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- PDB-7dbb: SSE in complex with tubulin -

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Basic information

Entry
Database: PDB / ID: 7dbb
TitleSSE in complex with tubulin
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / SSE / tUbulin / protein-drug complex
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / 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. / 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 / Chem-H1F / Tubulin beta chain / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsWu, C.Y. / Wang, Y.X.
CitationJournal: To Be Published
Title: SSE in complex with tubulin
Authors: Wu, C.Y. / Wang, Y.X.
History
DepositionOct 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,19323
Polymers261,6316
Non-polymers3,56217
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22340 Å2
ΔGint-137 kcal/mol
Surface area81140 Å2
Unit cell
Length a, b, c (Å)105.000, 157.573, 181.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACBDEF

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


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7
#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.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63042
#4: Protein Tubulin tyrosine ligase


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

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Non-polymers , 7 types, 17 molecules

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


Mass: 523.180 Da / Num. of mol.: 3 / 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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-H1F / 5-phenyl-3-(3,4,5-trimethoxyphenyl)-3,4-dihydropyrazole-2-carbothioamide


Mass: 371.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O3S / 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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG, 5% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCL2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 74418 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.049 / Rrim(I) all: 0.178 / Χ2: 0.455 / Net I/σ(I): 2.6 / Num. measured all: 975739
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8513.21.0636810.7890.31.1020.421100
2.85-2.9130.94336790.8240.2690.9810.43100
2.9-2.96130.86536700.8550.2480.90.422100
2.96-3.0212.90.72636760.890.2090.7550.42999.9
3.02-3.0812.30.61137080.9070.1810.6380.44599.8
3.08-3.1511.90.50736600.9230.1530.530.437100
3.15-3.2313.30.46336550.9550.1310.4810.446100
3.23-3.3213.70.38837000.9670.1080.4020.448100
3.32-3.4213.60.32536770.9760.0910.3380.464100
3.42-3.5313.60.27236870.9840.0760.2830.479100
3.53-3.6513.60.22536870.9870.0630.2330.473100
3.65-3.813.50.18837270.990.0530.1950.506100
3.8-3.9713.20.15436950.9940.0440.160.509100
3.97-4.1812.10.12337240.9940.0370.1290.499100
4.18-4.4414.10.10637360.9970.0290.110.487100
4.44-4.7913.90.08737280.9980.0240.090.481100
4.79-5.2713.70.0937540.9980.0250.0930.459100
5.27-6.0312.50.09837550.9970.0290.1020.44199.9
6.03-7.5913.20.08438300.9970.0240.0880.44299.9
7.59-5012.20.04639890.9990.0140.0480.37199.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55
Resolution: 2.805→29.877 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1994 2.7 %
Rwork0.1725 71868 -
obs0.1741 73862 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.07 Å2 / Biso mean: 54.2724 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: final / Resolution: 2.805→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17380 0 214 0 17594
Biso mean--53.69 --
Num. residues----2199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.805-2.8750.31571390.233501498
2.875-2.95270.28761420.2295122100
2.9527-3.03950.30861420.21875083100
3.0395-3.13750.26111420.19765103100
3.1375-3.24950.26051420.25124100
3.2495-3.37940.27311420.19485116100
3.3794-3.5330.25861410.19195107100
3.533-3.7190.20581430.1725126100
3.719-3.95150.22391420.15645147100
3.9515-4.25580.2171440.15015143100
4.2558-4.68260.18691430.1328514599
4.6826-5.35680.20471440.1457519099
5.3568-6.73620.24071440.1897519999
6.7362-29.8770.19681440.1676524996
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)
10.005-0.0039-0.00570.0027-0.0005-0.00350.0717-0.00020.0052-0.03480.0886-0.0165-0.15110.034200.255-0.05930.06710.1685-0.05790.182328.9498.99754.966
20.0004-0.0017-0.00030.0008-0.00120.004-0.0020.0097-0.0209-0.030.00040.0046-0.0372-0.0089-00.3715-0.060.03990.2842-0.01150.234627.230289.721443.4636
30.00010-0.0045-0.0005-0.00180.00240.06870.0530.0081-0.01680.0462-0.0181-0.06490.126400.2093-0.14090.07560.2499-0.13870.237837.922780.514846.2517
40.0056-0.0126-0.00750.0154-0.0010.00480.0314-0.01930.00230.02980.0609-0.0303-0.01750.1093-00.1605-0.02530.00770.2257-0.07730.227733.064477.198458.1425
50.0023-0.0095-0.00120.00480.01270.00210.0271-0.00650.00160.01850.05380.02020.0234-0.0455-00.10580.03710.00240.1945-0.02690.135211.792779.202959.974
60.00680.0161-0.00370.01650.02910.03510.0964-0.067-0.08590.12760.02970.0296-0.1003-0.0394-0-0.05520.17530.1946-0.0423-0.1628-0.035518.718886.848968.5812
70.00940.00020.00850.00030.00560.00590.0055-0.0176-0.02750.03520.02180.00430.00490.0153-00.25030.01490.01710.1222-0.02470.14516.830787.373180.691
80.01360.0098-0.00510.01030.0070.00580.06350.0329-0.03070.04340.02330.01180.00280.0073-00.1507-0.0013-0.00540.1211-0.02070.119718.214389.146273.796
9-0.0060.0065-0.00440.00370.0027-0.00060.08510.055-0.0230.0420.04070.00740.04610.0694-00.11920.05860.0247-0.0181-0.25140.111927.180261.394458.0295
100.00060.00240.00080.00020.001700.02090.0188-0.03060.0699-0.0038-0.01070.00370.0242-00.14360.0569-0.01810.1109-0.06940.125131.905763.673869.6671
110.0067-0.0061-0.00030.00220.00320.00530.04020.10740.0656-0.0596-0.00610.0608-0.0708-0.0328-00.21370.01760.01840.17220.00190.206616.313970.166919.5787
120.0152-0.0262-0.01720.0210.07810.04250.05970.06710.0203-0.0628-0.05910.0176-0.04050.005200.0603-0.00790.00620.1498-0.0280.148420.527854.229623.4747
130.0047-0.0062-0.0190.0160.00090.03670.0125-0.0425-0.0643-0.0006-0.01830.0116-0.0815-0.0874-00.1730.03850.01870.213-0.06110.19628.167961.542241.0323
140.0116-0.00880.0270.00490.00020.0242-0-0.0358-0.01310.0132-0.05060.03470.0252-0.05100.10670.01220.02510.1393-0.03910.151411.903952.403639.3176
15-0.0005-0.00110.0022-0.00880.00440.00010.0348-0.0016-0.04930.1867-0.063-0.0548-0.01960.05660-0.11350.0629-0.07120.0227-0.00350.030925.456938.424531.4035
160.0473-0.02640.02410.050.01850.0787-0.02880.0292-0.0007-0.04110.0119-0.003-0.0210.0213-00.0694-0.0301-0.00810.0854-0.01070.088120.211632.9452-12.0722
170.03350.02160.03890.00960.11060.07540.05120.20050.18260.1640.13490.14340.0529-0.20350-0.3551-0.4045-0.2197-0.4001-0.2888-0.11147.668126.04263.0958
180.0030.00040.0022-0.0030.0020.003-0.04040.0378-0.0098-0.0440.01970.0230.0651-0.027100.3746-0.1106-0.00490.5159-0.03880.248417.17024.589-40.574
190.0043-0.01270.00560.00080.00190.004-0.08780.12490.0509-0.03890.029-0.01760.0033-0.026200.4182-0.108-0.0050.56570.00150.238617.131111.5731-45.6636
200.00350.0032-0.01070.00050.00260.0016-0.03270.07520.0163-0.0122-0.0095-0.0234-0.00280.022900.4817-0.12880.11140.6037-0.13870.370333.7591-1.1216-43.9299
21-0.002-0.0051-0.0015-0.00740.00880.0181-0.14510.11650.0041-0.0741-0.0282-0.06750.1985-0.124700.3133-0.14050.06110.1738-0.30020.038522.2629-6.0257-33.475
22-0.00320.00350.00020.00050.00290.0018-0.05920.04840.0735-0.02740.05230.02510.0225-0.034500.2037-0.03690.01050.2233-0.02070.154615.26273.6888-27.8052
23-0.0023-0.0052-0.00110.00150.0063-0.0057-0.06290.01820.0283-0.0258-0.01340.02430.0712-0.044100.3155-0.10090.03130.3249-0.10050.33694.4352-5.6386-23.4717
240.01420.02170.01080.017-0.00560.0192-0.10460.1516-0.0299-0.08180.0988-0.02070.107-0.1671-00.2017-0.0530.0380.222-0.07760.20659.0698-2.7442-21.0446
250.00080.0004-0.00080.0216-0.00970.00160.0832-0.0052-0.11510.03730.0521-0.00560.03320.0121-00.38560.09190.27110.158-0.25180.268530.1987-16.6033-23.943
260.00890.0060.015-0.00050.01250.0030.03650.02120.05770.03840.02130.00240.01670.03300.3613-0.0491-0.02350.2858-0.07930.321627.610193.159681.9856
270.0277-0.0049-0.0561-0.08990.1689-0.0779-0.144-0.01830.03760.15-0.3477-0.2191-0.11060.2123-00.01690.18630.3523-0.0646-0.577-0.440942.735427.37043.8356
280.0170.0034-0.0132-0.0142-0.00030.0061-0.14480.0215-0.0824-0.0935-0.0666-0.07820.1804-0.001300.35-0.02640.0520.199-0.04250.24587.701356.42274.4571
290.0079-0.01780.00910.0113-0.00170.0013-0.0498-0.0741-0.02050.0515-0.03690.064-0.0010.080800.40920.05240.01370.48530.10640.349116.446356.9262107.191
30-0.02180.0220.00690.0069-0.0142-0.0008-0.14650.0517-0.12750.03230.06690.03460.0788-0.03600.42110.03010.1989-0.20450.20880.2474-1.966947.708499.7506
310.02850.0176-0.0122-0.0006-0.00460.0233-0.1980.0335-0.00130.06970.10950.01580.042-0.070300.2660.0090.06170.1591-0.00310.2115-1.429461.157488.0792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 64 )A1 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 88 )A65 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 128 )A89 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 199 )A129 - 199
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 223 )A200 - 223
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 306 )A224 - 306
7X-RAY DIFFRACTION7chain 'A' and (resid 307 through 338 )A307 - 338
8X-RAY DIFFRACTION8chain 'A' and (resid 339 through 381 )A339 - 381
9X-RAY DIFFRACTION9chain 'A' and (resid 382 through 414 )A382 - 414
10X-RAY DIFFRACTION10chain 'A' and (resid 415 through 438 )A415 - 438
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 88 )B1 - 88
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 238 )B89 - 238
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 338 )B239 - 338
14X-RAY DIFFRACTION14chain 'B' and (resid 339 through 401 )B339 - 401
15X-RAY DIFFRACTION15chain 'B' and (resid 402 through 438 )B402 - 438
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 197 )C1 - 197
17X-RAY DIFFRACTION17chain 'C' and (resid 198 through 440 )C198 - 440
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 28 )D2 - 28
19X-RAY DIFFRACTION19chain 'D' and (resid 29 through 88 )D29 - 88
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 127 )D89 - 127
21X-RAY DIFFRACTION21chain 'D' and (resid 128 through 223 )D128 - 223
22X-RAY DIFFRACTION22chain 'D' and (resid 224 through 266 )D224 - 266
23X-RAY DIFFRACTION23chain 'D' and (resid 267 through 311 )D267 - 311
24X-RAY DIFFRACTION24chain 'D' and (resid 312 through 401 )D312 - 401
25X-RAY DIFFRACTION25chain 'D' and (resid 402 through 441 )D402 - 441
26X-RAY DIFFRACTION26chain 'E' and (resid 6 through 46 )E6 - 46
27X-RAY DIFFRACTION27chain 'E' and (resid 47 through 143 )E47 - 143
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 83 )F1 - 83
29X-RAY DIFFRACTION29chain 'F' and (resid 84 through 198 )F84 - 198
30X-RAY DIFFRACTION30chain 'F' and (resid 199 through 283 )F199 - 283
31X-RAY DIFFRACTION31chain 'F' and (resid 284 through 384 )F284 - 384

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