[English] 日本語
Yorodumi
- PDB-1mqt: Swine Vesicular Disease Virus coat protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mqt
TitleSwine Vesicular Disease Virus coat protein
Components
  • (Polyprotein Capsid ...) x 3
  • Polyprotein
KeywordsVIRUS / swine vesicular disease virus / SVDV coat protein / enterovirus / Icosahedral virus
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Few Secondary Structures ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SPL / Genome polyprotein
Similarity search - Component
Biological speciesSwine vesicular disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsVerdaguer, N. / Jimenez-Clavero, M.A. / Fita, I. / Ley, V.
CitationJournal: J.Virol. / Year: 2003
Title: STRUCTURE OF SWINE VESICULAR DISEASE VIRUS: MAPPING OF CHANGES OCCURRING DURING ADAPTATION OF HUMAN COXSACKIE B5 VIRUS TO INFECT SWINE
Authors: Verdaguer, N. / Jimenez-Clavero, M.A. / Fita, I. / Ley, V.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The first residue of chain D is a myristic acid covalently attached to GLY D2 (not ...HETEROGEN The first residue of chain D is a myristic acid covalently attached to GLY D2 (not visible in the electron density)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7265
Polymers93,3004
Non-polymers4261
Water54030
1
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,623,540300
Polymers5,597,999240
Non-polymers25,54160
Water4,324240
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: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 5


  • icosahedral pentamer
  • 469 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)468,62825
Polymers466,50020
Non-polymers2,1285
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 562 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)562,35430
Polymers559,80024
Non-polymers2,5546
Water43224
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: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.41 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,405,88575
Polymers1,399,50060
Non-polymers6,38515
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)318.350, 349.960, 371.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)
6generate(-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699)
7generate(1), (1), (1)
8generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)
9generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)
10generate(-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699)
11generate(-1), (-1), (1)
12generate(-0.30901699, -0.5, -0.80901699), (-0.5, 0.80901699, -0.30901699), (0.80901699, 0.30901699, -0.5)
13generate(-0.80901699, -0.30901699, -0.5), (0.30901699, 0.5, -0.80901699), (0.5, -0.80901699, -0.30901699)
14generate(-0.80901699, 0.30901699, -0.5), (0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699)
15generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polyprotein


Mass: 31370.240 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP1 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4

-
Polyprotein Capsid ... , 3 types, 3 molecules BCD

#2: Protein Polyprotein Capsid Protein


Mass: 28505.158 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP2 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4
#3: Protein Polyprotein Capsid Protein


Mass: 26071.531 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP3 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4
#4: Protein Polyprotein Capsid Protein


Mass: 7353.049 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP4 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4

-
Non-polymers , 2 types, 31 molecules

#5: Chemical ChemComp-SPL / OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE / CERAMIDE


Mass: 425.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H51NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, Potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Details: Jimenez-Clavero, M.A., (2003) Acta Cryst., D59, 541.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlvirus solution1drop
21.2 Mammonium sulfate1reservoir
30.1 Msodium potassium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 214790 / Num. obs: 214790 / % possible obs: 60 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 4.6
Reflection shellResolution: 3.3→3.5 Å / Rmerge(I) obs: 0.27 / % possible all: 44.1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 288614 / % possible obs: 70 % / Num. measured all: 459326 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 51 % / Rmerge(I) obs: 0.191

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COV

1cov


Resolution: 3.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 9509 -RANDOM
Rwork0.257 ---
all-214655 --
obs-192613 62.6 %-
Displacement parametersBiso mean: 11.97 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6333 0 30 30 6393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.5
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / Num. reflection obs: 266789 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.9

+
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