[English] 日本語
Yorodumi
- PDB-5sb4: Tubulin-todalam-8-complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5sb4
TitleTubulin-todalam-8-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 / microtubule-based process / 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 / regulation of microtubule polymerization or depolymerization / microtubule-based process / 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 / 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
Chem-4B6 / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsMuehlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
Funding support Italy, Switzerland, 3items
OrganizationGrant numberCountry
NEON/Regione LombardiaID239047 Italy
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action.
Authors: Muhlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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)264,87422
Polymers261,6316
Non-polymers3,24216
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.575, 157.329, 180.728
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, 346 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-4B6 / N-{4-[2-(2-fluoroanilino)-1,3-thiazol-4-yl]phenyl}acetamide


Mass: 327.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14FN3OS / 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.: 330 / 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: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.5→49.62 Å / Num. obs: 103407 / % possible obs: 99.9 % / Redundancy: 13.557 % / Biso Wilson estimate: 52.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.277 / Rrim(I) all: 0.287 / Χ2: 0.751 / Net I/σ(I): 10.14 / Num. measured all: 1401930 / Scaling rejects: 87
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
2.5-2.5713.2743.2650.76100193759675480.273.39599.4
2.57-2.6413.5572.5131.0699696735573540.4062.611100
2.64-2.7113.2852.1631.2795347717771770.4742.25100
2.71-2.813.3211.7571.692808696769670.5911.827100
2.8-2.8913.9861.4482.0594865678467830.6941.503100
2.89-2.9913.5481.1582.5888996656965690.781.203100
2.99-3.113.4170.843.5884918632963290.8710.873100
3.1-3.2314.2840.6844.5787058609560950.920.71100
3.23-3.3714.1730.515683368588258820.9570.534100
3.37-3.5413.9690.3688.2877749556655660.9750.382100
3.54-3.7313.6880.2711.0973301535553550.9850.28100
3.73-3.9512.7450.18414.764374505250510.9930.192100
3.95-4.2313.870.14318.9166231477447750.9960.149100
4.23-4.5713.0210.10423.6357761443644360.9980.108100
4.57-513.9020.09226.9957302412341220.9980.096100
5-5.5913.9510.10724.0152078373337330.9970.111100
5.59-6.4613.4810.11422.544715331733170.9970.118100
6.46-7.9112.6720.07929.0536027284328430.9980.082100
7.91-11.1912.8970.04744.8528593221722170.9990.049100
11.19-49.6212.8490.04350.6916550130712880.9990.04598.5

-
Processing

Software
NameVersionClassificationNB
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT
Resolution: 2.5→49.62 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.18 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 9954 5.01 %
Rwork0.1983 188885 -
obs0.1999 198839 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.16 Å2 / Biso mean: 66.7152 Å2 / Biso min: 31.04 Å2
Refinement stepCycle: final / Resolution: 2.5→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17268 0 195 330 17793
Biso mean--59.72 53.54 -
Num. residues----2182
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 (%)
2.5-2.530.35773280.3586202653098
2.53-2.560.37343300.34763016631100
2.56-2.590.34623330.326663226655100
2.59-2.620.34823310.326362956626100
2.62-2.660.37053290.315262576586100
2.66-2.690.33743350.319363796714100
2.69-2.730.34213290.323962286557100
2.73-2.770.30393330.300863296662100
2.77-2.820.29783350.292463426677100
2.82-2.860.31673310.281662626593100
2.86-2.910.31923320.275863076639100
2.91-2.970.30583300.266962986628100
2.97-3.020.29453310.251262736604100
3.02-3.080.29693340.242163176651100
3.08-3.150.23853290.236763396668100
3.15-3.220.26463270.251362236550100
3.22-3.310.26963310.226663356666100
3.31-3.390.26553360.222163046640100
3.39-3.490.21973350.204563406675100
3.49-3.610.22653330.18762446577100
3.61-3.740.21133400.183363546694100
3.74-3.890.20773290.171462466575100
3.89-4.060.19023330.162862946627100
4.06-4.280.18993310.151863076638100
4.28-4.540.17923360.139763156651100
4.54-4.890.17963350.135762816616100
4.89-5.390.18113350.155862916626100
5.39-6.160.27023310.172263226653100
6.17-7.760.18583310.171162796610100
7.76-49.620.15443210.146162996620100
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)
11.35620.0366-0.19483.60590.88092.23170.01880.05290.2221-0.65250.3235-0.4458-0.81680.4254-0.33030.6117-0.15230.13370.5157-0.16020.472832.23989.43551.041
21.4620.1652-1.33164.04320.40912.62990.1407-0.0058-0.0060.60420.0149-0.00110.40590.3917-0.10120.44560.02680.00650.4748-0.15280.470330.12674.01759.132
31.89170.07990.27583.24530.79063.86030.1091-0.05690.09140.2976-0.08690.2003-0.1742-0.0615-0.0210.43030.01370.0740.3529-0.10150.454917.12184.32867.005
40.8214-0.09330.40113.70551.63433.0057-0.0778-0.17130.09650.73240.00540.3418-0.0048-0.05880.06580.4831-0.03230.12320.475-0.08110.473219.0282.99873.395
51.52290.1319-0.06353.21782.00824.4558-0.0946-0.0718-0.36170.67780.3873-0.39730.67221.2125-0.29970.45510.1329-0.10290.5217-0.09590.504132.63261.87660.998
63.7234-1.2914-0.79153.19190.17293.20610.04880.1230.4962-0.23630.02340.0742-0.7393-0.2465-0.07570.53460.05230.0080.3415-0.01660.500716.22469.97919.317
71.519-0.24-0.39322.10921.27043.4920.01730.00820.2099-0.1467-0.0240.087-0.2638-0.0718-0.02810.2860.0246-0.00320.3548-0.06880.39320.32455.93325.377
82.5527-0.47261.08892.51360.113.1753-0.2366-0.14270.16680.1997-0.04830.4026-0.0961-0.87890.2620.440.05350.04860.6752-0.18970.51946.27360.00542.744
90.7999-0.36720.46223.23610.86693.1285-0.0859-0.1125-0.13870.64790.02210.09340.67210.12330.01710.3245-0.04090.01010.3791-0.02920.352321.00140.16932.099
101.089-0.34930.16953.34630.31451.6299-0.05860.17240.0559-0.3560.0843-0.0363-0.17120.1767-0.01920.3502-0.08670.02980.4417-0.02990.380520.15732.927-11.986
110.81-0.32160.07581.63670.9961.7625-0.021-0.04870.07720.0294-0.06060.15820.0434-0.19530.07820.2802-0.06950.04190.3382-0.02580.35827.77825.8583.144
123.3682-1.00440.32383.502-0.04811.8336-0.06340.53070.169-0.65520.1934-0.0091-0.0265-0.0733-0.12230.7042-0.14350.03440.8476-0.05670.426717.2869.525-43.914
131.922-0.0199-0.36671.46260.02972.3047-0.12760.371-0.1561-0.41220.2062-0.22080.31330.2541-0.07490.6058-0.04950.08550.604-0.19110.467622.75-2.517-34.036
142.7548-2.3445-0.22583.2888-0.3030.4970.12070.1534-0.1799-0.5676-0.29010.62040.4207-0.70930.14080.6993-0.1723-0.02950.8079-0.20540.63912.168-6.372-24.703
151.6243-0.2425-0.25131.2482-0.13442.6065-0.15930.2295-0.2387-0.0960.13080.07070.2194-0.28260.03810.4999-0.09980.03390.4541-0.12410.37528.621-1.86-20.765
163.4634-0.6879-1.3631.364-1.11692.2953-0.20640.1827-0.8807-0.0365-0.11710.0610.59730.3110.26220.89520.01140.07910.6428-0.24650.75230.231-17.392-24.409
172.2276-1.0147-0.39652.69530.70470.8533-0.0634-0.26150.07550.72790.2388-0.33310.18240.5361-0.16311.0246-0.0554-0.04640.7604-0.23070.64727.56392.40582.113
180.2097-0.2645-0.46880.18330.4280.7655-0.0668-0.0207-0.01060.26510.4972-0.45270.4020.7252-0.44830.53040.08830.01690.7987-0.25160.680143.03427.8184.215
192.83420.2757-1.95243.11170.35374.001-0.32990.3906-0.5915-0.20180.0203-0.0421.0394-0.47840.27080.8381-0.10150.12140.5338-0.1170.60156.10454.67369.672
203.36490.12262.00822.3-2.30144.4945-0.131-0.5709-0.00470.4483-0.3779-0.8972-0.29631.44380.44960.72880.0662-0.11831.18170.09390.746715.59663.872103.054
212.8033-0.26911.11762.4907-0.40972.4851-0.2307-0.6563-0.6340.702-0.3957-0.76560.91441.52120.54891.11810.26320.06951.23370.4110.972310.86551.505105.726
220.43320.4978-0.47180.8189-0.32920.6632-0.4602-0.0783-0.75120.11160.0481-0.26480.94660.06820.21721.23790.12310.2880.52810.12730.9425-3.17249.98998.708
232.86380.1984-1.56280.7985-0.14973.2385-0.3141-0.0336-0.46970.07350.1784-0.08510.6366-0.04850.11370.8139-0.01850.12190.4629-0.03010.59661.05757.96587.726
242.5196-0.2807-0.0762.6844-1.14238.6058-0.15060.1502-0.70470.161-0.2150.11180.347-0.56420.35690.6616-0.06030.02080.58080.04260.6828-3.87259.13283.27
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:160 )A1 - 160
2X-RAY DIFFRACTION2( CHAIN A AND RESID 161:199 )A161 - 199
3X-RAY DIFFRACTION3( CHAIN A AND RESID 200:311 )A200 - 311
4X-RAY DIFFRACTION4( CHAIN A AND RESID 312:401 )A312 - 401
5X-RAY DIFFRACTION5( CHAIN A AND RESID 402:437 )A402 - 437
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:88 )B1 - 88
7X-RAY DIFFRACTION7( CHAIN B AND RESID 89:259 )B89 - 259
8X-RAY DIFFRACTION8( CHAIN B AND RESID 260:372 )B260 - 372
9X-RAY DIFFRACTION9( CHAIN B AND RESID 373:437 )B373 - 437
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:197 )C1 - 197
11X-RAY DIFFRACTION11( CHAIN C AND RESID 198:440 )C198 - 440
12X-RAY DIFFRACTION12( CHAIN D AND RESID 1:88 )D1 - 88
13X-RAY DIFFRACTION13( CHAIN D AND RESID 89:273 )D89 - 273
14X-RAY DIFFRACTION14( CHAIN D AND RESID 274:311 )D274 - 311
15X-RAY DIFFRACTION15( CHAIN D AND RESID 312:399 )D312 - 399
16X-RAY DIFFRACTION16( CHAIN D AND RESID 400:441 )D400 - 441
17X-RAY DIFFRACTION17( CHAIN E AND RESID 6:46 )E6 - 46
18X-RAY DIFFRACTION18( CHAIN E AND RESID 47:143 )E47 - 143
19X-RAY DIFFRACTION19( CHAIN F AND RESID 1:66 )F1 - 66
20X-RAY DIFFRACTION20( CHAIN F AND RESID 67:140 )F67 - 140
21X-RAY DIFFRACTION21( CHAIN F AND RESID 141:207 )F141 - 207
22X-RAY DIFFRACTION22( CHAIN F AND RESID 208:297 )F208 - 297
23X-RAY DIFFRACTION23( CHAIN F AND RESID 298:354 )F298 - 354
24X-RAY DIFFRACTION24( CHAIN F AND RESID 355:380 )F355 - 380

+
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