[English] 日本語
Yorodumi
- PDB-7zx2: Tubulin-Pelophen B complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zx2
TitleTubulin-Pelophen B complex
Components
  • (Tubulin beta-2B ...) x 2
  • Stathmin-4
  • Tubulin alpha-1B chain
KeywordsCELL CYCLE/INHIBITOR / Tubulin / Pelophen / Peloruside / Laulimalide / CELL CYCLE-INHIBITOR complex
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-K9I / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsEstevez-Gallego, J. / Diaz, J.F. / Van der Eycken, J. / Oliva, M.A.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-104545RBI00/AEI/10.13039/501100011033 Spain
H2020 Marie Curie Actions of the European CommissionH2020-MSCA-ITN-2019 860070 TUBINTRAINEuropean Union
CitationJournal: Structure / Year: 2023
Title: Chemical modulation of microtubule structure through the laulimalide/peloruside site.
Authors: Estevez-Gallego, J. / Alvarez-Bernad, B. / Pera, B. / Wullschleger, C. / Raes, O. / Menche, D. / Martinez, J.C. / Lucena-Agell, D. / Prota, A.E. / Bonato, F. / Bargsten, K. / Cornelus, J. / ...Authors: Estevez-Gallego, J. / Alvarez-Bernad, B. / Pera, B. / Wullschleger, C. / Raes, O. / Menche, D. / Martinez, J.C. / Lucena-Agell, D. / Prota, A.E. / Bonato, F. / Bargsten, K. / Cornelus, J. / Gimenez-Abian, J.F. / Northcote, P. / Steinmetz, M.O. / Kamimura, S. / Altmann, K.H. / Paterson, I. / Gago, F. / Van der Eycken, J. / Diaz, J.F. / Oliva, M.A.
History
DepositionMay 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 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 beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,07830
Polymers266,9126
Non-polymers4,16624
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.709, 156.973, 181.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 3 molecules ACE

#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 / Details: Alpha-tubulin-1B / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 22125.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Stathmin-4 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043

-
Tubulin beta-2B ... , 2 types, 3 molecules BDF

#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Beta-tubulin-2B / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#4: Protein Tubulin beta-2B chain


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

-
Non-polymers , 11 types, 164 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.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#10: 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
#11: 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
#12: Chemical ChemComp-K9I / (3R,4S,7S,9S,11S)-3,4,11-trihydroxy-7-((R,Z)-4-(hydroxymethyl)hex-2-en-2-yl)-9-methoxy-12,12-dimethyl-6-oxa-1(1,3)-benzenacyclododecaphan-5-one


Mass: 464.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H40O7
#13: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#14: 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
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Mes, imidazole, calcium chloride, magnesium chloride, L-tyrosine, glycerol, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→49.66 Å / Num. obs: 103744 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 54.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Net I/σ(I): 13.5 / Num. measured all: 841601 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.548.31.0384222150730.6970.3841.1082100
13.69-49.666.70.07148427280.9940.030.0773498.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.16 Å49.61 Å
Translation8.16 Å49.61 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O2B

4o2b


Resolution: 2.5→49.66 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 5204 5.02 %
Rwork0.1971 98449 -
obs0.199 103653 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.92 Å2 / Biso mean: 67.1093 Å2 / Biso min: 26.27 Å2
Refinement stepCycle: final / Resolution: 2.5→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16666 0 256 140 17062
Biso mean--59.43 47.68 -
Num. residues----2105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.530.36091610.313332273388
2.53-2.560.33481730.286132333406
2.56-2.590.32371660.26932853451
2.59-2.620.27211750.264232383413
2.62-2.660.29161800.256132363416
2.66-2.690.30241690.26132653434
2.69-2.730.29741750.254432043379
2.73-2.770.32271690.251632793448
2.77-2.820.28861850.256632603445
2.82-2.860.30981530.259132433396
2.86-2.910.29021650.272232763441
2.91-2.960.33781890.283932083397
2.96-3.020.31321620.260332793441
3.02-3.080.29811730.249432753448
3.08-3.150.26361780.229132563434
3.15-3.220.27581830.234132203403
3.22-3.30.21951620.224432843446
3.3-3.390.28551660.222932823448
3.39-3.490.2531910.213532933484
3.49-3.610.2531770.216732353412
3.61-3.730.21111750.191833103485
3.73-3.880.20261920.176332283420
3.88-4.060.24871880.171332813469
4.06-4.270.20011500.162833163466
4.27-4.540.1941870.149833183505
4.54-4.890.18231620.14133063468
4.89-5.380.2011550.160933523507
5.38-6.160.22561810.17933533534
6.16-7.760.20031860.177233623548
7.76-49.660.1891760.173135453721
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)
10.3941-0.3221-0.22990.18530.15580.36850.02630.1265-0.0764-0.34920.14730.027-0.34630.27520.03060.6421-0.09090.09690.386-0.09740.377528.581898.577754.912
20.06540.0331-0.01210.0905-0.09360.0782-0.2784-0.0849-0.1893-0.580.190.0285-0.54780.0515-00.7828-0.13990.07970.4751-0.08850.415327.258489.304243.8378
30.974-0.36440.64550.2368-0.0430.80750.09110.44-0.2499-0.31490.3806-0.1409-0.0860.74580.30730.326-0.20270.18890.5933-0.21850.472337.735680.500846.1307
4-0.0171-0.1175-0.15390.42760.05110.63780.11130.0296-0.01610.15230.1245-0.03170.03590.17490.00330.4011-0.01420.00990.4855-0.18810.495432.862176.900857.6837
50.36530.16550.41891.07010.63721.03950.10910.05450.01180.2694-0.09880.0941-0.0626-0.0555-0.00030.40160.0160.05860.3116-0.09260.350817.998384.173566.521
60.79650.46730.46541.05380.10650.18730.1067-0.08960.06380.2273-0.14410.19530.0079-0.045800.63950.00410.04260.4386-0.12720.427617.490987.887676.6893
7-0.08530.20250.00140.846-0.0480.47190.0780.1957-0.13490.53450.1419-0.07440.48730.22110.00680.49060.1057-0.07530.4211-0.12620.418329.507961.842861.9782
80.9981-0.0947-0.21730.2925-0.07780.63210.02860.24840.1043-0.24130.00390.0653-0.2503-0.045700.45520.05020.02440.387-0.01340.413117.235867.887818.1867
90.3249-0.2223-0.14980.96911.21011.4167-0.01270.055-0.0703-0.0168-0.002-0.0241-0.05490.0219-0.00710.2484-0.0120.02130.3558-0.07470.361520.259953.654124.5203
100.4128-0.22010.05750.75070.58380.6998-0.043-0.05410.0710.1101-0.19630.03120.053-0.2348-0.03140.36930.01040.05230.4582-0.15750.43088.713461.278942.1381
11-0.22270.19930.20870.61950.38250.9172-0.04920.1208-0.04790.31610.00080.03070.34820.018700.38120.0176-0.01590.3489-0.0340.376821.318540.088232.3853
120.783-0.00750.27530.90990.25590.5309-0.03820.0878-0.0066-0.05940.0505-0.0276-0.03580.0654-00.3082-0.04110.01910.3657-0.02970.344318.279131.4187-11.3012
130.478-0.35120.00920.84310.69620.7999-0.00390.01240.08420.0726-0.0590.0050.1172-0.127100.3061-0.0430.02760.3258-0.03870.3558.379126.42964.156
140.07960.0966-0.1350.0779-0.01640.1043-0.32020.30070.0702-0.15170.3819-0.01090.0644-0.32760.00010.6184-0.15970.03610.8671-0.14080.449817.83814.901-40.4819
150.15550.0126-0.09910.13340.05470.0505-0.37690.41510.1136-0.15480.1974-0.1257-0.01590.06760.00020.6164-0.0551-0.02350.79860.04090.48713.9317.6443-42.5049
160.55930.0957-0.05440.4952-0.41050.5314-0.2270.4899-0.0031-0.29830.271-0.24050.06940.1578-0.05460.6267-0.09660.13180.7963-0.2570.492529.49560.8412-42.7684
170.5945-0.2845-0.17460.0916-0.04280.3437-0.30160.3663-0.1408-0.26560.3466-0.16140.32830.0759-0.01840.6598-0.11180.09060.5473-0.24030.538321.8671-8.7355-32.1337
180.1106-0.0427-0.4690.29530.09340.4355-0.08970.24250.0346-0.16160.1348-0.12290.1001-0.2235-0.00190.489-0.12090.01240.5659-0.10590.411813.16410.3953-29.9609
190.39-0.1677-0.0650.5474-0.0821.3502-0.19630.256-0.0662-0.04160.1416-0.01040.2928-0.31730.00250.5014-0.11750.03360.5161-0.14290.45768.0767-3.7552-21.9403
200.368-0.12150.14150.2585-0.15290.0347-0.00760.0503-0.38860.1706-0.0388-0.08260.34830.08770.00940.8210.06380.050.5781-0.24210.654630.4219-16.4921-24.1427
210.9005-0.0341-0.08130.0239-0.00320.01260.00430.53920.4380.35870.1332-0.1193-0.01520.07070.01570.6892-0.09510.01240.4115-0.12880.616424.686598.995582.1465
220.15180.14650.12780.07220.1330.0701-0.14640.1469-0.45010.63190.061-0.4848-0.12840.2967-0.00011.34810.0358-0.09340.8576-0.1290.671631.841882.271882.1935
230.206-0.4198-0.4430.10020.3459-0.0707-0.142-0.07470.04340.28240.11170.04320.48350.3367-0.09560.43510.02750.02880.5808-0.24310.506642.844129.40655.9317
242.2055-0.6076-0.32570.65740.03850.67640.18540.511-0.05070.6405-0.2488-0.05520.9198-0.5624-0.13371.1639-0.31390.1440.4737-0.19110.52046.323954.233569.9883
250.12010.1003-0.10960.0778-0.14190.1385-0.6854-0.4984-0.2337-0.1690.11960.0682-0.43410.872200.96240.0279-0.00570.96170.1120.730313.597663.172199.5685
260.19250.3381-0.39640.2401-0.21420.6132-0.32790.3442-0.46150.0182-0.0235-0.0170.2043-0.0775-0.1171.08070.03920.21030.62080.20550.8776-2.753450.5865101.2518
270.9333-0.1768-0.5567-0.0935-0.12140.4148-0.12070.0447-0.22280.180.53810.10060.1709-0.04950.00011.0382-0.09410.17040.652-0.01020.6851-0.926359.660987.7705
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 197 )A129 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 306 )A198 - 306
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 381 )A307 - 381
7X-RAY DIFFRACTION7chain 'A' and (resid 382 through 437 )A382 - 437
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 102 )B1 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 238 )B103 - 238
10X-RAY DIFFRACTION10chain 'B' and (resid 239 through 372 )B239 - 372
11X-RAY DIFFRACTION11chain 'B' and (resid 373 through 438 )B373 - 438
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 223 )C1 - 223
13X-RAY DIFFRACTION13chain 'C' and (resid 224 through 440 )C224 - 440
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 27 )D1 - 27
15X-RAY DIFFRACTION15chain 'D' and (resid 28 through 64 )D28 - 64
16X-RAY DIFFRACTION16chain 'D' and (resid 65 through 160 )D65 - 160
17X-RAY DIFFRACTION17chain 'D' and (resid 161 through 214 )D161 - 214
18X-RAY DIFFRACTION18chain 'D' and (resid 215 through 266 )D215 - 266
19X-RAY DIFFRACTION19chain 'D' and (resid 267 through 401 )D267 - 401
20X-RAY DIFFRACTION20chain 'D' and (resid 402 through 441 )D402 - 441
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 20 )E6 - 20
22X-RAY DIFFRACTION22chain 'E' and (resid 21 through 46 )E21 - 46
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 140 )E47 - 140
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 66 )F1 - 66
25X-RAY DIFFRACTION25chain 'F' and (resid 67 through 147 )F67 - 147
26X-RAY DIFFRACTION26chain 'F' and (resid 148 through 283 )F148 - 283
27X-RAY DIFFRACTION27chain 'F' and (resid 284 through 380 )F284 - 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