[English] 日本語
Yorodumi
- PDB-1pgw: BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pgw
TitleBEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT
Components
  • BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
  • BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
KeywordsVIRUS / COMOVIRUS / VIRAL COAT PROTEIN / BEAN POD MOTTLE VIRUS (BPMV) / Icosahedral virus
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / GTP binding / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBean-pod mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLin, T. / Cavarelli, J. / Johnson, J.E.
Citation
Journal: Virology / Year: 2003
Title: Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus.
Authors: Lin, T. / Cavarelli, J. / Johnson, J.E.
#1: Journal: Science / Year: 1989
Title: Protein-/RNA Interactions in an Icosahedral Virus at 3.0 Angstroms Resolution
Authors: Chen, Z. / Stauffacher, C. / Li, Y. / Schmidt, T. / Bomu, W. / Kamer, G. / Shanks, M. / Lomonossoff, G. / Johnson, J.E.
History
DepositionMay 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT


Theoretical massNumber of molelcules
Total (without water)59,3142
Polymers59,3142
Non-polymers00
Water2,702150
1
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 60


Theoretical massNumber of molelcules
Total (without water)3,558,842120
Polymers3,558,842120
Non-polymers00
Water2,162120
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
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 5


  • icosahedral pentamer
  • 297 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)296,57010
Polymers296,57010
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 6


  • icosahedral 23 hexamer
  • 356 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)355,88412
Polymers355,88412
Non-polymers00
Water21612
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
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 30


  • crystal asymmetric unit, crystal frame
  • 1.78 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,779,42160
Polymers1,779,42160
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)311.200, 284.200, 350.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, -0.87337965, 0.37645249), (0.87337965, 0.41727875, 0.25117011), (-0.37645249, 0.25117011, 0.89173825)53.65068, -67.81269, 29.22928
3generate(-0.80901699, -0.53977831, 0.23266043), (0.53977831, -0.52558404, 0.65757189), (-0.23266043, 0.65757189, 0.71656705)140.45932, -41.91055, 18.06469
4generate(-0.80901699, 0.53977831, -0.23266043), (-0.53977831, -0.52558404, 0.65757189), (0.23266043, 0.65757189, 0.71656705)140.45932, 41.91055, -18.06469
5generate(0.30901699, 0.87337965, -0.37645249), (-0.87337965, 0.41727875, 0.25117011), (0.37645249, 0.25117011, 0.89173825)53.65068, 67.81269, -29.22928
6generate(-0.5, -0.18751829, -0.84548027), (-0.18751829, -0.92967378, 0.31708602), (-0.84548027, 0.31708602, 0.42967378)116.466, 14.55967, 65.64647
7generate(0.14608306, -0.98927233), (-0.98927233, -0.14451593, -0.02134026), (-0.14608306, 0.97865974, 0.14451592)77.644, 76.81106, 11.34247
8generate(0.5, -0.18751829, -0.84548027), (-0.42388564, 0.79834686, -0.42774204), (0.75519598, 0.57225796, 0.31968712)38.822, 32.91218, -58.63644
9generate(0.30901699, -0.7272966, -0.61281984), (0.7272966, 0.59591026, -0.34048587), (0.61281984, -0.34048587, 0.71310674)53.65068, -56.47022, -47.58178
10generate(-0.30901699, -0.7272966, -0.61281984), (0.87337965, -0.47206524, 0.11984319), (-0.37645249, -0.4981908, 0.78108223)101.63732, -67.81269, 29.22928
11generate(0.30901699, 0.7272966, 0.61281984), (0.7272966, -0.59591026, 0.34048587), (0.61281984, 0.34048587, -0.71310674)53.65068, -56.47022, -47.58178
12generate(0.5, 0.18751829, 0.84548027), (-0.42388564, -0.79834686, 0.42774204), (0.75519598, -0.57225796, -0.31968712)38.822, 32.91218, -58.63644
13generate(-0.14608306, 0.98927233), (-0.98927233, 0.14451592, 0.02134026), (-0.14608306, -0.97865974, -0.14451593)77.644, 76.81106, 11.34247
14generate(-0.5, 0.18751829, 0.84548027), (-0.18751829, 0.92967378, -0.31708602), (-0.84548027, -0.31708602, -0.42967378)116.466, 14.55967, 65.64647
15generate(-0.30901699, 0.7272966, 0.61281984), (0.87337965, 0.47206524, -0.11984319), (-0.37645249, 0.4981908, -0.78108223)101.63732, -67.81269, 29.22928
16generate(-0.30901699, -0.87337965, 0.37645249), (0.7272966, -0.47206524, -0.4981908), (0.61281984, 0.11984319, 0.78108223)101.63732, -56.47022, -47.58178
17generate(-1), (-0.95731948, -0.28903185), (-0.28903185, 0.95731948)155.288
18generate(-0.30901699, 0.87337965, -0.37645249), (-0.7272966, -0.47206524, -0.4981908), (-0.61281984, 0.11984319, 0.78108223)101.63732, 56.47022, 47.58178
19generate(0.80901699, 0.53977831, -0.23266043), (-0.44949402, 0.31309262, -0.83661708), (-0.37874349, 0.78141691, 0.49592437)14.82868, 34.90051, 29.40716
20generate(0.80901699, -0.53977831, 0.23266043), (0.44949402, 0.31309262, -0.83661708), (0.37874349, 0.78141691, 0.49592437)14.82868, -34.90051, -29.40716
21generate(0.98927233, 0.14608306), (0.14608306, 0.14451593, -0.97865974), (-0.98927233, 0.02134026, -0.14451593)77.644, -11.34247, 76.81106
22generate(0.80901699, 0.44949402, 0.37874349), (0.53977831, -0.31309262, -0.78141691), (-0.23266043, 0.83661708, -0.49592437)14.82868, -41.91055, 18.06469
23generate(0.5, -0.42388564, 0.75519598), (0.18751829, -0.79834686, -0.57225796), (0.84548027, 0.42774204, -0.31968712)38.822, -14.55967, -65.64647
24generate(-0.5, -0.42388564, 0.75519598), (-0.42388564, -0.64064193, -0.64023346), (0.75519598, -0.64023346, 0.14064193)116.466, 32.91218, -58.63644
25generate(-0.80901699, 0.44949402, 0.37874349), (-0.44949402, -0.05792068, -0.89140357), (-0.37874349, -0.89140357, 0.24890369)140.45932, 34.90051, 29.40716
26generate(-0.5, 0.42388564, -0.75519598), (-0.42388564, 0.64064193, 0.64023346), (0.75519598, 0.64023346, -0.14064193)116.466, 32.91218, -58.63644
27generate(0.5, 0.42388564, -0.75519598), (0.18751829, 0.79834686, 0.57225796), (0.84548027, -0.42774204, 0.31968712)38.822, -14.55967, -65.64647
28generate(0.80901699, -0.44949402, -0.37874349), (0.53977831, 0.31309262, 0.78141691), (-0.23266043, -0.83661708, 0.49592437)14.82868, -41.91055, 18.06469
29generate(-0.98927233, -0.14608306), (0.14608306, -0.14451592, 0.97865974), (-0.98927233, -0.02134026, 0.14451592)77.644, -11.34247, 76.81106
30generate(-0.80901699, -0.44949402, -0.37874349), (-0.44949402, 0.05792068, 0.89140357), (-0.37874349, 0.89140357, -0.24890369)140.45932, 34.90051, 29.40716

-
Components

#1: Protein BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT / BPMV / GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37 / COAT PROTEIN VP23]


Mass: 20638.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bean-pod mottle virus (strain Kentucky G7)
Genus: Comovirus / Species: Bean pod mottle virus / Strain: Kentucky G7 / References: UniProt: P23009
#2: Protein BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT / BPMV / GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37 / COAT PROTEIN VP23]


Mass: 38675.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bean-pod mottle virus (strain Kentucky G7)
Genus: Comovirus / Species: Bean pod mottle virus / Strain: Kentucky G7 / References: UniProt: P23009
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal growpH: 7
Details: PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Crystal grow
*PLUS
Method: other / Details: Chen, Z., (1989) Science, 245, 154.

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.566
DetectorType: KODAK / Detector: FILM / Details: MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.566 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 315015 / % possible obs: 46.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 12.1 Å2
Reflection shellResolution: 2.9→3.08 Å / % possible all: 39.1
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.099

-
Processing

Software
NameVersionClassification
MGROSCdata collection
MGROSCdata reduction
X-PLOR3.851refinement
MGROSCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BEAN POD MOTTLE VIRUS, MIDDEL COMPONENT

Resolution: 2.9→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rwork0.212 ---
obs0.212 306813 46.4 %-
Rfree---RANDOM
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4156 0 0 150 4306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.297 42638 -
obs--39.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.55
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57

+
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