[English] 日本語
Yorodumi
- PDB-1s58: The structure of B19 parvovirus capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s58
TitleThe structure of B19 parvovirus capsid
ComponentsB19 parvovirus capsid
KeywordsVIRUS / icosahedral capsid / beta-barrel / Icosahedral virus
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / phospholipase A2 / T=1 icosahedral viral capsid / lipid catabolic process / viral penetration into host nucleus ...phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / phospholipase A2 / T=1 icosahedral viral capsid / lipid catabolic process / viral penetration into host nucleus / viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / receptor-mediated virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Minor capsid protein VP1 / Minor capsid protein VP1
Similarity search - Component
Biological speciesHuman parvovirus B19
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, NCS averaging / Resolution: 3.5 Å
AuthorsKaufmann, B. / Simpson, A.A. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The structure of human parvovirus B19.
Authors: Kaufmann, B. / Simpson, A.A. / Rossmann, M.G.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999sequence The sequence for this protein has not been deposited to any sequence database at the time ...sequence The sequence for this protein has not been deposited to any sequence database at the time of processing this file

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: B19 parvovirus capsid


Theoretical massNumber of molelcules
Total (without water)60,9301
Polymers60,9301
Non-polymers00
Water00
1
A: B19 parvovirus capsid
x 60


Theoretical massNumber of molelcules
Total (without water)3,655,80360
Polymers3,655,80360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: B19 parvovirus capsid
x 5


  • icosahedral pentamer
  • 305 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)304,6505
Polymers304,6505
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: B19 parvovirus capsid
x 6


  • icosahedral 23 hexamer
  • 366 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)365,5806
Polymers365,5806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: B19 parvovirus capsid
x 20


  • crystal asymmetric unit, crystal frame
  • 1.22 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,218,60120
Polymers1,218,60120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)351.393, 351.393, 351.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30995633, -0.69837337, -0.6451401), (0.66293147, 0.64514026, -0.37987898), (0.68150694, -0.30994532, 0.66293739)-122.61112, -62.43289, -54.54407
3generate(-0.80656821, -0.46705588, -0.36235538), (0.37427343, 0.07097398, -0.9245949), (0.4575613, -0.88137884, 0.11756025)-81.82517, -163.27348, -154.91292
4generate(-0.80657467, 0.37427957, 0.45755529), (-0.46705853, 0.07097944, -0.88136886), (-0.36235163, -0.92459886, 0.11756125)65.99304, -163.16351, -162.40021
5generate(0.30994588, 0.66293598, 0.68150324), (-0.69837223, 0.64514909, -0.30993778), (-0.64514007, -0.37987678, 0.662939)116.56378, -62.25495, -66.65876
6generate(-0.93160182, -0.08480892, 0.35344687), (-0.08480886, -0.89484299, -0.4382489), (0.35344915, -0.43825203, 0.82644481)-14.60707, -332.72325, -77.0096
7generate(-0.10410188, 0.48634305, 0.86754397), (-0.91817629, -0.3822378, 0.10411406), (0.3822506, -0.78572621, 0.48633969)85.6341, -242.55323, -138.06272
8generate(0.88138231, 0.11757028, 0.45753613), (-0.46703756, 0.36236321, 0.80657756), (-0.07095778, -0.92459597, 0.37428846)20.71497, -111.7892, -162.40268
9generate(0.66294511, -0.6814958, -0.30995974), (0.64514893, 0.30994676, 0.69836092), (-0.3798574, -0.66294802, 0.64514211)-119.64844, -121.14261, -116.39248
10generate(-0.4575407, -0.80657302, -0.37429045), (0.88137926, -0.46704941, -0.07098415), (-0.1175595, -0.36237093, 0.92459011)-141.47866, -257.68736, -63.61666
11generate(-0.89485529, 0.43823274, 0.08480516), (0.43821989, 0.82645711, 0.35344916), (0.08480269, 0.35344925, -0.93160182)77.18444, -30.47758, 61.79741
12generate(0.07094752, 0.88137973, 0.46705214), (0.92459151, 0.11758974, -0.36235226), (-0.37429533, 0.45754602, -0.80657125)154.9179, -155.08487, 80.14615
13generate(0.92458426, 0.37430507, -0.07096241), (0.11759136, -0.45753883, -0.8813778), (-0.36237744, 0.80657224, -0.46704544)65.71694, -256.02737, 141.46668
14generate(0.48635798, -0.3822313, -0.78572066), (-0.86753379, -0.10412047, -0.48635181), (0.10408624, 0.91818553, -0.38223752)-67.14574, -193.80598, 161.01611
15generate(-0.63811749, -0.34272183, -0.68945101), (-0.66937445, 0.68943266, 0.27681322), (0.38045876, 0.63814012, -0.66934915)-60.05843, -54.40854, 111.77779
16generate(0.82645711, -0.35342382, -0.43825204), (-0.35341103, -0.93161412, 0.08479974), (-0.43825185, 0.08480278, -0.894843)-62.08537, -339.07917, 14.70019
17generate(-0.27680196, -0.66934941, -0.68945601), (-0.66934669, -0.38049221, 0.63811718), (-0.68946221, 0.63812551, -0.34270583)-117.44888, -242.20901, 111.94863
18generate(-0.99939835, -0.02481948, -0.02421834), (-0.02482722, 0.02420163, 0.99939514), (-0.02422609, 0.99940257, -0.02480327)-4.11473, -171.18994, 175.33692
19generate(-0.34272842, 0.68944753, 0.63812511), (0.68944338, -0.27680573, 0.66935975), (0.63812279, 0.66936135, -0.38046584)121.29314, -224.16791, 117.26458
20generate(0.78571231, 0.48635887, 0.38223822), (0.48636742, -0.86753234, 0.10410871), (0.3822408, 0.10410759, -0.91817996)85.46531, -327.92915, 17.98563

-
Components

#1: Protein B19 parvovirus capsid


Mass: 60930.047 Da / Num. of mol.: 1 / Fragment: VP2 capsid protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus B19 / Genus: Erythrovirus / Gene: vp2 / Plasmid: AcMNPV-VP2 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q90201, UniProt: Q9PZT0*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% MPD, 0.1M Na Cacodylate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.107 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2003
RadiationMonochromator: Diamond(111) double-bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.107 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 123514 / Num. obs: 123514 / % possible obs: 68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 76.4 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 7.2
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.38 / Num. unique all: 9414 / Rsym value: 0.436 / % possible all: 52.6

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
ENVELOPEmodel building
CNSrefinement
REFMACrefinement
ENVELOPEphasing
RefinementMethod to determine structure: molecular replacement, NCS averaging
Starting model: cryo-electron microscopy reconstruction

Resolution: 3.5→20 Å / Isotropic thermal model: individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: above statistics are for model refined with individual isotropic temparature-factors, followed by TLS refinement using REFMAC, which gave the following displacement parameters (rigid unit is ...Details: above statistics are for model refined with individual isotropic temparature-factors, followed by TLS refinement using REFMAC, which gave the following displacement parameters (rigid unit is the crystal ASU). ORIGIN (0.120 -175.570 -0.120) T (0.0000 0.0000 0.0000 0.0000 0.0000 0.0000) L (0.1990 0.2145 0.2016 0.0769 -0.0807 -0.0731) S (-0.0063 0.0057 0.0213 -0.0161 -0.0188 -0.0151 -0.0390 0.0000)
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1065 -random
Rwork0.313 ---
all0.313 123514 --
obs0.313 104679 62.4 %-
Displacement parametersBiso mean: 96.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.8 Å
Luzzati d res low-5 Å
Luzzati sigma a1.3 Å1.6 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 0 0 4108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011307
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
3.5-3.650.4751090.521X-RAY DIFFRACTION993753
3.65-4.080.4252310.458X-RAY DIFFRACTION2106456
4.08-4.710.3242350.343X-RAY DIFFRACTION2370661
4.71-5.770.312370.297X-RAY DIFFRACTION2227666
5.77-8.160.2151760.207X-RAY DIFFRACTION1855871
8.16-200.284770.245X-RAY DIFFRACTION912968

+
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