593237-0.2890517432950.2454341829520.4311583735730.402831357665-0.5315067388990.04953748712760.847673027889-0.192956166337-0.0274802079590.95677298188-0.211329475030.8004136665558.97472829961-3.49405638547-24.2251226032
204.98189728495-1.03924875291-0.3237248873532.87824233597-1.615423438591.08915764626-0.1439904645320.437547713205-0.960012305123-0.130508076274-0.03829933424740.1658360769990.6471879338860.05950338465440.08068483559841.3269874481-0.06823184109540.1552835998110.896640097645-0.3879999492111.2131088464830.3796472273-17.1904094351-22.7506712422
213.35866197405-0.915103392792-2.145475438213.891994482642.28191721334.042983859980.00374827376028-0.8999524124060.826504706121.259079862830.115497275163-0.154087685814-0.3013956753690.919114748163-0.07542654521441.42377000828-0.246034227504-0.1525477555981.30638115255-0.2494842312311.0078548207428.376424953591.688105376482.5865725161
220.462810423482-0.180471345899-0.6693856040692.086225319472.58880736922.92201606395-0.175628315891-0.06680714419960.02934096532670.5786307388860.49832369493-0.3726944095590.700179851580.691849378424-0.480949084510.9337663190510.138734552328-0.02698672267031.06845468392-0.2727168977961.0149970446542.762202710127.52150074794.30869305181
235.98138700710.76250891585-1.473996814793.674319285130.3794817795434.84347776346-0.07086725708010.489726233747-1.028038909570.6969623391170.1904530652280.1401895236611.62936346765-0.920037713457-0.1109815970371.57625166951-0.1724693487830.1564765788171.17216550326-0.1770379967611.093032793916.2121295297254.252710434469.4294430794
247.20585255172.20652508113-0.2218517051395.65189669315-5.485140030065.896889414360.221269321493-0.726705745589-0.2060665083640.996431702047-0.391763112283-0.647169583575-1.184945564561.259057259930.1051606143971.503972917970.02379254479490.03655643275391.482057230840.1856981681971.1293549368511.302772589564.570288754997.2072671358
254.989805153371.80676655435-2.436103071.09723520375-0.4383387339662.73788572727-0.169456537139-1.33543497917-1.285934751820.403657156824-0.419284166721-0.5250687940660.3717192391242.875078547940.594023873841.343787301170.316985699465-0.2265760581572.098225337210.3924074469471.4781244976720.933646082655.1955923845108.269466238
262.654805904331.11052638156-0.002248148387471.57543219816-0.5626925658095.47078621396-0.172012941095-0.216523206411-0.744574108701-0.0443806412720.0327901841829-0.1031197249171.438216692250.3737986116040.07684923201311.731254734990.2821565812030.3089744859331.179453201440.2454729199811.440144488922.1908852156950.552584959199.1918866018
271.92351132717-0.401738180673-0.7331865505131.926794891530.216894307251.3773661137-0.9587646006550.00307615988007-1.60074711936-0.04470424160680.248167297745-0.3287644453631.391662235640.3709699681050.7508002675712.533336619780.150593741230.5089533244271.484537348080.2025672410932.08664186093-2.0134549342740.5236409599100.799029178
284.017359823791.47957806194-3.037174235121.73688290108-2.023837034546.34109277589-0.27930313046-0.0641000482172-0.5102993613350.006604315984050.3528496784680.1573820156890.914788500702-0.0448718359118-0.04685320045771.467085891220.002135084678950.1514664027540.9318523297320.03725138679521.12378714908-2.0571317650958.992725130388.7641697873
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 79 )AA1 - 791 - 79
22chain 'A' and (resid 80 through 160 )AA80 - 16080 - 160
33chain 'A' and (resid 161 through 199 )AA161 - 199161 - 199
44chain 'A' and (resid 200 through 259 )AA200 - 259200 - 259
55chain 'A' and (resid 260 through 306 )AA260 - 306260 - 306
66chain 'A' and (resid 307 through 338 )AA307 - 338307 - 338
77chain 'A' and (resid 339 through 414 )AA339 - 414339 - 414
88chain 'A' and (resid 415 through 438 )AA415 - 438415 - 438
99chain 'B' and (resid 1 through 102 )BG1 - 1021 - 100
1010chain 'B' and (resid 103 through 259 )BG103 - 259101 - 257
1111chain 'B' and (resid 260 through 373 )BG260 - 373258 - 359
1212chain 'B' and (resid 374 through 437 )BG374 - 437360 - 423
1313chain 'C' and (resid 1 through 102 )CO1 - 1021 - 102
1414chain 'C' and (resid 103 through 199 )CO103 - 199103 - 199
1515chain 'C' and (resid 200 through 311 )CO200 - 311200 - 311
1616chain 'C' and (resid 312 through 440 )CO312 - 440312 - 440
1717chain 'D' and (resid 1 through 64 )DT1 - 641 - 62
1818chain 'D' and (resid 65 through 214 )DT65 - 21463 - 212
1919chain 'D' and (resid 215 through 401 )DT215 - 401213 - 387
2020chain 'D' and (resid 402 through 441 )DT402 - 441388 - 427
2121chain 'E' and (resid 6 through 46 )EX6 - 461 - 26
2222chain 'E' and (resid 47 through 143 )EX47 - 14327 - 123
2323chain 'F' and (resid 1 through 66 )FY1 - 661 - 66
2424chain 'F' and (resid 67 through 96 )FY67 - 9667 - 96
2525chain 'F' and (resid 97 through 174 )FY97 - 17497 - 152
2626chain 'F' and (resid 175 through 235 )FY175 - 235153 - 208
2727chain 'F' and (resid 236 through 274 )FY236 - 274209 - 247
2828chain 'F' and (resid 275 through 381 )FY275 - 381248 - 344

+
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://pdbjlc1.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