[English] 日本語
Yorodumi
- PDB-5s4t: Tubulin-Z328695024-complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5s4t
TitleTubulin-Z328695024-complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine LigaseTubulin—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 / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / 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 / neuron projection development / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
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. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / Chem-K1G / 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: 2.27 Å
AuthorsMuehlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.
Funding supportEuropean Union, Italy, Switzerland, 4items
OrganizationGrant numberCountry
iNEXT/Horizon 2020PID2692European Union
NEON/Regione LombardiaID239047 Italy
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation31030A_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Comprehensive Analysis of Binding Sites in Tubulin.
Authors: Muhlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionNov 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,75222
Polymers261,6316
Non-polymers3,12016
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.770, 158.420, 179.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: Q6B856
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein Tubulin-Tyrosine Ligase / Tubulin—tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 395 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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 / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-K1G / N,1-dimethyl-N-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 205.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.27→62.53 Å / Num. obs: 137603 / % possible obs: 99.8 % / Redundancy: 6.838 % / Biso Wilson estimate: 65.301 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.098 / Χ2: 1.021 / Net I/σ(I): 11.21 / Num. measured all: 940983 / Scaling rejects: 162
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.27-2.337.0972.4690.77134610085100530.342.66399.7
2.33-2.397.0641.7821.0169252982298030.4861.92399.8
2.39-2.466.9961.3721.3466872958195590.6151.48199.8
2.46-2.546.8961.0591.7363810927092530.7231.14599.8
2.54-2.626.7210.7882.2660677904690280.8090.85499.8
2.62-2.716.5320.6292.8157067875387360.8530.68499.8
2.71-2.826.7470.4663.7556742842184100.9230.50599.9
2.82-2.937.0880.3435.1557587813781250.9590.3799.9
2.93-3.067.0060.2457.0254826783378260.9770.26599.9
3.06-3.216.9520.1769.4751643744074280.9870.1999.8
3.21-3.386.7620.13112.2448142712971190.9920.14299.9
3.38-3.596.4720.09815.443659675167460.9950.10799.9
3.59-3.846.9120.0819.3643686632563200.9970.08699.9
3.84-4.147.0450.06125.3841856594259410.9980.065100
4.14-4.546.8860.04830.437701547754750.9980.052100
4.54-5.086.4240.04431.9731762494649440.9980.048100
5.08-5.866.5950.04631.2329165442644220.9980.0599.9
5.86-7.186.8970.04533.0925884375337530.9980.049100
7.18-10.156.2640.03540.7618547296329610.9990.03899.9
10.15-62.536.3250.03247.7110759172017010.9980.03598.9

-
Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5lxt
Resolution: 2.27→62.53 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 6768 4.92 %
Rwork0.2058 130809 -
obs0.2078 137577 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.56 Å2 / Biso mean: 78.158 Å2 / Biso min: 38.92 Å2
Refinement stepCycle: final / Resolution: 2.27→62.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17425 0 202 379 18006
Biso mean--72.92 63.2 -
Num. residues----2200
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 (%)
2.27-2.30.38162070.371142954502100
2.3-2.320.36292570.3642904547100
2.32-2.350.38772270.345442844511100
2.35-2.380.38172330.331743234556100
2.38-2.410.37032410.326843164557100
2.41-2.450.37062310.321142764507100
2.45-2.480.3322510.304242844535100
2.48-2.520.33282220.299543194541100
2.52-2.560.37162340.292643274561100
2.56-2.60.35152370.276643244561100
2.6-2.640.29992070.273143254532100
2.64-2.690.31412420.267743174559100
2.69-2.740.30551990.261543494548100
2.74-2.80.31932340.2643094543100
2.8-2.860.31372510.251642954546100
2.86-2.930.28472160.26143784594100
2.93-30.32362300.24843504580100
3-3.080.30252130.242143604573100
3.08-3.170.26472130.230443614574100
3.17-3.270.26752150.233443644579100
3.27-3.390.28582160.225443694585100
3.39-3.530.25772040.220543984602100
3.53-3.690.23892290.209243484577100
3.69-3.880.22882220.188144034625100
3.88-4.120.20752100.173143904600100
4.12-4.440.20682360.165744014637100
4.44-4.890.18572010.154244474648100
4.89-5.60.22552360.173644514687100
5.6-7.050.23232240.194745004724100
7.05-62.530.18172300.16144656488699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.9356-0.441-0.02395.10581.11563.6316-0.01480.12220.2907-0.49310.303-0.3392-0.86570.3469-0.29910.6287-0.12990.1380.5662-0.13540.509432.163589.84250.4621
22.6447-0.6439-2.36354.8617-0.22982.73180.0866-0.3409-0.1450.475-0.0692-0.20670.19740.2328-0.00920.54080.0605-0.0530.5537-0.13950.48530.063774.457158.7814
31.8535-0.15420.58594.750.99215.4270.0951-0.02240.06790.375-0.01320.328-0.2244-0.2399-0.08670.45240.04940.07170.4188-0.10280.482817.163184.83366.5547
41.4333-0.39550.24576.71241.43632.5113-0.0452-0.19930.21770.84030.10160.2942-0.0982-0.1006-0.07290.65140.01690.11740.593-0.07890.510319.095983.607972.9663
52.28870.54180.84475.93654.33056.62-0.0835-0.2730.01260.78770.4877-0.59630.71420.9535-0.31910.56340.1604-0.06890.5118-0.09670.587132.557162.541961.4168
66.101-1.5378-0.9637.87040.78594.96270.17970.2530.8529-0.2569-0.12370.3651-1.0607-0.14440.00590.57690.02030.00150.40170.0070.539415.972370.134818.9509
72.43560.5292-0.2392.43031.51023.90370.0343-0.00270.0997-0.0279-0.03560.0687-0.24780.002-0.01590.38970.01270.00710.4735-0.08770.46520.261556.384625.2749
85.5003-3.02561.47834.7447-0.64334.2784-0.294-0.0388-0.13750.29570.03310.653-0.2665-1.23480.23770.57990.01890.09490.7798-0.1930.58665.778860.262642.223
91.0208-1.0578-0.68444.60222.57355.15450.0081-0.3267-0.0740.78160.1159-0.07910.74120.4271-0.13980.4513-0.0692-0.02340.5629-0.06480.524821.044342.00331.4124
101.6753-0.3542-0.07933.28120.31132.0379-0.0490.20130.0749-0.31630.12130.0376-0.16660.1034-0.06720.4276-0.07760.02520.5136-0.05930.440820.312733.1709-12.0346
111.4111-0.7899-0.02691.79110.98261.9233-0.0336-0.01210.0310.1018-0.04470.1260.025-0.24260.07730.3588-0.06320.04550.4264-0.03610.43917.98926.08133.1303
125.2331-2.0311-0.01326.9494-0.57350.555-0.03820.69070.1676-0.87010.1601-0.02030.0584-0.1812-0.12940.7179-0.12980.07620.935-0.04350.40617.36429.8711-44.1389
132.18530.0846-0.56131.77830.03722.7201-0.09770.4593-0.2257-0.33140.1789-0.29930.28460.0499-0.08180.6477-0.0690.09090.7503-0.23010.552922.9127-2.1501-34.3193
141.056-1.5126-0.69913.98490.63870.54260.16030.3058-0.5504-0.5995-0.29490.71470.4159-0.65030.12520.7259-0.1396-0.03850.9789-0.26260.69322.0086-6.1683-25.274
153.2687-0.9605-0.30362.2337-0.11963.153-0.21020.4072-0.3125-0.08420.13940.24830.2163-0.45470.07940.5978-0.15910.0310.5863-0.15710.52848.8187-1.5626-20.969
165.26740.3674-2.75561.7385-1.54442.6396-0.43070.1215-0.7540.21370.1107-0.09630.90340.24820.14950.92940.09690.02460.6733-0.26080.921930.5328-17.0598-24.6647
175.7361-3.47590.35487.56151.48843.0134-0.0244-0.69470.26681.37780.3332-0.7232-0.17880.14-0.31231.1428-0.1508-0.07960.9296-0.20370.775127.80793.27681.3948
180.1682-0.4478-0.80525.7456.147.0912-0.1593-0.0943-0.03880.87550.7789-0.53890.98351.1643-0.73510.61360.11490.02140.9761-0.25360.863543.158428.18993.9526
194.85160.8806-1.51616.07590.83055.9401-0.41930.4816-0.7782-0.1240.211-0.22931.6572-0.30850.14441.0635-0.16610.12890.7183-0.14880.64736.471555.082269.5309
205.43331.20653.61434.7351-2.34545.940.1293-0.55270.19410.4162-0.38-0.873-0.3481.99250.24250.8330.0629-0.06751.28950.01730.746116.574264.5665102.483
214.42271.07231.81254.2852-0.83835.4668-0.0105-0.5844-0.68690.7919-0.2142-0.85571.13081.91260.19521.14740.39130.03771.23680.22540.91111.543752.6396105.6187
222.52660.7291-1.12193.772-0.89282.4489-0.53880.0362-0.87250.28540.2309-0.31611.20490.04280.17581.32830.1020.26380.63620.07950.9571-2.205450.27199.23
233.1734-0.4948-2.11730.31671.2356.6374-0.19950.136-0.51940.07460.1593-0.05491.08860.0138-0.0030.99960.01540.06570.54280.00980.74981.082358.60487.4488
246.6724-5.0323-3.49775.81772.07152.91540.15280.7976-0.3772-0.16090.35610.5018-0.5571-1.0753-0.39010.6556-0.1020.07680.9646-0.03440.6771-8.161563.589779.1723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 160 )A1 - 160
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 199 )A161 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 311 )A200 - 311
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 401 )A312 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 438 )A402 - 438
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 88 )B1 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 259 )B89 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 372 )B260 - 372
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 438 )B373 - 438
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 197 )C1 - 197
11X-RAY DIFFRACTION11chain 'C' and (resid 198 through 440 )C198 - 440
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 88 )D1 - 88
13X-RAY DIFFRACTION13chain 'D' and (resid 89 through 273 )D89 - 273
14X-RAY DIFFRACTION14chain 'D' and (resid 274 through 311 )D274 - 311
15X-RAY DIFFRACTION15chain 'D' and (resid 312 through 399 )D312 - 399
16X-RAY DIFFRACTION16chain 'D' and (resid 400 through 441 )D400 - 441
17X-RAY DIFFRACTION17chain 'E' and (resid 6 through 46 )E6 - 46
18X-RAY DIFFRACTION18chain 'E' and (resid 47 through 143 )E47 - 143
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 66 )F1 - 66
20X-RAY DIFFRACTION20chain 'F' and (resid 67 through 140 )F67 - 140
21X-RAY DIFFRACTION21chain 'F' and (resid 141 through 207 )F141 - 207
22X-RAY DIFFRACTION22chain 'F' and (resid 208 through 297 )F208 - 297
23X-RAY DIFFRACTION23chain 'F' and (resid 298 through 354 )F298 - 354
24X-RAY DIFFRACTION24chain 'F' and (resid 355 through 382 )F355 - 382

+
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