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- PDB-8pxv: Targeting extended blood antigens by Akkermansia muciniphila enzy... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8pxv
TitleTargeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / Beta-hexosaminidase / Akkermansia muciniphila / GalNAc-B converting / CBM
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-lactose / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWeikum, J. / Jensen, M. / Abou Hachem, M. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Technology and Production Sciences0136-00086A Denmark
Citation
Journal: Nat Microbiol / Year: 2024
Title: Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood.
Authors: Jensen, M. / Stenfelt, L. / Ricci Hagman, J. / Pichler, M.J. / Weikum, J. / Nielsen, T.S. / Hult, A. / Morth, J.P. / Olsson, M.L. / Abou Hachem, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2May 15, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,7277
Polymers219,9273
Non-polymers8004
Water8,215456
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4012
Polymers73,3091
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6512
Polymers73,3091
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6743
Polymers73,3091
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.260, 170.420, 171.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 376 or resid 389 through 647))
d_2ens_1(chain "B" and resid 4 through 647)
d_3ens_1(chain "C" and resid 4 through 647)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNGLYGLYAA4 - 3764 - 376
d_12ALAALAPROPROAA389 - 647389 - 647
d_21GLNGLNPROPROBB4 - 6474 - 647
d_31GLNGLNPROPROCC4 - 6474 - 647

NCS oper:
IDCodeMatrixVector
1given(-0.0703558484111, 0.0588012447892, 0.995787360939), (0.997521918654, 0.00442389617667, 0.0702171698863), (-0.000276402903946, 0.998259907416, -0.0589667774901)33.1289555446, -51.7832582874, 20.0401290705
2given(0.0740885084786, 0.986249026426, -0.147728639018), (-0.0239837790495, 0.149855078905, 0.988417034287), (0.996963224625, -0.0696872527876, 0.0347565180215)49.8998831735, -16.9325823896, -32.4147175307

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Components

#1: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 73309.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_0369 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UN02
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 11% PEG8000, 0.5 M NaCl, 0.1M NaCacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→54.32 Å / Num. obs: 93815 / % possible obs: 95.34 % / Redundancy: 4.8 % / Biso Wilson estimate: 45.99 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.069 / Rrim(I) all: 0.163 / Net I/σ(I): 10.36
Reflection shellResolution: 2.5→2.589 Å / Mean I/σ(I) obs: 1.34 / Num. unique obs: 9509 / CC1/2: 0.457 / Rpim(I) all: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→54.32 Å / SU ML: 0.3221 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1242
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 4657 4.96 %
Rwork0.1782 89149 -
obs0.1799 93806 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→54.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15081 0 53 456 15590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002715514
X-RAY DIFFRACTIONf_angle_d0.669321005
X-RAY DIFFRACTIONf_chiral_restr0.05292261
X-RAY DIFFRACTIONf_plane_restr0.00492707
X-RAY DIFFRACTIONf_dihedral_angle_d12.1195711
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.14080583705
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS2.29609416411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.3571660.31813021X-RAY DIFFRACTION97.22
2.53-2.560.30711500.29412996X-RAY DIFFRACTION98.31
2.56-2.590.28581580.26963018X-RAY DIFFRACTION98.15
2.59-2.620.30531570.2633014X-RAY DIFFRACTION97.69
2.62-2.660.31741580.25653021X-RAY DIFFRACTION97.94
2.66-2.690.27551550.25142982X-RAY DIFFRACTION96.91
2.69-2.730.31231660.23892993X-RAY DIFFRACTION97.62
2.73-2.770.30481560.23233018X-RAY DIFFRACTION96.74
2.77-2.820.27491460.23592972X-RAY DIFFRACTION97.26
2.82-2.860.27281570.23322996X-RAY DIFFRACTION96.81
2.86-2.910.29741300.23462997X-RAY DIFFRACTION96.45
2.91-2.960.2731660.23082990X-RAY DIFFRACTION96.87
2.96-3.020.2711430.22952990X-RAY DIFFRACTION96.16
3.02-3.080.261610.20692986X-RAY DIFFRACTION96.95
3.08-3.150.26621830.21212946X-RAY DIFFRACTION95.98
3.15-3.220.2841490.22132989X-RAY DIFFRACTION95.5
3.22-3.30.23881640.20872951X-RAY DIFFRACTION96.02
3.3-3.390.24121390.19952974X-RAY DIFFRACTION95.55
3.39-3.490.21791640.18432933X-RAY DIFFRACTION94.8
3.49-3.610.22521410.17752947X-RAY DIFFRACTION94.32
3.61-3.730.20561260.1672970X-RAY DIFFRACTION94.07
3.73-3.880.18641800.15682927X-RAY DIFFRACTION94.99
3.88-4.060.19241770.14282939X-RAY DIFFRACTION94.71
4.06-4.270.16431470.1292950X-RAY DIFFRACTION93.99
4.27-4.540.15181820.12842903X-RAY DIFFRACTION93.63
4.54-4.890.16181660.12212939X-RAY DIFFRACTION93.38
4.89-5.380.14081670.12912904X-RAY DIFFRACTION92.39
5.38-6.160.16511400.14522936X-RAY DIFFRACTION91.9
6.16-7.760.19361200.15352951X-RAY DIFFRACTION90.94
7.76-54.320.15271430.15462996X-RAY DIFFRACTION88.67
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)
10.13712064638-0.1142329872980.2639820731150.269853159233-0.3592961489230.4852493954360.01103104538250.0393082181817-0.0546405106117-0.32704801591-0.121206385124-0.1012780553920.1377899208660.137414546481-1.9141069904E-50.5564766064110.0675701945439-0.05787907128680.415914410697-0.0164667519470.44526205441658.7797646473-19.039689942818.2937342167
20.756766752734-0.2732461705160.1163477649220.765589633020.3861777513660.365543368514-0.136994719204-0.208045600136-0.0535401118775-0.0398535183340.03963293398150.037148878087-0.00282731938386-0.0291570513291-0.0006176232853960.450628340814-0.0572203244472-0.05407803348330.558243855950.02703354105540.42806496820367.0817296310.65675070437412.9614441108
30.7653291685010.1145517769720.03833423339630.5499951931220.03668027577850.2179362000530.01393694231230.0124404919696-0.07381595566260.0508520321009-0.0736436378370.002604785994410.144922738472-0.1642625275451.36769775981E-50.467848793188-0.09308459808330.04247377971090.5298187160470.003146221920010.41883081119731.4162819399-6.2057391244-18.3599502959
41.341351874160.638270925603-0.3934470272480.476989570417-0.3481558619990.5935385951020.0596502596298-0.03066713031330.05118110003020.00817960436732-0.0235756875924-0.0114989241498-0.0278917734954-0.0219759210559-3.05620477602E-60.378637052823-0.002376566883070.01446311278260.3596228080830.004830330857360.34487876947761.52561488111.5670019332-27.835139158
50.146142409113-0.245848009607-0.06063553269640.1521320835680.2254341607150.05567242756390.124218949358-0.05940188623120.09744227031460.07679558252060.164987416081-0.3288817688910.0737206419712-0.0152314447278-4.04251888009E-50.457686097614-0.1045288191130.0570952984650.6230115535360.03515785963740.40083864730648.69224515069.02650713684-1.37326827693
60.7342109238720.152259646232-0.5921314289240.7981403836540.5567348096620.6256294980570.0227277726731-0.1175351650070.2264272830090.07037184760790.122578600786-0.3441873299960.04819965876210.1354711603760.000384231379440.378095441387-0.05651909303390.005224641652280.4986077809-0.03030170141340.56826079057645.408885239419.70400386117.0272830847
70.1308199049030.0257586827747-0.05792411632150.2936471824470.1321275277560.0581587869918-0.02924447395290.108379913095-0.219285620092-0.1968915101010.04438372241640.248511764660.457526527565-0.0589963984022-2.06763164786E-50.608617088892-0.0598397690018-0.01115035660880.480261822419-0.07063457757590.54575726289116.2591324073-19.188378522417.7170395187
80.5376049751620.24107741610.02627891540850.4999503512010.1515503652770.6249050769910.01630543745060.131197341273-0.279697955911-0.110750923462-0.01049108159260.04321322280720.164672861071-0.110177682062-0.0001319927252860.535998547154-0.09793671493910.0089219137210.487331041064-0.06214597386180.48711778111812.5351587117-16.127400649414.0039419282
90.2359253283320.148326973895-0.06714917293880.1380749787380.0173107798790.0261889168762-0.02217651254220.134654861662-0.0747701502902-0.231653669697-0.1337566983780.0732429448060.0941019705832-0.1470931181852.26447963513E-50.396262699209-0.0710125524928-0.009969322107950.455213670923-0.009896621528590.3354040027159.51728741856.5671346048219.9946024752
101.03023921192-0.4335249369930.112218483920.584456422315-0.1137981782530.774196787356-0.02261724862810.1501145708340.221000352491-0.1357101258940.03843411422350.332481867556-0.0776959026234-0.197370439064-1.81237734398E-50.396293798277-0.00593851360282-0.04645334570310.4757522011660.01484368841260.4632491482360.36152836039421.845657552418.8092730048
110.292402708608-0.03356546768090.1292095622820.2555165991440.01293075179530.191456842247-0.033357655578-0.05350307082830.269885779790.1396280868390.08530519584060.435065579309-0.193209501767-0.228838455796-1.39764544244E-50.4065915734670.05763048355820.09622655250680.588573778125-0.03346777459160.620608181904-7.3027183959824.279167920935.5183693862
120.405290391751-0.117486603178-0.2808916829470.630601342734-0.1683521982280.33105552104-0.0429186223426-0.07366610928420.2086920651270.09499327662420.0811603730233-0.0265229011607-0.0235901074215-0.174095090843-1.83606272555E-50.408091138446-0.0356541164391-0.01431479008080.485898472776-0.03747914472530.39303301964910.93836869859.7418925344334.3021758533
130.19111246546-0.231571809530.1064367437130.2170599859150.08847068002350.0838842771814-0.171860907437-0.227951449892-0.008414189930210.09693800772550.0809434255646-0.0822042305132-0.123900959624-0.271743452705-3.86810098183E-50.377682425323-0.02250159574260.03043287651380.453027165229-0.007935153757270.49398699528830.72046451610.021648249935727.6625741833
140.658480839908-0.09768575483580.07900056683310.2497229413020.05088676580420.07318612769520.0194551710717-0.0945440979310.1248633508870.0757615525130.150165571571-0.365739597205-0.01868924582240.06850074775832.38694342183E-50.4067767022940.0269480873684-0.003613045642760.370750050441-0.04338000979870.51262518513749.706427644-3.9552184345639.8770725286
150.6098582919140.0938078314533-0.05749658568230.3789486340350.1148285772780.62644932935-0.05616708051380.09574992019770.06812835543020.05826703630190.0527345270597-0.39033179715-0.06241689841020.197316654567-9.18120500668E-60.4577124024680.02101037230280.01124162127120.410001491284-0.03117712297810.46334269728649.4522174837-5.9416282426336.5458935608
160.14581444427-0.08860147543110.1509981546920.535753278502-0.1184107913950.2652932340310.2309003043860.488490968171-0.078745654306-0.722713793069-0.3473792817260.108890864686-0.39961988279-0.227651556166-0.6588396146581.001993629040.344448744081-0.2563604697010.669171887431-0.1392110197460.41538069790648.3477007605-34.69256559310.0145345802771
170.2357359079720.217159206279-0.2587999307340.34521185816-0.3754604446980.467479010869-0.0481192794760.507421257751-0.298231267439-0.555741692842-0.1818409073150.2435039583080.271710370815-0.36780198147-0.4051886711890.9075620760430.167758684899-0.2822677940480.704033260763-0.26429620460.6403481146942.4688950399-43.93533044711.20359831838
180.2273261337020.1187324420390.04616988089210.124635408139-0.06484948674880.05075540063890.5048165711810.575689727569-0.349664206512-0.676693010361-0.544543139910.246811647881-0.198231615424-0.111662187457-0.1876940179350.8079544551150.262641079371-0.2189253638190.607325472905-0.1673294639760.44054149954146.6975978991-36.58725714596.34121395643
190.546705281438-0.4418113404140.07281478859480.919886245883-0.1897025100291.127505632420.1098485371310.0378290590849-0.142747313375-0.184097469849-0.1164781133720.08720771105160.0557409762449-0.01064264728-0.006312187480260.3923912179830.00387746249192-0.03435021960670.312463809637-0.03470758658670.41552680340959.5551580635-45.267842826732.9021651085
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 499 through 542 )BC499 - 542486 - 529
22chain 'B' and (resid 543 through 647 )BC543 - 647530 - 634
33chain 'C' and (resid 4 through 144 )CE4 - 1441 - 141
44chain 'C' and (resid 145 through 498 )CE145 - 498142 - 483
55chain 'C' and (resid 499 through 542 )CE499 - 542484 - 527
66chain 'C' and (resid 543 through 647 )CE543 - 647528 - 632
77chain 'A' and (resid 2 through 34 )AA2 - 341 - 33
88chain 'A' and (resid 35 through 144 )AA35 - 14434 - 143
99chain 'A' and (resid 145 through 185 )AA145 - 185144 - 184
1010chain 'A' and (resid 186 through 323 )AA186 - 323185 - 322
1111chain 'A' and (resid 324 through 375 )AA324 - 375323 - 374
1212chain 'A' and (resid 376 through 498 )AA376 - 498375 - 497
1313chain 'A' and (resid 499 through 542 )AA499 - 542498 - 541
1414chain 'A' and (resid 543 through 588 )AA543 - 588542 - 587
1515chain 'A' and (resid 589 through 647 )AA589 - 647588 - 646
1616chain 'B' and (resid 2 through 34 )BC2 - 341 - 33
1717chain 'B' and (resid 35 through 82 )BC35 - 8234 - 81
1818chain 'B' and (resid 83 through 130 )BC83 - 13082 - 129
1919chain 'B' and (resid 131 through 498 )BC131 - 498130 - 485

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