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- PDB-1bmv: PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1bmv
TitlePROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION
Components
  • PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
  • PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
  • RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
KeywordsVirus/RNA / PROTEIN-RNA COMPLEX / SINGLE STRAND / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / virus-mediated perturbation of host defense response / 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
RNA / RNA (> 10) / RNA2 polyprotein
Similarity search - Component
Biological speciesBean pod mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsChen, Z. / Stauffacher, C. / Li, Y. / Schmidt, T. / Bomu, W. / Kamer, G. / Shanks, M. / Lomonossoff, G. / Johnson, J.E.
CitationJournal: Science / Year: 1989
Title: Protein-RNA interactions in an icosahedral virus at 3.0 A resolution.
Authors: Chen, Z.G. / Stauffacher, C. / Li, Y. / Schmidt, T. / Bomu, W. / Kamer, G. / Shanks, M. / Lomonossoff, G. / Johnson, J.E.
History
DepositionOct 9, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 9, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 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_rmsd_angle / pdbx_validate_rmsd_bond / 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[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _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_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_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 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET DOMAIN *1* CONTAINS A TEN-STRANDED BETA BARREL DESIGNATED * S1* ON THE SHEET RECORDS BELOW. ...SHEET DOMAIN *1* CONTAINS A TEN-STRANDED BETA BARREL DESIGNATED * S1* ON THE SHEET RECORDS BELOW. DOMAIN *2* AND DOMAIN *3* EACH CONTAIN AN EIGHT-STRANDED BETA BARREL DESIGNATED *S21* AND * S3* RESPECTIVELY. A BETA BARREL IS REPRESENTED BY A SET OF SHEET RECORDS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THUS THESE THREE BETA BARRELS ARE REPRESENTED BY SETS OF SHEET RECORDS WITH NINE OR ELEVEN STRANDS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
1: PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
2: PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)


Theoretical massNumber of molelcules
Total (without water)66,6683
Polymers66,6683
Non-polymers00
Water00
1
M: RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
1: PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
2: PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
x 60


Theoretical massNumber of molelcules
Total (without water)4,000,100180
Polymers4,000,100180
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
M: RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
1: PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
2: PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
x 5


  • icosahedral pentamer
  • 333 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)333,34215
Polymers333,34215
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
M: RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
1: PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
2: PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
x 6


  • icosahedral 23 hexamer
  • 400 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)400,01018
Polymers400,01018
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
M: RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
1: PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
2: PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
x 30


  • crystal asymmetric unit, crystal frame
  • 2 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,000,05090
Polymers2,000,05090
Non-polymers00
Water0
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, -0.87340982, 0.3763848), (0.87340815, 0.41723961, 0.25113314), (-0.37638408, 0.25113314, 0.89177738)53.6571, -67.82301, 29.22746
3generate(-0.80901699, -0.53979695, 0.23261859), (0.53979592, -0.52568651, 0.65747509), (-0.23261815, 0.65747509, 0.71666952)140.4761, -41.91692, 18.06356
4generate(-0.80901699, 0.53979695, -0.23261859), (-0.53979592, -0.52568651, 0.65747509), (0.23261815, 0.65747509, 0.71666952)140.4761, 41.91692, -18.06356
5generate(0.30901699, 0.87340982, -0.3763848), (-0.87340815, 0.41723961, 0.25113314), (0.37638408, 0.25113314, 0.89177738)53.6571, 67.82301, -29.22746
6generate(-0.5, -0.18745258, -0.84549569), (-0.18745222, -0.92972319, 0.3169801), (-0.84549407, 0.3169801, 0.42972319)116.47992, 14.55628, 65.65539
7generate(0.14616028, -0.98926189), (-0.98926, -0.14459052, -0.02136279), (-0.14616, 0.97863722, 0.14459052)77.65328, 76.81928, 11.3498
8generate(0.5, -0.18745258, -0.84549569), (-0.42394407, 0.7983356, -0.42770474), (0.75516222, 0.57229526, 0.31969838)38.82664, 32.92065, -58.64082
9generate(0.30901699, -0.72724954, -0.61287709), (0.72724815, 0.59596332, -0.34049499), (0.61287592, -0.34049499, 0.71305368)53.6571, -56.4732, -47.59183
10generate(-0.30901699, -0.72724954, -0.61287709), (0.87340815, -0.47203575, 0.11974555), (-0.37638408, -0.49828844, 0.78105274)101.64946, -67.82301, 29.22746
11generate(0.30901699, 0.72724954, 0.61287709), (0.72724815, -0.59596332, 0.34049499), (0.61287592, 0.34049499, -0.71305368)53.6571, -56.4732, -47.59183
12generate(0.5, 0.18745258, 0.84549569), (-0.42394407, -0.7983356, 0.42770474), (0.75516222, -0.57229526, -0.31969838)38.82664, 32.92065, -58.64082
13generate(-0.14616028, 0.98926189), (-0.98926, 0.14459052, 0.02136279), (-0.14616, -0.97863722, -0.14459052)77.65328, 76.81928, 11.3498
14generate(-0.5, 0.18745258, 0.84549569), (-0.18745222, 0.92972319, -0.3169801), (-0.84549407, -0.3169801, -0.42972319)116.47992, 14.55628, 65.65539
15generate(-0.30901699, 0.72724954, 0.61287709), (0.87340815, 0.47203575, -0.11974555), (-0.37638408, 0.49828844, -0.78105274)101.64946, -67.82301, 29.22746
16generate(-0.30901699, -0.87340982, 0.3763848), (0.72724815, -0.47203575, -0.49828844), (0.61287592, 0.11974555, 0.78105274)101.64946, -56.4732, -47.59183
17generate(-1), (-0.95727443, -0.28918104), (-0.28918104, 0.95727443)155.30656
18generate(-0.30901699, 0.87340982, -0.3763848), (-0.72724815, -0.47203575, -0.49828844), (-0.61287592, 0.11974555, 0.78105274)101.64946, 56.4732, 47.59183
19generate(0.80901699, 0.53979695, -0.23261859), (-0.44946408, 0.31309692, -0.83663133), (-0.37877815, 0.78140266, 0.49592007)14.83046, 34.90236, 29.41337
20generate(0.80901699, -0.53979695, 0.23261859), (0.44946408, 0.31309692, -0.83663133), (0.37877815, 0.78140266, 0.49592007)14.83046, -34.90236, -29.41337
21generate(0.98926189, 0.14616028), (0.14616, 0.14459052, -0.97863722), (-0.98926, 0.02136279, -0.14459052)77.65328, -11.3498, 76.81928
22generate(0.80901699, 0.44946494, 0.37877887), (0.53979592, -0.31309692, -0.78140266), (-0.23261815, 0.83663133, -0.49592007)14.83046, -41.91692, 18.06356
23generate(0.5, -0.42394488, 0.75516367), (0.18745222, -0.7983356, -0.57229526), (0.84549407, 0.42770474, -0.31969838)38.82664, -14.55628, -65.65539
24generate(-0.5, -0.42394488, 0.75516367), (-0.42394407, -0.64054215, -0.64029433), (0.75516222, -0.64029433, 0.14054215)116.47992, 32.92065, -58.64082
25generate(-0.80901699, 0.44946494, 0.37877887), (-0.44946408, -0.05778176, -0.89142746), (-0.37877815, -0.89142746, 0.24876477)140.4761, 34.90236, 29.41337
26generate(-0.5, 0.42394488, -0.75516367), (-0.42394407, 0.64054215, 0.64029433), (0.75516222, 0.64029433, -0.14054215)116.47992, 32.92065, -58.64082
27generate(0.5, 0.42394488, -0.75516367), (0.18745222, 0.7983356, 0.57229526), (0.84549407, -0.42770474, 0.31969838)38.82664, -14.55628, -65.65539
28generate(0.80901699, -0.44946494, -0.37877887), (0.53979592, 0.31309692, 0.78140266), (-0.23261815, -0.83663133, 0.49592007)14.83046, -41.91692, 18.06356
29generate(-0.98926189, -0.14616028), (0.14616, -0.14459052, 0.97863722), (-0.98926, -0.02136279, 0.14459052)77.65328, -11.3498, 76.81928
30generate(-0.80901699, -0.44946494, -0.37877887), (-0.44946408, 0.05778176, 0.89142746), (-0.37877815, 0.89142746, -0.24876477)140.4761, 34.90236, 29.41337

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Components

#1: RNA chain RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')


Mass: 3530.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: M
#2: Protein PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)


Mass: 21914.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bean pod mottle virus / Genus: Comovirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P23009
#3: Protein PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)


Mass: 41223.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bean pod mottle virus / Genus: Comovirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P23009
Sequence detailsELEVEN RIBONUCLEOTIDES ARE LOCATED INSIDE THE CAPSID PROTEIN. THEIR BASE TYPES ARE QUITE ARBITRARY. ...ELEVEN RIBONUCLEOTIDES ARE LOCATED INSIDE THE CAPSID PROTEIN. THEIR BASE TYPES ARE QUITE ARBITRARY. ONLY THE CONFORMATION OF THE FIRST SEVEN RIBONUCLEOTIDES ARE DEFINED WITH CONFIDENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: Sehnke, P.C., (1988) J. Crystal Growth, 90, 222.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Type: CHESS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 698453 / Observed criterion σ(I): 2
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.096

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Processing

SoftwareClassification: refinement
RefinementResolution: 3→7 Å / Rfactor obs: 0.33 / σ(F): 3
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 238 0 0 4613
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 7 Å / σ(F): 3 / Rfactor obs: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS

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