[English] 日本語
Yorodumi
- PDB-7ccc: The structure of the actin filament uncapping complex mediated by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ccc
TitleThe structure of the actin filament uncapping complex mediated by twinfilin
Components
  • (F-actin-capping protein subunit ...) x 2
  • Actin, alpha skeletal muscle
  • Twinfilin-1
KeywordsSTRUCTURAL PROTEIN / actin filament regulator
Function / homology
Function and homology information


regulation of actin phosphorylation / Advanced glycosylation endproduct receptor signaling / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / WASH complex / F-actin capping protein complex / COPI-mediated anterograde transport / sequestering of actin monomers / negative regulation of actin filament polymerization / Factors involved in megakaryocyte development and platelet production ...regulation of actin phosphorylation / Advanced glycosylation endproduct receptor signaling / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / WASH complex / F-actin capping protein complex / COPI-mediated anterograde transport / sequestering of actin monomers / negative regulation of actin filament polymerization / Factors involved in megakaryocyte development and platelet production / cell junction assembly / MHC class II antigen presentation / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / cytoskeletal motor activator activity / tropomyosin binding / cortical cytoskeleton / myofibril / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / brush border / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / calcium-dependent protein binding / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / cell body / actin binding / actin cytoskeleton organization / hydrolase activity / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Twinfilin / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha ...Twinfilin / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / F-actin-capping protein subunit alpha-1 / Actin, alpha skeletal muscle / Twinfilin-1 / F-actin-capping protein subunit alpha / F-actin-capping protein subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsRobinson, R.C. / Mwangangi, D.M.
Funding support1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0028/2018
CitationJournal: Sci Adv / Year: 2021
Title: The structure of the actin filament uncapping complex mediated by twinfilin.
Authors: Mwangangi, D.M. / Manser, E. / Robinson, R.C.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Twinfilin-1
C: F-actin-capping protein subunit alpha
D: F-actin-capping protein subunit beta
E: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,1479
Polymers188,2125
Non-polymers9354
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23520 Å2
ΔGint-126 kcal/mol
Surface area63960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.759, 168.662, 176.989
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 AEB

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Twinfilin-1 / Protein A6 / Protein tyrosine kinase 9


Mass: 40341.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TWF1, PTK9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12792

-
F-actin-capping protein subunit ... , 2 types, 2 molecules CD

#3: Protein F-actin-capping protein subunit alpha


Mass: 32980.703 Da / Num. of mol.: 1 / Mutation: I222V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capza1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RKN9, UniProt: P47753*PLUS
#4: Protein F-actin-capping protein subunit beta


Mass: 30669.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capzb / Production host: Escherichia coli (E. coli) / References: UniProt: Q923G3

-
Non-polymers , 3 types, 58 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Sequence detailsTHE GENEBANK ACCESSION NUMBER IS 24771896 FOR THE PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 8000, 10% glycerol, 500 mM potassium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 34562 / % possible obs: 95.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.061 / Rrim(I) all: 0.198 / Χ2: 0.852 / Net I/σ(I): 4.5 / Num. measured all: 403423
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.057.22.0820970.4950.7612.2240.4594.4
3.05-3.117.81.78520900.5210.6321.9010.4792.5
3.11-3.178.31.54421000.5560.5291.6380.48694.6
3.17-3.238.81.29221050.6730.4311.3670.51493.5
3.23-3.39.21.12521400.7550.3671.1880.52795.1
3.3-3.389.40.96521200.8280.3081.0170.55694.3
3.38-3.469.60.85521480.8410.2710.90.65196
3.46-3.559.70.90921280.8930.2870.9560.6893.6
3.55-3.669.50.71721490.8550.2290.7551.36296.2
3.66-3.789.50.50221400.8770.160.5291.60994.4
3.78-3.919.80.35821340.9510.1130.3770.85694.7
3.91-4.069.70.30521500.9710.0960.3210.91395.2
4.06-4.259.80.20321310.9840.0640.2130.92693.8
4.25-4.479.60.16321690.9860.0520.1721.02694.7
4.47-4.759.40.13522050.990.0440.1421.01896.9
4.75-5.119.40.1322370.9920.0420.1371.01997.3
5.11-5.619.50.12722540.990.0410.1330.97698.3
5.61-6.49.60.11122950.9920.0360.1170.86698.8
6.4-7.989.60.08523390.9950.0280.090.86999.5
7.98-209.60.06724280.9970.0210.070.91799.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAW, 3AA7

3daw

3aa7


Resolution: 3.2→19.92 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 3431 9.93 %
Rwork0.1864 31131 -
obs0.1916 34558 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.22 Å2 / Biso mean: 55.7863 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: final / Resolution: 3.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12516 0 56 54 12626
Biso mean--34.09 39.79 -
Num. residues----1574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.240.35131230.2582966108973
3.24-3.290.296970.2461061115879
3.29-3.340.30571260.25591074120082
3.34-3.390.28751070.241137124483
3.39-3.450.37891220.24141142126486
3.45-3.510.31381420.26341130127286
3.51-3.570.36481220.28051181130387
3.57-3.640.31231220.25311210133291
3.64-3.710.3681300.27831199132989
3.71-3.790.25671180.22891253137193
3.79-3.880.23961190.19151271139093
3.88-3.970.2461330.20371259139293
3.97-4.080.23371300.18881275140595
4.08-4.20.23661480.16181263141193
4.2-4.330.2081420.14631265140794
4.33-4.490.17561420.14861285142796
4.49-4.660.17731590.13781294145396
4.66-4.870.21021300.14321315144597
4.87-5.130.19631710.15091303147497
5.13-5.440.19121500.15571346149698
5.44-5.850.20741800.17961312149298
5.85-6.420.21621430.18191367151099
6.42-7.310.20921470.18351386153399
7.31-9.060.2021610.151913921553100
9.07-19.920.20671670.14841445161299
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)
10.394-0.03330.36210.3254-0.29761.85560.01010.0010.4264-0.32250.1698-0.46930.21671.09290.050.4385-0.12640.10320.54520.04190.508328.2964-8.2652-35.9821
20.05740.0446-0.02590.0306-0.00730.01810.5030.6421-0.2279-0.2248-0.0909-0.6470.24610.51320.00041.08390.03870.04011.02550.15760.756433.5907-12.0358-53.7814
30.13530.13840.00171.5124-1.08130.86390.10540.72920.1218-0.93220.0522-0.32560.210.58530.1230.3271-0.08020.1880.7325-0.09380.628632.364-17.1802-40.4018
40.2207-0.20520.12480.285-0.14930.72840.03550.2285-0.0324-0.0151-0.0687-0.64610.15990.7953-0.00840.21-0.03870.01890.516-0.01980.490226.2202-16.9757-28.937
51.0766-0.0640.051.55440.45522.2536-0.0110.24070.2335-0.26950.0862-0.0464-0.1937-0.23490.00130.1934-0.0051-0.01570.35680.06040.29214.627-14.6757-42.0026
60.61590.9738-0.3741.7599-0.39450.37830.2118-0.0998-0.64880.1053-0.2041-0.81620.44070.5812-0.12140.5085-0.1047-0.06440.7436-0.00050.561730.4672-14.0652-21.949
71.47080.3775-0.38781.822-0.34810.7060.2144-0.2851-0.3868-0.35630.1870.31890.4159-0.5250.02230.7081-0.3601-0.22380.06410.46520.2499-0.9804-53.0026-71.2424
80.9818-0.03610.4060.6498-0.17320.18790.2626-0.6564-0.14490.68890.2805-0.54390.4379-0.29470.00010.67560.052-0.09330.62210.01950.519818.3362-43.0737-53.4576
90.68770.35350.15230.57540.0721.7536-0.29870.2867-0.36390.17270.1038-0.2640.86610.8036-0.02350.5580.0116-0.05610.44850.06230.578119.8961-16.8178-6.9297
101.84760.40920.45571.55460.14552.3645-0.1862-0.27320.13930.06370.0558-0.0269-0.076-0.1021-0.00170.24570.0372-0.02890.14590.02040.27838.3844-10.5104-5.1256
110.3770.1294-0.36440.33610.110.5459-0.01610.05820.02670.00860.16060.12390.206-0.30790.00020.2717-0.0498-0.1130.35060.07750.47912.4465-16.9615-6.8202
120.45910.23870.4240.28580.06190.55120.00270.24980.0206-0.33550.20950.29040.4833-0.0137-0.03080.6416-0.1413-0.04291.06130.08370.9252-18.1227-40.0072-29.5524
130.402-0.07730.21550.244-0.18690.2349-0.1293-0.1688-0.2890.23710.15380.36020.3053-0.33-0.01440.3057-0.26580.22660.62880.08490.4675-8.7112-60.4419-16.7797
140.4746-0.17410.0930.2924-0.21840.4585-0.1311-0.8925-0.10710.34290.05520.30650.2411-0.099-0.00380.4872-0.04980.03920.59660.11810.3829.4339-61.1041-5.8782
150.0323-0.0117-0.0060.0239-0.03070.0470.29090.1095-1.21490.2475-0.4461-0.72330.7023-0.0645-0.00060.90940.1413-0.0510.93020.05790.892317.758-70.4489-1.2379
163.224-0.33750.78561.1326-0.59341.7583-0.0020.26440.0673-0.0713-0.0357-0.31860.19550.30470.0040.3289-0.0547-0.01370.29130.04110.143918.3501-55.615-21.8064
170.8602-0.10670.18540.80140.00070.4483-0.0045-0.2276-0.101-0.54210.25610.55780.1395-0.10580.05720.45-0.2375-0.27360.4970.13340.339-1.4487-34.0194-52.7083
180.14320.12240.17160.51510.08030.2751-0.13770.06340.0040.17490.06390.65770.3726-0.5026-0.00110.574-0.2993-0.05710.89180.15430.7883-16.9223-52.0183-35.5403
190.3658-0.0838-0.14060.3454-0.17450.53190.02440.2839-0.0567-0.42760.36620.68920.2728-0.76983.22540.4547-0.413-0.48461.06450.38710.7948-19.9463-42.5499-52.2448
201.86460.67120.58661.58610.04211.74730.23960.78760.1294-0.5474-0.37160.45470.0757-0.2280.00830.4817-0.126-0.05370.58150.13170.3386-6.6031-41.1979-41.1515
211.35950.5259-0.00151.26360.26051.9348-0.24970.28771.0927-0.0205-0.0545-0.2306-0.5266-0.4318-0.03880.2294-0.118-0.06490.360.16620.3936-2.2997-33.4779-38.2092
220.70610.1622-0.25210.35020.1170.41280.34870.24980.4822-0.5011-0.13310.515-0.0529-0.5530.00390.53340.06570.03390.4430.17260.49760.7751-15.84-86.8357
230.0859-0.1292-0.09810.20650.15710.1194-0.05630.51320.7676-0.19290.1818-0.1010.12150.05260.12280.87610.12870.3420.5730.37270.6176.98-6.5105-82.221
240.586-0.0147-0.00990.9696-0.39980.73430.20020.31270.64330.15780.25420.532-0.1647-0.71270.04910.33810.1040.09750.44050.22850.5299-2.4547-20.5588-77.6726
251.08440.1905-0.17882.2593-0.43651.30610.1778-0.06430.0777-0.0942-0.1389-0.4401-0.13470.10840.00110.31020.01570.09010.1851-0.01890.322923.2517-23.4586-77.3758
260.142-0.46170.29592.52230.11551.76470.12530.33380.2368-0.12990.11110.82440.044-0.5542-0.75150.4722-0.0328-0.1020.35820.27180.3842-2.5011-32.0135-81.8262
270.2484-0.32610.2881.48670.20420.6675-0.196-0.95470.12150.6344-0.445-0.19540.463-0.0839-0.1050.60460.00270.16231.55090.47711.1605-16.8294-22.2319-71.5186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 38 )A5 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 68 )A39 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 92 )A69 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 165 )A93 - 165
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 334 )A166 - 334
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 370 )A335 - 370
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 123 )B1 - 123
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 165 )B124 - 165
9X-RAY DIFFRACTION9chain 'B' and (resid 166 through 194 )B166 - 194
10X-RAY DIFFRACTION10chain 'B' and (resid 195 through 285 )B195 - 285
11X-RAY DIFFRACTION11chain 'B' and (resid 286 through 310 )B286 - 310
12X-RAY DIFFRACTION12chain 'B' and (resid 311 through 341 )B311 - 341
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 60 )C8 - 60
14X-RAY DIFFRACTION14chain 'C' and (resid 61 through 106 )C61 - 106
15X-RAY DIFFRACTION15chain 'C' and (resid 107 through 118 )C107 - 118
16X-RAY DIFFRACTION16chain 'C' and (resid 119 through 252 )C119 - 252
17X-RAY DIFFRACTION17chain 'C' and (resid 253 through 276 )C253 - 276
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 70 )D2 - 70
19X-RAY DIFFRACTION19chain 'D' and (resid 71 through 137 )D71 - 137
20X-RAY DIFFRACTION20chain 'D' and (resid 138 through 195 )D138 - 195
21X-RAY DIFFRACTION21chain 'D' and (resid 196 through 249 )D196 - 249
22X-RAY DIFFRACTION22chain 'E' and (resid 5 through 55 )E5 - 55
23X-RAY DIFFRACTION23chain 'E' and (resid 56 through 78 )E56 - 78
24X-RAY DIFFRACTION24chain 'E' and (resid 79 through 165 )E79 - 165
25X-RAY DIFFRACTION25chain 'E' and (resid 166 through 334 )E166 - 334
26X-RAY DIFFRACTION26chain 'E' and (resid 335 through 355 )E335 - 355
27X-RAY DIFFRACTION27chain 'E' and (resid 356 through 372 )E356 - 372

+
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