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- PDB-6vzs: Engineered TTLL6 mutant bound to gamma-elongation analog -

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Basic information

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


positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / 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 ...positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / 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 / ciliary basal body / cilium / microtubule cytoskeleton organization / microtubule / 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-S3A / Tubulin polyglutamylase TTLL6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsMahalingan, K.K. / Keenen, E.K. / Strickland, M. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)220,05753
Polymers213,3824
Non-polymers6,67549
Water3,819212
1
A: 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
MethodPISA
2
B: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6239
Polymers53,3451
Non-polymers1,2778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91223
Polymers53,3451
Non-polymers2,56722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 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
MethodPISA
Unit cell
Length a, b, c (Å)74.738, 108.648, 170.888
Angle α, β, γ (deg.)90.000, 90.023, 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 111 or (resid 112...A57 - 350
121(chain 'A' and (resid 57 through 111 or (resid 112...A352 - 409
131(chain 'A' and (resid 57 through 111 or (resid 112...A414 - 460
141(chain 'A' and (resid 57 through 111 or (resid 112...A501
151(chain 'A' and (resid 57 through 111 or (resid 112...A601
161(chain 'A' and (resid 57 through 111 or (resid 112...A701
211(chain 'B' and (resid 57 through 102 or (resid 103...B57 - 350
221(chain 'B' and (resid 57 through 102 or (resid 103...B352 - 409
231(chain 'B' and (resid 57 through 102 or (resid 103...B414 - 460
241(chain 'B' and (resid 57 through 102 or (resid 103...B501
251(chain 'B' and (resid 57 through 102 or (resid 103...B601
261(chain 'B' and (resid 57 through 102 or (resid 103...B701
311(chain 'C' and (resid 57 through 87 or (resid 88...C57 - 350
321(chain 'C' and (resid 57 through 87 or (resid 88...C352 - 409
331(chain 'C' and (resid 57 through 87 or (resid 88...C414 - 460
341(chain 'C' and (resid 57 through 87 or (resid 88...C501
351(chain 'C' and (resid 57 through 87 or (resid 88...C601
361(chain 'C' and (resid 57 through 87 or (resid 88...C701
411(chain 'D' and (resid 57 through 98 or (resid 99...D57 - 350
421(chain 'D' and (resid 57 through 98 or (resid 99...D352 - 409
431(chain 'D' and (resid 57 through 98 or (resid 99...D414 - 460
441(chain 'D' and (resid 57 through 98 or (resid 99...D501
451(chain 'D' and (resid 57 through 98 or (resid 99...D601
461(chain 'D' and (resid 57 through 98 or (resid 99...D701

NCS ensembles :
ID
1
2
3
4

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Components

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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

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Non-polymers , 5 types, 261 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-S3A / (2~{S})-2-[[[(3~{R})-3-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 433.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21NO12P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 290 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

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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 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: 2.66→45.84 Å / Num. obs: 155180 / % possible obs: 99.68 % / Redundancy: 2 % / Biso Wilson estimate: 50.11 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04598 / Rpim(I) all: 0.045 / Rrim(I) all: 0.06503 / Net I/σ(I): 8.69
Reflection shellResolution: 2.66→2.755 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3283 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 15165 / CC1/2: 0.872 / Rpim(I) all: 0.3283 / Rrim(I) all: 0.4643 / % possible all: 98.85

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLR
Resolution: 2.66→45.84 Å / SU ML: 0.3735 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.5018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2555 7576 4.97 %
Rwork0.2185 144823 -
obs0.2203 152399 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.54 Å2
Refinement stepCycle: LAST / Resolution: 2.66→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12358 0 422 212 12992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001513054
X-RAY DIFFRACTIONf_angle_d0.4917710
X-RAY DIFFRACTIONf_chiral_restr0.03861932
X-RAY DIFFRACTIONf_plane_restr0.00252233
X-RAY DIFFRACTIONf_dihedral_angle_d17.78984591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.690.4082250.3854452X-RAY DIFFRACTION91.21
2.69-2.720.36222310.31314823X-RAY DIFFRACTION98.5
2.72-2.750.33622310.29334908X-RAY DIFFRACTION98.66
2.75-2.790.43831990.28914839X-RAY DIFFRACTION99.1
2.79-2.830.29083010.28094803X-RAY DIFFRACTION99.18
2.83-2.860.32672610.27074979X-RAY DIFFRACTION99.39
2.86-2.910.32982660.28924700X-RAY DIFFRACTION99.52
2.91-2.950.35092910.27934878X-RAY DIFFRACTION99.38
2.95-30.32172680.26774935X-RAY DIFFRACTION99.07
3-3.040.29712500.2544740X-RAY DIFFRACTION98.93
3.04-3.10.29882490.24844898X-RAY DIFFRACTION98.92
3.1-3.150.29062590.24894791X-RAY DIFFRACTION98.12
3.15-3.210.30382700.23884800X-RAY DIFFRACTION97.91
3.21-3.280.24432170.2224844X-RAY DIFFRACTION98.41
3.28-3.350.28452370.22184778X-RAY DIFFRACTION98.31
3.35-3.430.26332440.21534875X-RAY DIFFRACTION98.8
3.43-3.510.23732940.22924760X-RAY DIFFRACTION98.94
3.51-3.610.23123110.21644846X-RAY DIFFRACTION99.52
3.61-3.720.26592330.2164871X-RAY DIFFRACTION98.72
3.72-3.840.2522790.18354757X-RAY DIFFRACTION99.15
3.84-3.970.22822400.20724946X-RAY DIFFRACTION99.22
3.97-4.130.25992220.19534873X-RAY DIFFRACTION98.66
4.13-4.320.25332380.18464816X-RAY DIFFRACTION99
4.32-4.550.2242670.17934824X-RAY DIFFRACTION99.03
4.55-4.830.21092900.17694815X-RAY DIFFRACTION99.71
4.83-5.20.24092680.18764878X-RAY DIFFRACTION99.52
5.2-5.730.20762230.21294942X-RAY DIFFRACTION99.37
5.73-6.550.29512110.22864851X-RAY DIFFRACTION98.69
6.55-8.250.25052660.23454840X-RAY DIFFRACTION99.26
8.25-45.840.17392350.18584761X-RAY DIFFRACTION97.18
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)
17.218198200532.180854894340.9421364232835.06473288348-1.756188624039.896397564630.171853615308-0.6882821650360.132499014420.841311686813-0.06714092230740.798700092349-0.499955749329-0.875342163894-0.04769647550890.3677118511470.0263899962910.1299595008980.3711368228340.02489434403360.612426599373-1.62930068458-25.237528414821.4379701377
22.600557406330.9124724051930.1973832993.44232176519-0.4679685866924.549305154990.226673567319-0.420834761940.3091273288970.575716081977-0.224101925257-0.845940286543-0.1272423802790.616179039750.02107145392010.341376818029-0.0130037685305-0.1646693732740.396038456679-0.02792077817070.74119245306429.395202983-9.4957803891816.491871245
31.97576366211-0.131715752432-0.6067810031782.17415104286-0.4309823029462.636870530920.003994424090480.0829705726365-0.160732460190.2175971694090.0127339940045-0.2237184970210.09908495613710.0404468676989-0.03951033029550.2247285771750.024765921406-0.06362799863490.24892962531-0.03018412467690.59946392438319.6428419996-23.29503309638.25833665993
42.93841714842-0.320929668063-0.7224114044633.64840456695-0.8630855425892.66739708196-0.165306264328-0.56199856484-0.4842256163360.7872087896110.001026867902340.01792323674850.4409193062890.02359111447110.1060039761960.555532171340.0265744102971-0.04463427638220.3616720785910.06839358118690.75099739257612.1171754525-33.898221388522.0240206731
53.467516223941.787222907872.859205141991.490455723412.111507858467.543893774960.1048799780380.8709562726610.167932185616-1.23113788317-0.210315695104-0.513539320278-0.4148881022490.4488639407280.1958897835561.321652043820.1725229416910.128637103060.666962322941-0.06227126239330.47019932097940.0068819485-46.634324070965.0499913908
61.82759085992-0.523631011059-0.1981538498912.36570961756-0.3088507506720.6871542310360.1211442811640.119280159853-0.0469605933622-0.457002850349-0.04763764428830.2533408595190.08009905612810.116110369201-0.07651378593391.101422623180.00919375869168-0.1040822393160.458644766035-0.0428019055720.38051849377316.2077011176-40.647592006374.4008091901
70.0104249604182-0.0981609000040.003732490258490.6914373812480.00416726104677-0.00145896039875-0.159079641194-0.5340339673710.369018216367-0.205077071668-0.2824914198040.417383661973-0.0504901595868-0.623295996360.4861152366552.139096746040.07526913079130.2283301970590.818969242543-0.5562948528451.1800619875831.3059231712-60.559730855743.1287114224
82.976109141381.328648410521.389926376271.92728013082.976290137034.816064449540.1617247640660.262465625697-1.08239299729-0.4634539438490.00290731032320.3148642285250.6051331201290.113111905951-0.1546710907521.364336500830.0928744019187-0.1512269090220.495783435291-0.1085753985770.65249125439219.1360211127-60.614084066263.2413611478
97.728099549513.68924422842-0.8556584618139.890188174862.185545639655.589048201420.251346651125-1.10686444861-0.06630135181021.36184049545-0.381581983269-0.9581246166860.1639845346250.6558000851060.1636735736730.532533814391-0.088053870557-0.1440307640770.473411046982-0.07188474417710.67042608824439.753227987522.17670909720.7062926614
101.88000408754-0.204825189979-0.2883987052071.97909081553-0.4366382850283.181479244680.184233994049-0.3459321796960.003793036435840.5956578867710.005645278538070.9610512850730.00427293964313-0.518875299373-0.1432361985870.400001503058-0.01222119206360.2209643776410.376031766989-0.01332207634030.7486954324298.594798770737.188660846616.0996254169
112.369939966080.19433909190.6399255972972.748945198680.1911793253611.969446551340.0623983920259-0.01229506660440.2542983725260.359064828165-0.06489287830270.114427390303-0.1207240885340.0426672269794-0.005243308544350.268191478013-0.008412906015710.1089935675280.231653115754-0.0218961734990.56819330766420.813724665521.41359543659.52528480014
122.210009893050.828181241956-0.05009046544571.703454279131.424676632921.508658840460.362037423639-0.5887308254460.7201854462111.17729751874-0.3348656139610.284039623525-0.422182650652-0.144749854973-0.1838505515021.03229918705-0.07018010865930.1248958001840.518854428217-0.2613080029490.94000514535320.624487872236.307482755627.8884274502
132.06509570865-2.85613703177-6.131849383146.546960973890.610167426788.62791001904-0.05898836526280.743391030473-0.29215692601-0.585004702439-0.1057829848420.4952265057970.502399267162-0.6855169327050.1272616730490.872461994947-0.0681375393308-0.1290984196720.7027827927130.03152705680010.458059205472-1.608647156060.79625537464463.7707552584
145.49371089971-1.38383808486-1.359876182012.18670598165-0.1189345540294.744090002060.1495918322440.717995050579-0.417090135803-0.704330638471-0.215213558952-0.2045446097620.2871522297090.2206238499720.06710869963141.04193609857-0.01649188522660.1199807929540.481073732619-0.08115436725630.46397257991629.0598371591-14.573126723869.4213624176
152.8662978415-0.1191044437440.2803770965922.732446734080.1203390700940.969920952472-0.03111672637860.107051580852-0.0361325851397-0.1934738420890.057309695727-0.175724480527-0.0826857428845-0.0736124051496-0.0309407319220.9195369931770.001918748726840.05495566548620.40055799236-0.03061178258260.35769544061418.3643249009-1.1600928453477.0545551343
162.777930047991.39343777661-1.752487337653.77181908078-3.46067118963.26176872438-0.02362077869530.4318759853860.176312569052-0.5818768020770.161082059404-0.0301011214863-0.210900887724-0.130608961396-0.09643434701111.08068446509-0.05732010384140.09313775780120.520325657557-0.04360839102970.5458870389611.707252134313.965391386257.8681130486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 57:117)
2X-RAY DIFFRACTION2(chain A and resid 118:208)
3X-RAY DIFFRACTION3(chain A and resid 209:353)
4X-RAY DIFFRACTION4(chain A and resid 354:460)
5X-RAY DIFFRACTION5(chain B and resid 57:112)
6X-RAY DIFFRACTION6(chain B and resid 113:394)
7X-RAY DIFFRACTION7(chain B and resid 395:420)
8X-RAY DIFFRACTION8(chain B and resid 421:460)
9X-RAY DIFFRACTION9(chain C and resid 57:114)
10X-RAY DIFFRACTION10(chain C and resid 115:210)
11X-RAY DIFFRACTION11(chain C and resid 211:406)
12X-RAY DIFFRACTION12(chain C and resid 407:460)
13X-RAY DIFFRACTION13(chain D and resid 58:117)
14X-RAY DIFFRACTION14(chain D and resid 118:210)
15X-RAY DIFFRACTION15(chain D and resid 211:379)
16X-RAY DIFFRACTION16(chain D and resid 380:460)

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