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- PDB-5o03: GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-32 -

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Basic information

Entry
Database: PDB / ID: 5o03
TitleGII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-32
Components
  • Capsid proteinCapsid
  • Nanobody (VHH) Nano-32
KeywordsVIRAL PROTEIN / Norovirus / Protruding domain / capsid / VHH / Nanobody
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
IMIDAZOLE / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsKoromyslova, A.D. / Hansman, G.H.
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
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
Revision 1.2Sep 12, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant

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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
C: Nanobody (VHH) Nano-32
D: Nanobody (VHH) Nano-32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,40021
Polymers97,3314
Non-polymers1,06917
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint21 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.660, 109.660, 268.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA224 - 538
211chain BB224 - 538
112chain CC1 - 135
212chain DD1 - 135

NCS ensembles :
ID
1
2

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Components

#1: Protein Capsid protein / Capsid


Mass: 34506.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Variant (production host): WK6 / References: UniProt: Q5F4T5
#2: Antibody Nanobody (VHH) Nano-32


Mass: 14158.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.19→49.041 Å / Num. obs: 84293 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.641 % / Biso Wilson estimate: 45.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Χ2: 1.049 / Net I/σ(I): 23.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.19-2.338.4860.7732.66132580.9250.82498.9
2.33-2.4910.9950.4845.01126380.9740.508100
2.49-2.6911.3660.2679.14118270.990.28100
2.69-2.9410.8060.14315.43108720.9960.15100
2.94-3.2911.5550.07627.6999220.9990.08100
3.29-3.7911.3620.04842.3188110.9990.05100
3.79-4.6410.4750.03454.2375090.9990.036100
4.64-6.5311.0920.03260.759380.9990.034100
6.53-49.0419.7410.03662.9835180.9990.03899.4

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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: 2.194→49.041 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1
RfactorNum. reflection% reflection
Rfree0.1929 4212 5 %
Rwork0.1722 --
obs0.1732 84222 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.51 Å2 / Biso mean: 63.0572 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.194→49.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 70 235 6943
Biso mean--75.26 54.41 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056955
X-RAY DIFFRACTIONf_angle_d0.8739487
X-RAY DIFFRACTIONf_chiral_restr0.0351052
X-RAY DIFFRACTIONf_plane_restr0.0041248
X-RAY DIFFRACTIONf_dihedral_angle_d12.2922433
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2778X-RAY DIFFRACTION4.91TORSIONAL
12B2778X-RAY DIFFRACTION4.91TORSIONAL
21C1074X-RAY DIFFRACTION4.91TORSIONAL
22D1074X-RAY DIFFRACTION4.91TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1942-2.21920.28491290.25992452258194
2.2192-2.24530.27771400.232626512791100
2.2453-2.27270.22751360.229526022738100
2.2727-2.30140.24851370.236326052742100
2.3014-2.33170.28291410.229226782819100
2.3317-2.36370.29841370.21525912728100
2.3637-2.39740.25461390.209626412780100
2.3974-2.43320.22351400.201526402780100
2.4332-2.47120.23471390.197526332772100
2.4712-2.51170.25821390.206726412780100
2.5117-2.55510.26341400.203926532793100
2.5551-2.60150.23571380.197526372775100
2.6015-2.65160.2291380.196226152753100
2.6516-2.70570.25771390.195126622801100
2.7057-2.76450.20991400.179626562796100
2.7645-2.82880.22821400.190326572797100
2.8288-2.89950.18991380.189126512789100
2.8995-2.97790.22341410.18626642805100
2.9779-3.06550.20271400.188326672807100
3.0655-3.16450.24051410.185926742815100
3.1645-3.27750.18731400.194826612801100
3.2775-3.40870.23221410.184826832824100
3.4087-3.56380.17831420.183626832825100
3.5638-3.75170.22061410.169326712812100
3.7517-3.98660.18581430.163327242867100
3.9866-4.29430.1571420.138926952837100
4.2943-4.72610.13391440.119627292873100
4.7261-5.40920.15571450.138627472892100
5.4092-6.81220.16121480.158627982946100
6.8122-49.05370.17021540.17482949310399
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)
13.08850.0215-0.73313.3865-1.28493.7018-0.00410.3891-0.2794-0.1384-0.0522-0.0188-0.0639-0.14940.08050.26930.0231-0.05510.5129-0.03490.31190.666439.9474-37.6771
26.6055-4.52224.90074.2135-5.25338.5477-0.0189-0.28320.0085-0.00940.06720.06690.1094-0.4231-0.01030.2741-0.0475-0.00830.4424-0.05380.3122.342532.1183-22.2796
32.8708-0.61881.0260.606-1.26953.08310.0855-0.0335-0.13920.1166-0.1562-0.00270.1179-0.1520.10270.3371-0.0962-0.04460.5473-0.02760.45772.601224.0618-20.3488
44.22341.66151.23223.28110.75772.87760.0111-0.1922-0.30850.2223-0.179-0.32850.21620.46820.12680.25520.0462-0.06670.4770.06180.444313.96923.2896-19.7518
52.08270.20110.03141.3651-0.40882.98160.06820.1905-0.35370.0092-0.098-0.01590.3097-0.1802-0.02290.2472-0.0116-0.03920.4707-0.08880.39714.252325.4247-32.2303
63.9255-0.70370.56272.1915-0.06913.83520.02350.44770.1788-0.1376-0.11880.021-0.4314-0.31170.09860.32130.0676-0.02330.60990.00970.3435-2.427446.71-40.8326
78.05390.10324.26584.10283.21598.4148-0.41570.32930.6655-0.4434-0.12210.4423-0.8263-1.12780.56130.58660.19160.00310.75560.12110.3932-8.937951.0952-45.4968
83.12320.2105-0.63431.47850.38172.50150.1005-0.39180.25160.3702-0.2159-0.3264-0.73250.54980.07050.5476-0.1822-0.08830.52270.02520.371914.43750.0644-16.7274
95.9972-3.7622-2.41592.60460.7212.84510.04510.3595-0.17750.2455-0.3311-0.2862-0.55160.60660.00030.3493-0.1297-0.0910.66990.1260.403821.53646.0029-31.9383
101.0259-0.1566-0.80610.97961.39332.3349-0.0020.26450.09-0.1752-0.1233-0.1687-0.31460.98760.14330.4161-0.1793-0.08181.00190.13710.551629.624342.6854-33.7181
117.13412.81462.54664.14060.71761.6561-0.16120.5156-0.4648-0.2796-0.0365-0.4649-0.21591.10550.0680.2580.02870.00810.83720.05870.496525.920931.8363-35.1906
120.89781.0821-0.32962.14620.09831.8017-0.07970.015-0.12990.1798-0.1115-0.53970.07350.90450.08750.2997-0.0428-0.1030.97450.09690.587529.713634.0554-28.5535
135.56860.32690.11522.5799-1.1070.49410.12140.29780.45170.3373-0.2077-0.797-0.96960.8656-0.0690.6119-0.478-0.17151.04050.11230.665831.891252.3141-24.2827
142.7959-0.232-0.50150.1010.5292.9089-0.0473-0.43110.14650.635-0.0891-0.1146-0.64480.76080.00320.6422-0.2559-0.17390.71630.0350.427920.196247.0815-10.4341
151.9684-0.3469-0.76265.311-0.18794.88670.1332-0.01470.24160.231-0.11470.1844-1.18090.12730.03070.6227-0.1294-0.06140.4471-0.0040.38127.425256.0566-15.7995
165.01181.0461-0.14013.16170.96524.7629-0.014-0.01050.44040.8369-0.0559-0.0791-0.77980.59790.1530.6925-0.1544-0.16170.5152-0.01080.37713.033452.9163-7.5281
173.55572.56974.93717.26922.78357.0042-0.1125-0.370.53420.0222-0.12270.139-1.73730.28470.33470.9985-0.13080.05380.6101-0.03050.45967.447862.8512-8.7962
182.7189-0.40780.79094.4635-0.3472.09070.24340.4667-0.577-0.4053-0.1762-0.74010.10590.16860.02470.45320.04320.06421.03640.11860.547625.734643.7682-56.1103
197.1316-1.7208-1.78983.58630.07714.03960.22591.16690.1906-0.5808-0.2229-0.5817-0.28980.6704-0.00450.5191-0.01390.1141.0660.14890.575927.262347.0695-61.6216
204.1782.7517-5.49799.7119-6.18528.48850.49381.53811.8091-0.95740.29051.5435-0.862-1.3341-0.72620.94460.17380.01781.11310.15530.720513.780454.0648-59.4972
217.41141.3629-1.68033.97880.97332.41610.140.0051-0.16970.1847-0.2431-0.5343-0.33920.47240.11150.4012-0.0161-0.03670.90520.13710.527725.792548.5631-50.4399
223.60995.1905-0.72478.41440.49237.53980.4629-0.5482-1.2959-0.057-0.3251-0.79030.6181-0.15370.12660.7088-0.098-0.21810.63610.19050.82344.281521.57951.0877
234.43172.05330.4416.7253-0.46766.4070.6798-0.8624-0.62990.7799-0.4911-0.25070.2676-0.3862-0.16380.7106-0.2588-0.10370.59960.08290.44930.367429.85255.5808
242.6130.9462-1.09886.273-3.46384.95980.6168-0.6663-0.58140.536-0.27470.14371.0563-0.3884-0.2370.9288-0.3514-0.25040.74290.11520.6324-4.113522.75771.3543
257.47544.0028-1.46974.2621-3.29043.52590.4931-0.11830.30840.3966-0.3287-0.01180.0289-0.8612-0.18390.6604-0.1413-0.12550.6225-0.06840.4118-2.312233.1725-1.2823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 266 )A224 - 266
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 294 )A267 - 294
3X-RAY DIFFRACTION3chain 'A' and (resid 295 through 332 )A295 - 332
4X-RAY DIFFRACTION4chain 'A' and (resid 333 through 370 )A333 - 370
5X-RAY DIFFRACTION5chain 'A' and (resid 371 through 455 )A371 - 455
6X-RAY DIFFRACTION6chain 'A' and (resid 456 through 520 )A456 - 520
7X-RAY DIFFRACTION7chain 'A' and (resid 521 through 538 )A521 - 538
8X-RAY DIFFRACTION8chain 'B' and (resid 224 through 266 )B224 - 266
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 294 )B267 - 294
10X-RAY DIFFRACTION10chain 'B' and (resid 295 through 332 )B295 - 332
11X-RAY DIFFRACTION11chain 'B' and (resid 333 through 370 )B333 - 370
12X-RAY DIFFRACTION12chain 'B' and (resid 371 through 409 )B371 - 409
13X-RAY DIFFRACTION13chain 'B' and (resid 410 through 429 )B410 - 429
14X-RAY DIFFRACTION14chain 'B' and (resid 430 through 455 )B430 - 455
15X-RAY DIFFRACTION15chain 'B' and (resid 456 through 500 )B456 - 500
16X-RAY DIFFRACTION16chain 'B' and (resid 501 through 520 )B501 - 520
17X-RAY DIFFRACTION17chain 'B' and (resid 521 through 538 )B521 - 538
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 51 )C1 - 51
19X-RAY DIFFRACTION19chain 'C' and (resid 52 through 99 )C52 - 99
20X-RAY DIFFRACTION20chain 'C' and (resid 100 through 112 )C100 - 112
21X-RAY DIFFRACTION21chain 'C' and (resid 113 through 135 )C113 - 135
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 17 )D1 - 17
23X-RAY DIFFRACTION23chain 'D' and (resid 18 through 83 )D18 - 83
24X-RAY DIFFRACTION24chain 'D' and (resid 84 through 99 )D84 - 99
25X-RAY DIFFRACTION25chain 'D' and (resid 100 through 135 )D100 - 135

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