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- PDB-5o04: GII.10 Vietnam 026 norovirus protruding domain in complex with Na... -

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Basic information

Entry
Database: PDB / ID: 5o04
TitleGII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-26 and Nano-85
Components
  • Capsid protein
  • Nanobody (VHH) Nano-26
  • Nanobody (VHH) Nano-85
KeywordsVIRAL PROTEIN / Norovirus / Protruding domain / capsid / VHH / Nanobody Nanobody (VHH) Nano-4
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorwalk virus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKoromyslova, A.D. / Hansman, A.D.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization.
Authors: Koromyslova, A.D. / Hansman, G.S.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: 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.name
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Capsid protein
B: Capsid protein
E: Nanobody (VHH) Nano-26
D: Nanobody (VHH) Nano-85
F: Nanobody (VHH) Nano-26
C: Nanobody (VHH) Nano-85
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,76924
Polymers121,6526
Non-polymers1,11718
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint7 kcal/mol
Surface area42260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.250, 91.480, 118.120
Angle α, β, γ (deg.)90.000, 127.120, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
12chain E and segid
22chain F and segid CAAA

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
112chain E and segidE0
212chain F and segid CAAAF0

NCS ensembles :
ID
1
2

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Components

#1: Protein Capsid protein


Mass: 34506.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Variant: Vietnam 026 / Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Antibody Nanobody (VHH) Nano-26


Mass: 12917.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Antibody Nanobody (VHH) Nano-85


Mass: 13401.786 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate, 40% PEG600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→47.978 Å / Num. obs: 58206 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 2.823 % / Biso Wilson estimate: 39.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.097 / Χ2: 0.923 / Net I/σ(I): 10.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.442.7330.5922.2991740.7630.72790.1
2.44-2.612.6950.4293.1488270.8310.52792.1
2.61-2.812.8930.2884.7484160.9150.34994.3
2.81-3.082.8780.1717.5677030.960.20893.5
3.08-3.442.7730.09411.9468080.9830.11591.5
3.44-3.972.9730.05318.3961310.9940.06492.5
3.97-4.862.8330.03524.2350400.9970.04390.2
4.86-6.842.9360.03324.9239300.9970.0489.8
6.84-47.9782.7650.03129.5721770.9970.03986.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.978 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21
RfactorNum. reflection% reflection
Rfree0.2415 2911 5 %
Rwork0.2116 --
obs0.2131 58188 91.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.68 Å2 / Biso mean: 52.2446 Å2 / Biso min: 21.95 Å2
Refinement stepCycle: final / Resolution: 2.3→47.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8045 0 72 81 8198
Biso mean--58.59 38.18 -
Num. residues----1076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028324
X-RAY DIFFRACTIONf_angle_d0.67411330
X-RAY DIFFRACTIONf_chiral_restr0.0281258
X-RAY DIFFRACTIONf_plane_restr0.0041486
X-RAY DIFFRACTIONf_dihedral_angle_d11.9662897
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2750X-RAY DIFFRACTION5.195TORSIONAL
12B2750X-RAY DIFFRACTION5.195TORSIONAL
21E792X-RAY DIFFRACTION5.195TORSIONAL
22F792X-RAY DIFFRACTION5.195TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2993-2.3370.39441220.37492304242680
2.337-2.37730.30231400.31052673281395
2.3773-2.42050.36091420.30522684282694
2.4205-2.46710.3231410.29782671281294
2.4671-2.51750.26831380.28532628276693
2.5175-2.57220.33641370.29452608274591
2.5722-2.6320.32461410.2792680282194
2.632-2.69780.31291410.28692675281695
2.6978-2.77080.28811420.27262693283594
2.7708-2.85230.31081400.26722672281294
2.8523-2.94430.30061410.25992678281994
2.9443-3.04960.28971420.25322690283294
3.0496-3.17160.24961400.23442671281193
3.1716-3.3160.26831360.22442581271791
3.316-3.49070.22991400.21142647278792
3.4907-3.70940.25561390.20112650278993
3.7094-3.99560.23361400.18542652279292
3.9956-4.39750.19491380.15742636277491
4.3975-5.03320.1521350.14242556269189
5.0332-6.3390.19771390.16832637277691
6.339-47.9880.18941370.16822591272888
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)
11.99210.6158-1.16191.1323-0.59191.5598-0.0521-0.18430.00140.05620.04410.0149-0.0029-0.006-0.03520.43670.0379-0.01940.3213-0.02110.2383-36.6067-32.408325.5636
21.58710.19430.85812.14780.581.36890.0079-0.3842-0.03730.409-0.04370.0627-0.0704-0.09760.04120.4730.03030.04370.43830.02670.2394-43.7313-38.142434.146
31.7210.4411-0.51381.1138-0.32210.8484-0.0788-0.07850.1455-0.049-0.0108-0.0936-0.15980.04660.08590.36670.0244-0.01740.21690.00310.2185-29.5538-23.113514.3051
43.5661-0.27090.91840.624-0.10571.0238-0.04990.0264-0.3036-0.08080.0320.05230.07210.01880.00390.38470.00390.01790.1763-0.00570.2516-35.7763-51.068911.9158
50.7202-0.09470.12631.0451-0.17020.9588-0.0428-0.1015-0.21110.09220.06190.14620.0768-0.0142-0.02650.30560.00660.0480.21610.00320.2546-42.4569-52.416315.0096
64.0843-1.1877-0.75724.00620.3064.3343-0.0185-0.3511-0.24170.2262-0.0959-0.41620.17970.18910.14050.30150.04230.0070.31870.09020.392-13.4338-56.162320.9333
74.16161.24193.32936.2573-0.3783.00270.4281-0.0944-0.3276-0.63350.1227-0.08590.02180.412-0.34450.655-0.10260.16970.6482-0.18310.4682-21.3769-52.0784-8.5901
83.28780.26110.5724.3984-3.81233.73620.19410.86890.4383-1.39760.06370.14940.07560.3095-0.10140.959-0.10710.01120.91690.00490.445-25.1672-48.1873-23.0521
93.05171.10690.35387.07552.73474.83740.12670.2444-0.3153-0.69650.0282-1.2557-0.43070.1746-0.18690.27080.06870.05030.31260.00290.3229-23.209-42.3816-0.8953
102.70951.68812.59374.9674-0.78175.89730.68820.6338-0.2577-1.1947-0.11-1.0554-0.34810.6044-0.57630.6772-0.00260.23250.5588-0.0550.5041-11.5983-46.3368-18.265
112.792-3.5334-4.69824.71716.12518.05450.5402-0.45270.4925-0.74520.3153-0.9079-1.22110.2829-0.60280.7386-0.02750.02520.36410.04480.4653-16.8638-35.2242-12.1891
123.93020.0895-1.05580.87581.43437.83580.05581.4380.4674-1.29050.2247-0.1228-0.5932-0.3585-0.2281.2080.05260.11970.72650.08970.4002-19.8378-36.1122-20.3863
133.9270.9876-1.28773.19172.45283.06230.26890.98230.2653-0.8364-0.40480.22760.4288-1.08320.22620.78620.14380.01670.6835-0.0350.3538-27.019-42.6396-12.9275
146.5732-1.0121-5.96691.16031.67896.0503-0.46110.26420.2866-1.09240.56440.0427-0.7299-0.649-0.10771.33590.21580.01411.444-0.03330.5206-18.8167-43.9197-30.6411
151.25630.12812.64613.75692.8857.4963-0.36430.6919-0.5956-0.0856-0.1805-0.28210.35890.12050.55320.6506-0.03030.24270.6081-0.10170.3707-15.4095-45.8342-12.1756
163.81160.72822.35434.19862.40386.97320.13670.7299-0.9495-0.54350.6608-0.58890.12230.5464-0.54430.4386-0.01770.19510.4988-0.09370.5173-15.9788-49.9654-14.5788
179.7499-5.61683.71826.3935-2.57868.17440.7522-0.50140.4293-0.3492-0.0996-0.9463-0.31580.6207-0.62820.37180.00270.17970.61860.16561.050212.6313-65.222312.51
189.4071-1.2387-4.2270.16540.47718.6637-1.3780.2938-0.1166-0.02980.3096-0.28670.2498-0.22670.86850.6717-0.0581-0.03390.60460.23480.908312.0596-86.058420.1323
190.92512.7044-0.75358.0362-1.62794.8999-0.00290.00860.32880.2464-0.0605-0.53980.51040.46130.31350.31530.07640.16840.50010.19410.96811.7075-69.48918.8294
201.0635-0.11760.14266.58210.8850.4133-0.07770.343-0.2853-0.70770.135-1.2977-0.04420.0131-0.10050.38570.0650.22390.43950.15940.83953.6802-65.848814.8262
214.68051.63060.97482.0513-2.04394.74860.4182-0.05980.3764-0.56570.1656-0.0462-0.4748-0.9989-0.38931.0194-0.05540.34710.9475-0.32831.12440.8559-83.12135.0647
222.9806-1.5153-0.19625.59941.60265.3559-0.2888-0.2917-1.05010.5854-0.21980.9190.3548-0.63750.41040.3690.07070.14590.45310.14950.8607-2.7414-73.827620.4423
234.22762.124-0.89012.782-2.62433.0189-0.0126-0.7152-0.42151.5649-0.2517-0.586-0.79040.24320.23760.84030.15580.07020.5950.21160.75926.5642-67.750824.7762
243.19714.5826-0.09069.61910.52161.1915-0.2127-0.25760.6124-0.2909-0.1601-0.12950.0390.17640.14390.53070.0711-0.01150.41910.16950.7748.4034-70.974122.3913
251.3382-1.77550.95842.7554-0.6442.56740.1390.1029-0.3112-0.7041-0.0368-0.13560.7876-0.1163-0.06030.45330.04460.1970.44540.13260.8534.2642-75.771514.6483
269.3499-4.188-0.81885.40150.1675.2602-0.15420.41350.27480.51860.29140.36020.09580.1405-0.21640.37020.11760.1490.47620.22980.6061-0.1463-55.64249.4606
270.8469-2.0210.94875.4019-1.99161.1787-0.2536-0.1705-1.089-0.5888-0.06630.22730.5026-0.10580.20960.69370.14110.28930.44510.12641.141711.0338-81.473312.1248
286.42470.60975.07940.07590.49984.006-1.1188-1.20081.01990.3867-0.2242-0.4902-1.0083-0.47211.20850.98110.0654-0.141.082-0.08470.5558-8.9407-25.627543.8184
297.38012.58145.38255.15892.7837.813-0.5598-0.3128-0.3328-0.29190.2676-0.9281-0.72550.55580.29130.4429-0.0647-0.03450.54910.08710.4618-6.4699-32.305834.4308
300.7024-1.4653-0.84513.77650.40653.70950.2124-1.2919-0.32170.4319-0.1752-1.34130.21770.7339-0.00830.6723-0.0974-0.34471.10120.15870.6404-0.5268-37.820440.8447
313.7645-1.52861.30371.8655-0.43917.5844-0.0364-1.30690.62440.8825-0.2176-1.0652-1.0392-0.12710.1720.7259-0.1656-0.19120.8169-0.10840.7294-5.0319-28.041939.1401
321.8541-2.9990.80326.9164-0.49552.8981-0.3031-0.16590.24030.18290.1955-1.0355-0.560.41230.08540.4002-0.09380.04860.37610.07840.5724-11.92416.54371.255
336.5315-0.7093-0.21627.5686-0.75943.2751-0.2945-0.18380.65420.729-0.123-0.264-0.27510.31550.36340.3225-0.0316-0.08090.28160.08090.3907-17.1843-2.58588.0843
347.4319-2.0345-2.04934.23990.72845.6268-0.21180.5369-0.2663-0.0145-0.0787-0.1839-0.2532-0.03320.31830.3492-0.0601-0.05630.34640.01030.3016-20.19981.71360.6185
352.27390.19531.75845.4245-3.53993.8424-0.3979-0.23630.04961.0526-0.0509-0.7209-0.82710.0560.44750.3652-0.004-0.05220.35860.01340.396-16.74574.89467.9733
362.4108-1.96170.67418.1412-0.78141.61940.1246-0.06330.52020.3122-0.4498-1.1955-0.58880.20980.3530.3713-0.03230.03960.34760.05230.4435-11.89854.27578.6531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 226 through 307 )A226 - 307
2X-RAY DIFFRACTION2chain 'A' and (resid 308 through 417 )A308 - 417
3X-RAY DIFFRACTION3chain 'A' and (resid 418 through 538 )A418 - 538
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 327 )B224 - 327
5X-RAY DIFFRACTION5chain 'B' and (resid 328 through 472 )B328 - 472
6X-RAY DIFFRACTION6chain 'B' and (resid 473 through 538 )B473 - 538
7X-RAY DIFFRACTION7chain 'E' and (resid 1 through 7 )E1 - 7
8X-RAY DIFFRACTION8chain 'E' and (resid 8 through 23 )E8 - 23
9X-RAY DIFFRACTION9chain 'E' and (resid 24 through 32 )E24 - 32
10X-RAY DIFFRACTION10chain 'E' and (resid 33 through 45 )E33 - 45
11X-RAY DIFFRACTION11chain 'E' and (resid 46 through 56 )E46 - 56
12X-RAY DIFFRACTION12chain 'E' and (resid 57 through 72 )E57 - 72
13X-RAY DIFFRACTION13chain 'E' and (resid 73 through 82 )E73 - 82
14X-RAY DIFFRACTION14chain 'E' and (resid 83 through 90 )E83 - 90
15X-RAY DIFFRACTION15chain 'E' and (resid 91 through 99 )E91 - 99
16X-RAY DIFFRACTION16chain 'E' and (resid 100 through 114 )E100 - 114
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 7 )D1 - 7
18X-RAY DIFFRACTION18chain 'D' and (resid 8 through 17 )D8 - 17
19X-RAY DIFFRACTION19chain 'D' and (resid 18 through 26 )D18 - 26
20X-RAY DIFFRACTION20chain 'D' and (resid 27 through 39 )D27 - 39
21X-RAY DIFFRACTION21chain 'D' and (resid 40 through 45 )D40 - 45
22X-RAY DIFFRACTION22chain 'D' and (resid 46 through 66 )D46 - 66
23X-RAY DIFFRACTION23chain 'D' and (resid 67 through 75 )D67 - 75
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 82 )D76 - 82
25X-RAY DIFFRACTION25chain 'D' and (resid 83 through 100 )D83 - 100
26X-RAY DIFFRACTION26chain 'D' and (resid 101 through 110 )D101 - 110
27X-RAY DIFFRACTION27chain 'D' and (resid 111 through 119 )D111 - 119
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 23 )F1 - 23
29X-RAY DIFFRACTION29chain 'F' and (resid 24 through 51 )F24 - 51
30X-RAY DIFFRACTION30chain 'F' and (resid 52 through 72 )F52 - 72
31X-RAY DIFFRACTION31chain 'F' and (resid 73 through 111 )F73 - 111
32X-RAY DIFFRACTION32chain 'C' and (resid 1 through 26 )C1 - 26
33X-RAY DIFFRACTION33chain 'C' and (resid 27 through 59 )C27 - 59
34X-RAY DIFFRACTION34chain 'C' and (resid 60 through 82 )C60 - 82
35X-RAY DIFFRACTION35chain 'C' and (resid 83 through 100 )C83 - 100
36X-RAY DIFFRACTION36chain 'C' and (resid 101 through 123 )C101 - 123

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