[English] 日本語
Yorodumi
- PDB-6vzq: Engineered TTLL6 mutant bound to alpha-elongation analog -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vzq
TitleEngineered TTLL6 mutant bound to alpha-elongation analog
ComponentsTubulin polyglutamylase TTLL6
KeywordsLIGASE / Protein engineering / TTLL6 / amino acid ligase / glutamylation
Function / homology
Function and homology information


positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / 9+0 non-motile cilium / microtubule severing / regulation of cilium beat frequency involved in ciliary motility ...positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / 9+0 non-motile cilium / microtubule severing / regulation of cilium beat frequency involved in ciliary motility / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / microtubule bundle formation / tubulin binding / microtubule / ciliary basal body / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-RZP / Chem-RZY / Tubulin polyglutamylase TTLL6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsMahalingan, K.K. / Keenen, E.K. / Strickland, E.K. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)ZIA NS 003163 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)ZIA NS 003122 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structural basis for polyglutamate chain initiation and elongation by TTLL family enzymes.
Authors: Mahalingan, K.K. / Keith Keenan, E. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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: Tubulin polyglutamylase TTLL6
B: Tubulin polyglutamylase TTLL6
C: Tubulin polyglutamylase TTLL6
D: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,61738
Polymers213,3824
Non-polymers5,23634
Water1,72996
1
A: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1965
Polymers53,3451
Non-polymers8514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,89912
Polymers53,3451
Non-polymers1,55411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3476
Polymers53,3451
Non-polymers1,0015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,17515
Polymers53,3451
Non-polymers1,83014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.038, 109.491, 171.700
Angle α, β, γ (deg.)90.000, 90.014, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 57 through 64 or (resid 65...A57 - 331
121(chain 'A' and (resid 57 through 64 or (resid 65...A333 - 350
131(chain 'A' and (resid 57 through 64 or (resid 65...A352 - 410
141(chain 'A' and (resid 57 through 64 or (resid 65...A418 - 460
151(chain 'A' and (resid 57 through 64 or (resid 65...A501
211(chain 'B' and ((resid 57 through 60 and (name N...B57 - 331
221(chain 'B' and ((resid 57 through 60 and (name N...B333 - 350
231(chain 'B' and ((resid 57 through 60 and (name N...B352 - 410
241(chain 'B' and ((resid 57 through 60 and (name N...B418 - 460
251(chain 'B' and ((resid 57 through 60 and (name N...B501
311(chain 'C' and ((resid 57 through 60 and (name N...C57 - 331
321(chain 'C' and ((resid 57 through 60 and (name N...C333 - 350
331(chain 'C' and ((resid 57 through 60 and (name N...C352 - 410
341(chain 'C' and ((resid 57 through 60 and (name N...C418 - 460
351(chain 'C' and ((resid 57 through 60 and (name N...C501
411(chain 'D' and ((resid 57 through 60 and (name N...D57 - 331
421(chain 'D' and ((resid 57 through 60 and (name N...D333 - 350
431(chain 'D' and ((resid 57 through 60 and (name N...D352 - 410
441(chain 'D' and ((resid 57 through 60 and (name N...D418 - 460
451(chain 'D' and ((resid 57 through 60 and (name N...D501

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Tubulin polyglutamylase TTLL6 / Tubulin--tyrosine ligase-like protein 6


Mass: 53345.398 Da / Num. of mol.: 4 / Mutation: C179A, Q180R, H362I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttll6 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Q9E8, Ligases

-
Non-polymers , 6 types, 130 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-RZY / (2~{S})-2-[[[(1~{S})-1-acetamidoethyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 375.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19NO10P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-RZP / (2~{S})-2-[[[(1~{R})-1-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 433.242 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H21NO12P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.31 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Sodium Citrate, pH 6.2, 200 mM MgCl2, 12% Peg 20000
PH range: 6.0-6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.08→46.16 Å / Num. obs: 101188 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 57.3 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06054 / Rpim(I) all: 0.0605 / Rrim(I) all: 0.08561 / Net I/σ(I): 7.16
Reflection shellResolution: 3.08→3.194 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2512 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 9901 / CC1/2: 0.918 / CC star: 0.978 / Rpim(I) all: 0.251 / Rrim(I) all: 0.3552 / % possible all: 98.36

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLR

4ylr


Resolution: 3.08→46.16 Å / SU ML: 0.3877 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.3173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2593 5094 5.14 %
Rwork0.2259 94093 -
obs0.2277 99187 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.88 Å2
Refinement stepCycle: LAST / Resolution: 3.08→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12026 0 328 96 12450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001812646
X-RAY DIFFRACTIONf_angle_d0.538717215
X-RAY DIFFRACTIONf_chiral_restr0.03871893
X-RAY DIFFRACTIONf_plane_restr0.00252191
X-RAY DIFFRACTIONf_dihedral_angle_d14.12697386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.120.37851620.34072967X-RAY DIFFRACTION92.46
3.12-3.160.33391860.29273092X-RAY DIFFRACTION99.21
3.16-3.190.34792100.26163169X-RAY DIFFRACTION99.12
3.19-3.230.26061920.24693153X-RAY DIFFRACTION98.79
3.23-3.280.33271890.24193075X-RAY DIFFRACTION99.03
3.28-3.320.2291940.22073083X-RAY DIFFRACTION98.08
3.32-3.370.29261870.24373121X-RAY DIFFRACTION97.81
3.37-3.420.37341630.23623175X-RAY DIFFRACTION98.58
3.42-3.470.31521310.25673129X-RAY DIFFRACTION98.16
3.47-3.530.28141660.24423098X-RAY DIFFRACTION97.64
3.53-3.590.28181500.2293161X-RAY DIFFRACTION99.31
3.59-3.660.25681340.23013172X-RAY DIFFRACTION98.8
3.66-3.730.27541880.22523176X-RAY DIFFRACTION98.94
3.73-3.80.30911210.20713227X-RAY DIFFRACTION98.91
3.8-3.890.2931580.21733137X-RAY DIFFRACTION99.04
3.89-3.980.25931670.21623147X-RAY DIFFRACTION98.93
3.98-4.080.21851340.21143193X-RAY DIFFRACTION98.99
4.08-4.190.21361580.19953165X-RAY DIFFRACTION98.96
4.19-4.310.25141580.21233148X-RAY DIFFRACTION98.92
4.31-4.450.25111700.19613161X-RAY DIFFRACTION98.2
4.45-4.610.21571610.19943107X-RAY DIFFRACTION98.76
4.61-4.790.23972000.19683150X-RAY DIFFRACTION99.23
4.79-5.010.27911840.21213179X-RAY DIFFRACTION99.76
5.01-5.270.28211890.22853156X-RAY DIFFRACTION99.73
5.27-5.60.32131840.2463121X-RAY DIFFRACTION99.34
5.6-6.030.29622000.25243159X-RAY DIFFRACTION98.71
6.03-6.640.28981300.24373144X-RAY DIFFRACTION97.91
6.64-7.60.23311770.24983120X-RAY DIFFRACTION98.8
7.6-9.560.17961710.20343177X-RAY DIFFRACTION99.79
9.56-46.160.17671800.21883031X-RAY DIFFRACTION95.4
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)
12.90640556703E-50.00476728203290.001897251813930.003704172798140.0006839216742290.00920759475772-0.00569615145753-0.00254345180415-0.01488404600040.00706939752616-0.0259919651659-0.02480069992770.0220693410255-0.0259803586022-4.70509315943E-80.979382409194-0.127721861487-0.004618970239350.772428225234-0.07984630049520.38193434237938.607023176425.015730558420.2454064123
2-0.00426413633190.0241706033312-0.001673309239370.0159917959187-0.01226243316060.02412587700810.0959408335044-0.0254834370779-0.08099969696970.0133967697138-0.002866381829950.104766087097-0.09708078024480.06447721081693.78521860765E-90.990463621285-0.07907078405840.1775418145190.703077189495-0.10744446902-0.048017676233312.384963640913.1306568710.4541707011
30.0146275890686-0.000495389421619-0.001879771248890.0262354106919-0.00735460893040.00522163614477-0.005172156714790.04645082667290.03633507276170.0665161791443-0.0250657844934-0.004687061042470.007525843750980.005253360907241.50242736535E-81.0008783713-0.01435813502770.1641177727630.808808933715-0.05374116421810.38595442288318.133109178928.42804882812.4302170628
4-0.0005764869141850.01263179977890.002949321010530.0221198480306-0.01485317460730.009275628916310.02452125329690.08005597143330.06576841407720.0609777115836-0.07123484660.0247701333157-0.009596476282970.00165314906854-9.92603064366E-100.983435528353-0.09333947530730.09707289135960.748680415993-0.1246661961170.24825918733923.373892459431.956117199518.2955502694
50.004574600780480.03938158702690.002394402295890.038721465480.0007484890044640.0283917771482-0.1551716703450.269621639199-0.00876565314375-0.4313980548610.0778364261831-0.0512042087516-0.176346008115-0.09441734737961.81779357168E-9-1.304580456160.46359673110.120878274479-0.189087730627-0.09565681303040.11846812284816.3319147329-6.7372721333466.9948047169
60.03260022343170.01825560785650.03268775364260.01892606379580.01905177657580.0003165315291580.073540174468-0.0939915909268-0.0413122456014-0.0383280670253-0.07481871201480.09343634979330.05189792320940.0755249391813-1.65351920494E-8-0.654255005468-0.5310344024890.0630666740431-0.1845327928480.01256511886060.36563204715920.5943656438-4.6421810594983.1523973897
70.03205535947250.01545947399120.005584876771340.0104128690710.0117671390316-0.00219794114274-0.00144361554756-0.04734446538170.0979263391292-0.307251037211-0.0479061622332-0.0324043461713-0.0285754771645-0.07973464637894.03181031202E-9-0.4045125313720.0540249346875-0.0415675659020.161106951916-0.02885732660190.50587238821218.42308650753.7749172999672.4954008059
8-0.00185130998256-0.00377553847192-0.009857603773220.00958112077687-0.030823657584-0.00516675436466-0.0118375815247-0.001713856329650.00302736910608-0.08987569824920.002867931731890.0319254711718-0.1494331846680.0297684481223-3.69104070532E-80.337735522804-0.0369127816422-0.01831423281080.2037880526730.2044325645230.45899404905612.754124770815.811197751858.6307579192
90.002446779188370.00241380009061-0.001269337954950.002809225285680.0002996130329850.00816705523115-0.0204209253504-0.01882448254740.005914050198810.011978775048-0.01915266989680.0466302057808-0.01734881384490.00708861703288-1.3110527087E-80.869130559931-0.002912878136720.03050602829560.9043977097230.0900377130940.35281670448-1.55265590916-22.51184189220.5449130869
10-0.0006502137620830.0196077674025-0.005419729747330.01172870819690.01284303660360.01767142735250.0365399547193-0.05579668884790.08802211255930.00313011954011-0.0137362155411-0.07952349774980.0569566243407-0.0407629168701-7.80246194342E-100.8987551689690.008107753151020.001795803892030.751613101775-0.0471906352977-0.014313862630824.9198283287-10.596588089810.9614104981
110.0182940789944-0.007822861167790.004500270199090.01854275753120.002327004882820.005833023099680.04391243851610.00179277181045-0.02325074229020.0227127639067-0.0288700366215-0.00369655357479-0.002218701688290.01711131988681.60595223875E-90.8844808138090.14522994206-0.07015072216580.876023508666-0.06253399565890.41157202527421.5519516949-25.12987222129.95245047273
12-0.0058842105503-0.00892021486558-0.002569203251260.00747834255939-0.001752559919710.00634665410647-0.00578027460374-0.0401728902039-0.08319302076910.01909339461140.02254612867040.024114278997-0.0439178112812-0.000170391565885-3.82352196673E-90.8606649919410.002090551014480.05241250482610.763459929120.06523340212910.26844047399913.818818374-29.564759518820.575104656
13-0.0105204212809-0.00941334694130.00267842891998-0.001799709969770.0003130788904520.00316267431715-0.0356254132380.0765984325371-0.00685625844649-0.0997180171772-0.0381645981745-0.04832876068920.01038471672210.04143109994099.44622669374E-9-0.06174870211140.3253474501980.156502765502-0.0839041750427-0.1702819526170.12194877859639.0384375771-45.420291163165.5528805587
140.0028837433524-0.001876502582270.03025568567630.00602133035287-0.0114315008045-0.01100936975770.0001676671825360.09850089120420.00570850509195-0.140785306518-0.04487840981690.02295268133970.0340495828975-0.1352505084097.23253620227E-9-0.834972318460.497388024555-0.364079419377-0.1841189504390.1210738694410.2459875280518.34941566223-29.685662096968.6376681901
150.074418335593-0.00517017685941-0.01063921918890.0069320178947-0.0526554836233-0.004628739180850.146619980584-0.169581572371-0.0567203478297-0.49408468521-0.172267408801-0.01117612895090.1505435195860.164043024647-4.727936986E-9-0.901368097280.054405811373-0.1597367808870.21250471141-0.004927777743330.38259946836216.8322559601-41.94886748178.2693025111
16-0.002379097900890.0170452911663-0.03723338212930.006496832478540.047451300228-0.0394559843955-0.02931597015120.0359788005276-0.113346233713-0.461543782751-0.117885049205-0.05029319992030.3771325779540.1779007813092.37245982315E-9-0.5781279660190.227056358852-0.0704865409338-0.651687431933-0.2381426954490.32288842155723.3289621745-52.216862895666.3498382857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 57:116)
2X-RAY DIFFRACTION2(chain A and resid 117:275)
3X-RAY DIFFRACTION3(chain A and resid 276:341)
4X-RAY DIFFRACTION4(chain A and resid 342:460)
5X-RAY DIFFRACTION5(chain B and resid 57:197)
6X-RAY DIFFRACTION6(chain B and resid 198:291)
7X-RAY DIFFRACTION7(chain B and resid 292:384)
8X-RAY DIFFRACTION8(chain B and resid 385:460)
9X-RAY DIFFRACTION9(chain C and resid 57:114)
10X-RAY DIFFRACTION10(chain C and resid 115:275)
11X-RAY DIFFRACTION11(chain C and resid 276:330)
12X-RAY DIFFRACTION12(chain C and resid 331:460)
13X-RAY DIFFRACTION13(chain D and resid 57:115)
14X-RAY DIFFRACTION14(chain D and resid 116:197)
15X-RAY DIFFRACTION15(chain D and resid 198:339)
16X-RAY DIFFRACTION16(chain D and resid 340:460)

+
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