[English] 日本語
Yorodumi
- PDB-6vzw: TTLL6 bound to the initiation analog -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vzw
TitleTTLL6 bound to the initiation analog
ComponentsTubulin polyglutamylase TTLL6
KeywordsLIGASE / TTLL6 / initiation / glutamylase / phosphinic acid
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 / regulation of cilium beat frequency involved in ciliary motility / 9+0 non-motile cilium / microtubule severing / 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 / regulation of cilium beat frequency involved in ciliary motility / 9+0 non-motile cilium / microtubule severing / 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
Chem-2TI / ADENOSINE-5'-DIPHOSPHATE / Tubulin polyglutamylase TTLL6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMahalingan, K.K. / Keenen, E.K. / Strickland, M. / Li, Y. / Liu, Y. / Ball, H.L. / Tanner, T.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)219,08040
Polymers213,4944
Non-polymers5,58636
Water5,296294
1
A: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4947
Polymers53,3731
Non-polymers1,1206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,04613
Polymers53,3731
Non-polymers1,67312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5868
Polymers53,3731
Non-polymers1,2127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tubulin polyglutamylase TTLL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,95412
Polymers53,3731
Non-polymers1,58111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.254, 110.585, 173.579
Angle α, β, γ (deg.)90.000, 90.139, 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 58 through 87 or (resid 88...A58 - 147
121(chain 'A' and (resid 58 through 87 or (resid 88...A149 - 180
131(chain 'A' and (resid 58 through 87 or (resid 88...A183 - 188
141(chain 'A' and (resid 58 through 87 or (resid 88...A190 - 331
151(chain 'A' and (resid 58 through 87 or (resid 88...A334 - 410
161(chain 'A' and (resid 58 through 87 or (resid 88...A418 - 460
171(chain 'A' and (resid 58 through 87 or (resid 88...A601
181(chain 'A' and (resid 58 through 87 or (resid 88...A701
191(chain 'A' and (resid 58 through 87 or (resid 88...A801
211(chain 'B' and (resid 58 through 81 or (resid 82...B58 - 147
221(chain 'B' and (resid 58 through 81 or (resid 82...B149 - 180
231(chain 'B' and (resid 58 through 81 or (resid 82...B183 - 188
241(chain 'B' and (resid 58 through 81 or (resid 82...B190 - 331
251(chain 'B' and (resid 58 through 81 or (resid 82...B334 - 410
261(chain 'B' and (resid 58 through 81 or (resid 82...B418 - 460
271(chain 'B' and (resid 58 through 81 or (resid 82...B601
281(chain 'B' and (resid 58 through 81 or (resid 82...B701
291(chain 'B' and (resid 58 through 81 or (resid 82...B901
311(chain 'C' and (resid 58 through 81 or (resid 82...C58 - 147
321(chain 'C' and (resid 58 through 81 or (resid 82...C149 - 180
331(chain 'C' and (resid 58 through 81 or (resid 82...C183 - 188
341(chain 'C' and (resid 58 through 81 or (resid 82...C190 - 331
351(chain 'C' and (resid 58 through 81 or (resid 82...C334 - 410
361(chain 'C' and (resid 58 through 81 or (resid 82...C418 - 460
371(chain 'C' and (resid 58 through 81 or (resid 82...C601
381(chain 'C' and (resid 58 through 81 or (resid 82...C701
391(chain 'C' and (resid 58 through 81 or (resid 82...C801
411(chain 'D' and (resid 58 through 81 or (resid 82...D58 - 147
421(chain 'D' and (resid 58 through 81 or (resid 82...D149 - 180
431(chain 'D' and (resid 58 through 81 or (resid 82...D183 - 188
441(chain 'D' and (resid 58 through 81 or (resid 82...D190 - 331
451(chain 'D' and (resid 58 through 81 or (resid 82...D334 - 410
461(chain 'D' and (resid 58 through 81 or (resid 82...D418 - 460
471(chain 'D' and (resid 58 through 81 or (resid 82...D601
481(chain 'D' and (resid 58 through 81 or (resid 82...D801
491(chain 'D' and (resid 58 through 81 or (resid 82...D1001

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 53373.387 Da / Num. of mol.: 4
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 , 5 types, 330 molecules

#2: Chemical
ChemComp-2TI / (2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid


Mass: 460.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H26N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.38 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Sodium Citrate, pH 6.2, 200 mM MgCl2, 8-12% 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: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→19.92 Å / Num. obs: 191456 / % possible obs: 99.67 % / Redundancy: 2 % / Biso Wilson estimate: 42.75 Å2 / CC1/2: 0.998 / CC star: 0.99 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.0643 / Net I/σ(I): 7.35
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3327 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 19357 / CC1/2: 0.827 / CC star: 0.952 / Rpim(I) all: 0.332 / Rrim(I) all: 0.4706 / % possible all: 99.77

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLR

4ylr


Resolution: 2.5→19.92 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 27.4744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2435 9423 4.92 %
Rwork0.217 182032 -
obs0.2184 191455 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12458 0 352 294 13104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001613122
X-RAY DIFFRACTIONf_angle_d0.515917792
X-RAY DIFFRACTIONf_chiral_restr0.03841928
X-RAY DIFFRACTIONf_plane_restr0.00282249
X-RAY DIFFRACTIONf_dihedral_angle_d15.70824648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.34832710.34235919X-RAY DIFFRACTION97.65
2.53-2.560.33423040.32126107X-RAY DIFFRACTION99.78
2.56-2.590.32294150.30056096X-RAY DIFFRACTION99.86
2.59-2.630.30992620.3076105X-RAY DIFFRACTION99.73
2.63-2.660.29073210.28735989X-RAY DIFFRACTION99.86
2.66-2.70.36842920.27866173X-RAY DIFFRACTION99.57
2.7-2.740.30493180.28396007X-RAY DIFFRACTION99.81
2.74-2.780.33073300.27566113X-RAY DIFFRACTION99.83
2.78-2.820.30823170.27466034X-RAY DIFFRACTION99.76
2.82-2.870.27673690.25335999X-RAY DIFFRACTION99.78
2.87-2.920.29093410.24716121X-RAY DIFFRACTION99.72
2.92-2.970.27252730.2466089X-RAY DIFFRACTION99.78
2.97-3.030.30183720.24316006X-RAY DIFFRACTION99.77
3.03-3.090.26763230.24216003X-RAY DIFFRACTION99.62
3.09-3.150.24323250.2336126X-RAY DIFFRACTION99.69
3.15-3.230.25322690.23416112X-RAY DIFFRACTION99.81
3.23-3.310.25252940.22776045X-RAY DIFFRACTION99.67
3.31-3.40.26743400.21956075X-RAY DIFFRACTION99.77
3.4-3.50.24812880.22386054X-RAY DIFFRACTION99.69
3.5-3.610.26742960.22266152X-RAY DIFFRACTION99.63
3.61-3.740.26663280.22576022X-RAY DIFFRACTION99.64
3.74-3.880.24933240.20016037X-RAY DIFFRACTION99.76
3.88-4.060.23153150.19166104X-RAY DIFFRACTION99.7
4.06-4.270.17763170.17526017X-RAY DIFFRACTION99.61
4.27-4.540.18742480.17246147X-RAY DIFFRACTION99.67
4.54-4.880.18083740.16756015X-RAY DIFFRACTION99.73
4.88-5.360.21843350.18716131X-RAY DIFFRACTION99.91
5.36-6.120.23073080.21256052X-RAY DIFFRACTION99.91
6.12-7.640.23722790.2096121X-RAY DIFFRACTION99.8
7.64-19.920.17752750.17096061X-RAY DIFFRACTION99
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)
16.87788969752-4.336174111491.589459816498.868753410090.2946036991295.74632958431-0.1230631973250.5660872932570.721983326273-0.3966131694610.235477655196-0.890269306969-0.1921774001120.594360304041-0.1169439504650.946468966465-0.07604577977920.07105903373280.80267541238-0.06033742839430.35023625307940.2031820565-29.467459808769.2148097854
24.771685780130.325400623856-0.153838421950.953887887026-1.368976076941.995474497880.3914745170411.5577775223-0.077952868819-0.545479549132-0.5998421550090.0186384958322-1.32200131528-0.3578357932150.1826293764811.248688803690.1207056902350.05512263950721.05096386337-0.0668603610770.37809070356132.5820688341-27.632692951157.4501430006
31.35455080241-0.906452708667-0.3366282405492.998260445961.428800106231.622879178590.09315856695180.2965964711060.0863743197178-0.345754107586-0.180551431330.246031168255-0.109687225774-0.145205678010.0802440635480.835634820590.0129187359206-0.03518597540420.6827938308430.02688572593970.3353843852210.0663263733-17.282045300772.2868284799
42.69461000348-0.1320559514740.688131205182.224325054810.0576071963081.401149719720.082011394963-0.02491898324170.116244252490.0987102338414-0.003005794729330.0339451518889-0.07741965762690.129569264525-0.07213428663630.889250174699-0.00322688391735-0.01144806892370.683660443308-0.03300308284710.27979522781416.3396070189-26.107603638880.8543104755
54.07029368165-0.749751279713-0.8105996440171.658090669970.5110388475410.2125420178750.04762964591480.145538938197-0.07440705809820.1021773926140.0704997411504-0.1391227318280.0451461132441-0.134034450624-0.1378891141090.881872920756-0.0451456684151-0.008834897562620.662083863322-0.0143414691620.25490796425525.6411713265-31.750318956972.5443659015
60.06678919126240.09585843199220.4071067855760.6326839131341.215599458672.596093508680.04301211709010.323344320278-0.298110422577-0.2045200349740.0004476118921640.2799278372270.103056623876-0.0700544972259-0.0215817060421.06123880674-0.0389612801836-0.05735730026080.808737038549-0.1317007651890.42225216374720.2311986662-43.758693231456.7269949647
77.528856552783.49921493337-0.7351411945145.22136329151-0.8194906086239.023643797750.216652380343-0.921618820810.1040780685460.546722599643-0.1730918068130.699183078084-0.0835846023908-0.5505788504420.01198417967250.277371652252-0.02091004612250.06425699814280.3976713399390.08162622172350.573594790859-1.92107121468-54.706374298418.2237791854
81.500666721940.520656033580.6616703730191.576784582760.4425849640251.223756354150.0847460810826-0.3036833826040.1069651791810.480334210089-0.103942930015-0.616025567623-0.1080561361510.2696291611060.01872217802440.292746180814-0.0222817881267-0.08631975056560.3761632584560.06738713198220.7367141626126.7564105131-41.270044081416.6411011852
91.846150701740.416182634442-1.26000340093.4978721148-1.374257681612.907811573790.09790258253190.201817640550.122062429060.0530806711819-0.111983454167-0.0571167060552-0.251673479051-0.02934474405330.002372420680480.1865715600670.0179599108495-0.07266938618320.3054440642210.04621897919210.61672956381619.9137200946-50.01466301960.887906437849
101.947609987570.0058876434718-0.323028933781.762391687890.4252043194391.915510170480.159357970949-0.0848265663388-0.1537383775630.390280868229-0.0302733225974-0.1255173209080.202663165063-0.117134673998-0.1015878303520.29112961683-0.0397758064925-0.08151208148060.2609820785760.07585274199920.66653868876116.9584306666-57.389877386214.4438245405
110.715155393397-0.09426711327370.8473964708430.222794772769-0.6672957386853.933200139650.435447457206-0.575607725358-0.6071942474071.35596579376-0.301563546139-0.2425401692420.126920286280.5468394756470.08134004518691.20867914129-0.234735065574-0.05639678676580.5809916762820.3027726885680.7572009490989.69357526525-70.07196805830.5444939757
127.40953699922-0.6967061633165.014554659440.907961095630.1095489949796.269172766970.3650683609250.209061600364-1.37125224041.49504790621-0.254848873123-0.6246381198120.733010348860.900311610769-0.1391593672290.5325338988980.00350282236282-0.175178772110.5099953271890.2171761341810.9694224855628.1342698789-64.914317166622.5320468223
134.361285712270.469416170795-2.217513261324.834186286084.685385434699.019849385740.09934887956770.546346755049-0.232894572468-0.760575327138-0.08753628107150.6176148529260.31102552272-0.264412358892-0.01741188518061.075479109880.0924698454849-0.0400646017460.7971205751550.04558249245420.28972432192-2.1916763030517.774469461768.5629226073
140.718980618816-0.9337832440770.207932764261.94082840199-0.03663405548040.09579294794060.08387538234910.155719964363-0.045082348542-0.615756707364-0.0305234704304-0.346573238186-0.0574641413523-0.0953809960526-0.04458150112561.065158076910.01417695348930.1376715178550.7663144727750.03981384821510.37915428357626.28559037184.4375603507269.9852155229
152.65645953339-0.4650697263561.215541240253.59571038786-1.485046648451.350038103370.0368813896084-0.393013291956-0.0664076909281-0.04665419342860.00616097576857-0.1966984444490.257606055261-0.170437910767-0.05709602175141.027278807220.01820924266060.09456618880940.7025599109770.0594300451530.29677615993719.308667518511.505044915285.185008575
161.99487166458-0.1865806456740.144000356631.414654953070.6470582483771.34698458330.1470275809030.1212814255940.00460004252657-0.317787027459-0.0509200153954-0.0936615865439-0.31384988179-0.0345224330372-0.07167810285781.01924147850.02211229366250.1210177404240.6283532168250.06827967177370.27218117598117.320928312720.577379460274.4145494821
171.36853746259-0.524223371790.329977673322.67313194873-3.382728864364.386660983710.1628972545710.1501996041170.843299565682-1.37363383509-0.2741729714080.0139255191365-0.186831133608-0.0215259577837-0.006812164899031.952763556730.287618066650.1661125989670.5881790206470.4551605404450.4655186077949.8312628292133.099613535356.0890503002
185.98984265952-2.59811275649-6.725048166071.128479923762.912937233277.564124213171.25924804740.528473383491.26837417947-0.837420994047-0.667443330457-1.34019194461-0.8949790951760.0111287944798-0.5925435935991.24992992254-0.09697186345860.3321807889220.7966999326140.1419493962080.67320572318127.906423475927.975487289664.2405250387
195.275906334184.19948603801-2.158336148136.085304399941.312428258155.807965718050.0553999696942-0.718929179489-0.2497478500380.3962340775880.0175316174838-0.86447731984-0.01701648916190.891093567356-0.04192441576130.269248262416-0.0183177332304-0.1060476744450.439239156661-0.03042475843370.73300118738240.1386763672-7.618664116717.6369706847
208.713112257682.292156435267.739715380863.175731558594.193211816448.721086654390.662225069839-1.32178083399-0.5967252539471.052012667740.183193614346-0.3912849791170.9659950758450.100502340111-0.8054609286370.562096861612-0.0352461970833-0.05796034233870.6432615576-0.03612333368060.34725785300732.0823924929-9.1746885014429.4670072983
212.188024603441.43857543338-0.3603861627921.52184881967-0.4560444614952.85555520274-0.0298129929921-0.402186053901-0.3275935053090.320407008344-0.07538951948090.7710820461680.108801212637-0.377205850120.1095825677540.271472435-0.02979830510230.0742563553440.38488998122-0.02202197197560.8387039384337.9081744198-24.171047192216.4047788297
222.292393829990.0989078944229-0.04400234817791.341197823770.002458653303741.895162115060.08014966671940.07681879225290.0310006954690.0915376928661-0.05570959552990.01418070806690.02498650792520.0469609893341-0.01555799988490.2031271064080.02576832971090.02382135778830.265146697604-0.01313575950530.6810645930816.1916131076-10.69034261477.21056301236
231.38144186545-0.194773515817-0.2058276080511.14527454506-0.018494179661.108893384740.0626971000557-0.04485561974280.01876291039360.3357202084720.1068997645540.0394648775957-0.08719274048860.297852340422-0.1645735697360.300502374405-0.02272913370850.04512132381030.292551091583-0.01791935640390.73443831141725.8388840026-3.2857864394719.2709599908
241.888284245181.1884665958-1.410146688273.56572206442.568342353975.250800559890.0413191537277-0.3147862137320.3978409798020.415023597274-0.1724106286340.517348682727-0.329981868098-0.1585165470130.0648769818780.4402995664360.06547746167820.03246091293890.352440104634-0.1164513091440.64960376236818.45593342496.3084109083824.4666418843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 57:98)
2X-RAY DIFFRACTION2(chain A and resid 99:117)
3X-RAY DIFFRACTION3(chain A and resid 118:235)
4X-RAY DIFFRACTION4(chain A and resid 236:336)
5X-RAY DIFFRACTION5(chain A and resid 337:404)
6X-RAY DIFFRACTION6(chain A and resid 405:460)
7X-RAY DIFFRACTION7(chain B and resid 57:104)
8X-RAY DIFFRACTION8(chain B and resid 105:210)
9X-RAY DIFFRACTION9(chain B and resid 211:294)
10X-RAY DIFFRACTION10(chain B and resid 295:394)
11X-RAY DIFFRACTION11(chain B and resid 395:445)
12X-RAY DIFFRACTION12(chain B and resid 446:460)
13X-RAY DIFFRACTION13(chain C and resid 57:104)
14X-RAY DIFFRACTION14(chain C and resid 105:210)
15X-RAY DIFFRACTION15(chain C and resid 211:283)
16X-RAY DIFFRACTION16(chain C and resid 284:394)
17X-RAY DIFFRACTION17(chain C and resid 395:445)
18X-RAY DIFFRACTION18(chain C and resid 446:460)
19X-RAY DIFFRACTION19(chain D and resid 58:98)
20X-RAY DIFFRACTION20(chain D and resid 99:118)
21X-RAY DIFFRACTION21(chain D and resid 119:198)
22X-RAY DIFFRACTION22(chain D and resid 199:336)
23X-RAY DIFFRACTION23(chain D and resid 337:419)
24X-RAY DIFFRACTION24(chain D and resid 420:460)

+
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