[English] 日本語
Yorodumi
- PDB-6y61: Structure of apo Sheep Polyomavirus VP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y61
TitleStructure of apo Sheep Polyomavirus VP1
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Biological speciesSheep polyomavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsStroh, L.J. / Rustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Mbio / Year: 2020
Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,67821
Polymers324,66510
Non-polymers1,01311
Water17,475970
1
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,88511
Polymers162,3335
Non-polymers5536
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24790 Å2
ΔGint-166 kcal/mol
Surface area46490 Å2
MethodPISA
2
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,79310
Polymers162,3335
Non-polymers4605
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24440 Å2
ΔGint-166 kcal/mol
Surface area46850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.430, 130.430, 221.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Capsid protein VP1


Mass: 32466.500 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheep polyomavirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3ZCF3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: KSCN, PEG 3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7711
pseudo-merohedral22K, H, -L20.2289
ReflectionResolution: 2.45→49.77 Å / Num. obs: 147085 / % possible obs: 94.81 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 21.58
Reflection shellResolution: 2.45→2.538 Å / Mean I/σ(I) obs: 4.69 / Num. unique obs: 13659 / CC1/2: 0.929 / Rrim(I) all: 0.526

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg


Resolution: 2.45→49.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.044 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1968 7336 4.988 %
Rwork0.161 --
all0.163 --
obs-147076 94.803 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.333 Å2
Baniso -1Baniso -2Baniso -3
1--18.848 Å2-0 Å2-0 Å2
2---18.848 Å2-0 Å2
3---37.696 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20395 0 66 970 21431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01320971
X-RAY DIFFRACTIONr_bond_other_d0.0030.01718744
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.65428504
X-RAY DIFFRACTIONr_angle_other_deg1.2691.5743456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97552644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26622.2961041
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.063153159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.27415118
X-RAY DIFFRACTIONr_chiral_restr0.0640.22740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024525
X-RAY DIFFRACTIONr_nbd_refined0.1870.23736
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.218142
X-RAY DIFFRACTIONr_nbtor_refined0.1670.29982
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.29058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2983
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.210
X-RAY DIFFRACTIONr_nbd_other0.230.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.29
X-RAY DIFFRACTIONr_mcbond_it2.0613.05210630
X-RAY DIFFRACTIONr_mcbond_other2.0613.05110629
X-RAY DIFFRACTIONr_mcangle_it3.1934.56513256
X-RAY DIFFRACTIONr_mcangle_other3.1934.56513257
X-RAY DIFFRACTIONr_scbond_it1.9783.11210341
X-RAY DIFFRACTIONr_scbond_other1.9783.11210342
X-RAY DIFFRACTIONr_scangle_it3.0264.61815248
X-RAY DIFFRACTIONr_scangle_other3.0264.61815249
X-RAY DIFFRACTIONr_lrange_it4.73834.47622325
X-RAY DIFFRACTIONr_lrange_other4.71634.44722240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5130.2664800.1869550X-RAY DIFFRACTION87.2629
2.513-2.5820.2584490.1729546X-RAY DIFFRACTION89.5128
2.582-2.6570.2444890.1889324X-RAY DIFFRACTION89.7886
2.657-2.7390.2414330.1819223X-RAY DIFFRACTION91.726
2.739-2.8290.2134880.1599052X-RAY DIFFRACTION92.5495
2.829-2.9280.2124020.1618795X-RAY DIFFRACTION93.456
2.928-3.0380.2133690.1558625X-RAY DIFFRACTION93.8341
3.038-3.1620.2014320.1558283X-RAY DIFFRACTION95.3292
3.162-3.3030.1953870.1678074X-RAY DIFFRACTION95.9188
3.303-3.4640.2064410.1697698X-RAY DIFFRACTION96.4337
3.464-3.6510.1943830.1677422X-RAY DIFFRACTION97.5625
3.651-3.8720.2013980.1657087X-RAY DIFFRACTION98.8119
3.872-4.1390.1813270.1516783X-RAY DIFFRACTION99.5659
4.139-4.470.1542780.1356322X-RAY DIFFRACTION99.9394
4.47-4.8960.1633760.1335743X-RAY DIFFRACTION99.8531
4.896-5.4730.163410.1485210X-RAY DIFFRACTION99.964
5.473-6.3170.1843140.1584518X-RAY DIFFRACTION100
6.317-7.7310.1772060.1663911X-RAY DIFFRACTION100
7.731-10.9080.1752060.1552976X-RAY DIFFRACTION100
10.908-49.770.2721370.2691598X-RAY DIFFRACTION98.9732

+
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