[English] 日本語
Yorodumi
- PDB-5o02: GII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o02
TitleGII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4
Components
  • Capsid protein
  • Nanobody (VHH) Nano-4
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 speciesNorovirus 13-BH-1/2013/GII.17
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsKoromyslova, A.D. / Hansman, G.S.
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 1.2Apr 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
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
C: Nanobody (VHH) Nano-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1149
Polymers47,6732
Non-polymers4417
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint17 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.470, 64.040, 70.030
Angle α, β, γ (deg.)90.000, 97.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

21A-1018-

HOH

31A-1033-

HOH

-
Components

#1: Protein Capsid protein


Mass: 34085.926 Da / Num. of mol.: 1 / Fragment: UNP residues 225-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus 13-BH-1/2013/GII.17 / Variant: Kawasaki323 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A7CJV4
#2: Antibody Nanobody (VHH) Nano-4


Mass: 13586.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: Phen6C / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 10% (w/v) PEG8000, 0.1 M imidazole

-
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: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.69→45.06 Å / Num. obs: 55894 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.165 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.082 / Χ2: 1.024 / Net I/σ(I): 11.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.82.930.4272.2684120.8490.52190.2
1.8-1.923.2980.2713.9485240.9280.32497.6
1.92-2.073.310.176.2879890.970.20498.1
2.07-2.273.2240.1189.1973920.9810.14298.3
2.27-2.542.9830.08511.9266410.9870.10497.8
2.54-2.933.2520.06116.8559150.9940.07397.8
2.93-3.593.2190.04423.4849550.9960.05397.5
3.59-5.052.960.03328.4538440.9970.04196.5
5.05-45.063.3780.03231.5122220.9970.03897.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.69 Å45.06 Å
Translation7.06 Å45.06 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4M and 4X4C

5f4m

4x4c


Resolution: 1.72→45.06 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.1805 2703 5 %
Rwork0.1503 --
obs0.1518 54046 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.32 Å2 / Biso mean: 20.9462 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.72→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 29 515 3869
Biso mean--43.64 33 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063628
X-RAY DIFFRACTIONf_angle_d1.0514960
X-RAY DIFFRACTIONf_chiral_restr0.045521
X-RAY DIFFRACTIONf_plane_restr0.005672
X-RAY DIFFRACTIONf_dihedral_angle_d12.0711322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.75130.3031400.26052665280597
1.7513-1.7850.23821410.23642665280697
1.785-1.82140.25731400.20242664280497
1.8214-1.8610.23921420.19162701284398
1.861-1.90430.21931410.18032681282298
1.9043-1.95190.21981430.17012707285098
1.9519-2.00470.22681410.16512685282698
2.0047-2.06370.20021430.16172711285498
2.0637-2.13030.19371440.15242732287698
2.1303-2.20640.18321410.14962692283398
2.2064-2.29480.171420.15062696283898
2.2948-2.39920.19331430.15182724286798
2.3992-2.52570.18461420.15412685282798
2.5257-2.68390.21421430.15542723286697
2.6839-2.89110.181420.15262700284298
2.8911-3.1820.16551440.14452725286998
3.182-3.64220.15011420.13532698284097
3.6422-4.58810.14081410.11622690283196
4.5881-45.07580.15111480.13592799294798
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)
10.70550.1930.21891.26860.89181.31690.01080.0943-0.0767-0.06860.0198-0.10190.03610.0684-0.00970.0770.00890.01620.10920.00020.0876-15.9811-63.1776204.5607
21.36890.4170.22850.56650.16840.79230.03420.1012-0.2507-0.07780.0166-0.11180.04630.0486-0.04430.09680.02580.01120.1024-0.02860.1143-14.2817-73.4175201.6517
30.75180.64710.28371.55440.33940.44610.0173-0.02250.01190.0554-0.0186-0.0139-0.0030.0332-0.00050.0779-0.00220.01290.11240.00050.0621-13.7728-51.0198219.7183
43.29044.7882.98826.96744.34832.7137-0.55160.73420.2049-0.72960.35430.0809-0.69630.75270.32430.2763-0.03920.04470.25070.00060.16712.3049-26.7987223.5207
51.7354-1.6663-1.42026.23-2.54314.4885-0.34010.06080.3423-0.00240.0926-0.1771-0.60620.78050.22760.1764-0.0715-0.02190.2236-0.01190.148912.6698-21.4852244.088
67.71426.39417.19825.33536.01396.7805-0.0396-0.01590.2119-0.2451-0.02590.0751-0.3148-0.07130.1460.19390.027-0.00750.1402-0.02420.1191-0.3918-23.2417230.71
78.6237-3.08297.87482.9436-3.58998.6309-0.22960.01160.08920.03020.0998-0.0489-0.2639-0.19020.14650.11570.00410.01740.1196-0.03890.0728-3.5198-31.6177232.1295
86.59340.35170.12062.2778-0.58454.9444-0.1001-0.4329-0.12710.34680.0308-0.56680.36480.3240.05170.16860.019-0.04610.1199-0.00260.14384.0836-36.6521239.5696
94.1896-0.05455.48943.1152-0.00527.25480.1004-0.3574-0.0430.2317-0.06650.21460.165-0.494-0.04030.13350.00980.02910.1734-0.01030.112-7.2286-30.7435242.008
104.58830.46740.20594.39492.64981.5987-0.0845-0.4213-0.05690.1681-0.07880.25490.0409-0.3191-0.00820.12010.00610.01770.1445-0.02880.0841-3.4357-25.3464242.577
114.2462-2.88555.66953.0896-3.55727.7358-0.13220.16860.2574-0.0416-0.00350.0528-0.33390.17940.1940.21750.0211-0.04630.18050.00220.1434-2.4684-21.686234.6013
123.65841.70672.54891.75081.70932.88130.0103-0.1503-0.05760.138-0.03260.02340.0563-0.050900.11960.01720.0190.1109-0.00090.0566-1.319-33.0757237.2116
133.07442.18831.78694.12972.19934.6125-0.28520.1369-0.0921-0.28440.2012-0.22840.00150.37460.09320.10420.01660.01660.0923-0.00330.06872.0218-35.1873227.9151
147.5453-0.41264.59467.8913-2.09183.2285-0.10210.07420.0365-0.05660.3547-0.44-0.50180.985-0.17660.10910.0058-0.00110.2668-0.05490.131714.3607-26.792240.6376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 315 )A225 - 315
2X-RAY DIFFRACTION2chain 'A' and (resid 316 through 426 )A316 - 426
3X-RAY DIFFRACTION3chain 'A' and (resid 427 through 528 )A427 - 528
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 7 )C1 - 7
5X-RAY DIFFRACTION5chain 'C' and (resid 8 through 17 )C8 - 17
6X-RAY DIFFRACTION6chain 'C' and (resid 18 through 28 )C18 - 28
7X-RAY DIFFRACTION7chain 'C' and (resid 29 through 39 )C29 - 39
8X-RAY DIFFRACTION8chain 'C' and (resid 40 through 51 )C40 - 51
9X-RAY DIFFRACTION9chain 'C' and (resid 52 through 64 )C52 - 64
10X-RAY DIFFRACTION10chain 'C' and (resid 65 through 73 )C65 - 73
11X-RAY DIFFRACTION11chain 'C' and (resid 74 through 83 )C74 - 83
12X-RAY DIFFRACTION12chain 'C' and (resid 84 through 108 )C84 - 108
13X-RAY DIFFRACTION13chain 'C' and (resid 109 through 117 )C109 - 117
14X-RAY DIFFRACTION14chain 'C' and (resid 118 through 124 )C118 - 124

+
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://pdbjlvh1.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