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- PDB-2bbv: THE REFINED THREE-DIMENSIONAL STRUCTURE OF AN INSECT VIRUS AT 2.8... -

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Entry
Database: PDB / ID: 2bbv
TitleTHE REFINED THREE-DIMENSIONAL STRUCTURE OF AN INSECT VIRUS AT 2.8 ANGSTROMS RESOLUTION
Components
  • (PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)) x 2
  • RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
KeywordsVirus/RNA / PROTEIN-RNA COMPLEX / DOUBLE HELIX / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


nodavirus endopeptidase / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / Capsid protein alpha
Similarity search - Component
Biological speciesBlack beetle virus
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsWery, J.-P. / Reddy, V.S. / Hosur, M.V. / Johnson, J.E.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The refined three-dimensional structure of an insect virus at 2.8 A resolution.
Authors: Wery, J.P. / Reddy, V.S. / Hosur, M.V. / Johnson, J.E.
#1: Journal: Nature / Year: 1993
Title: Ordered Duplex RNA Controls Capsid Architecture in an Icosahedral Animal Virus
Authors: Fisher, A.J. / Johnson, J.E.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Structural Homology Among Four Nodaviruses as Deduced by Sequencing and X-Ray Crystallography
Authors: Kaesberg, P. / Dasgupta, R. / Sgro, J.-Y. / Wery, J.-P. / Selling, B.H. / Hosur, M.V. / Johnson, J.E.
#3: Journal: Proteins / Year: 1987
Title: Structure of an Insect Virus at 3.0 Angstroms Resolution
Authors: Hosur, M.V. / Schmidt, T. / Tucker, R.C. / Johnson, J.E. / Gallagher, T.M. / Selling, B.H. / Rueckert, R.R.
History
DepositionJun 6, 1994Processing site: NDB
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET EACH SUBUNIT (A OR B OR C) IS ROUGHLY MADE UP OF TWO DOMAINS, A BETA-BARREL DOMAIN AND AN ...SHEET EACH SUBUNIT (A OR B OR C) IS ROUGHLY MADE UP OF TWO DOMAINS, A BETA-BARREL DOMAIN AND AN ALPHA-HELICAL DOMAIN. THE BETA-BARREL DOMAIN CONSISTS OF AN EIGHT-STRANDED ANTI-PARALLEL BETA-BARREL AND THE INSERTIONS BETWEEN THE STRANDS OF THE BARREL. THE BETA-BARREL CONTAINS TWO BETA SHEETS, ?BG AND ?CF (? CORRESPONDS TO A OR B OR C DEPENDING ON THE SUBUNIT). SHEETS ?BG AND ?CF EACH CONTAIN FOUR STRANDS (IN SHEET ?BG STRANDS 1, 2, 3, AND, 4 CORRESPOND TO STRANDS B, I, D, AND G, RESPECTIVELY, WHEREAS IN SHEET ?CF STRANDS 1, 2, 3, AND 4 CORRESPOND TO STRANDS C, H, E, AND F, RESPECTIVELY. THE LETTERS INDICATE THE ORDER OF THE STRANDS IN THE PRIMARY STRUCTURE). THERE IS ANOTHER SHEET ?EX, WHICH CONTAINS FOUR STRANDS (OF WHICH TWO ARE SHORT STRANDS) AND A PAIR OF PROTRUDING STRANDS, DESIGNATED AS ?PR BELONG TO THE SAME B-BARREL DOMAIN.
Remark 650HELIX THE ALPHA-HELICAL DOMAIN CONSISTS OF THREE ALPHA-HELICES (?H1, ?H2, AND ?H3), WHICH ARE ...HELIX THE ALPHA-HELICAL DOMAIN CONSISTS OF THREE ALPHA-HELICES (?H1, ?H2, AND ?H3), WHICH ARE LOCATED INSIDE THE PROTEIN CONTIGUOUS SHELL. (? CORRESPONDS TO A OR B OR C DEPENDING ON THE SUBUNIT).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
A: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
D: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
B: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
E: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
C: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
F: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,94912
Polymers134,7487
Non-polymers2005
Water3,747208
1
N: RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
A: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
D: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
B: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
E: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
C: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
F: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,096,922720
Polymers8,084,898420
Non-polymers12,023300
Water5,405300
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
N: RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
A: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
D: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
B: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
E: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
C: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
F: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
hetero molecules
x 5


  • icosahedral pentamer
  • 675 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)674,74360
Polymers673,74235
Non-polymers1,00225
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
N: RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
A: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
D: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
B: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
E: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
C: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
F: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 810 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)809,69272
Polymers808,49042
Non-polymers1,20230
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
N: RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')
A: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
D: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
B: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
E: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
C: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
F: PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 675 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)674,74360
Polymers673,74235
Non-polymers1,00225
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)362.000, 362.000, 362.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
DetailsBBV HAS AN ICOSAHEDRAL PENTAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THIS FIVE-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY WAS USED TO AVERAGE THE ELECTRON DENSITY MAP IN THE PHASE REFINEMENT PROCEDURE. THE FOUR TRANSFORMATIONS PRESENTED ON *MTRIX* RECORDS BELOW WILL GENERATE THE ADDITIONAL 12 OF THE 15 SUBUNITS COMPRISING THE PENTAMERIC UNIT WHEN APPLIED TO THE THREE SUBUNITS PRESENTED IN THIS ENTRY.

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Components

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


Mass: 3060.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)


Mass: 39436.656 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: GROWN IN DROSOPHILA MELANOGASTER / Source: (natural) Black beetle virus / Genus: Alphanodavirus / References: UniProt: P04329
#3: Protein/peptide PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)


Mass: 4459.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: GROWN IN DROSOPHILA MELANOGASTER / Source: (natural) Black beetle virus / Genus: Alphanodavirus / References: UniProt: P04329
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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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: vapor diffusion, hanging drop / PH range low: 7.2 / PH range high: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.0 mg/mlvirus1drop
20.05 Msodium phosphate1reservoir
30.55 Mammonium sulfate1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORrefinement
PROLSQrefinement
RefinementResolution: 2.8→6 Å / σ(F): 4
Details: THE ENDS OF THE THREE SUBUNITS (A, B AND C) AND ENDS OF THEIR CLEAVED PRODUCTS (BETA AND GAMMA) AND THE ORDERED PEPTIDE_ARM MIGHT HAVE UNACCEPTABLE STEREOCHEMISTRY. THESE RESIDUES ARE A 56, ...Details: THE ENDS OF THE THREE SUBUNITS (A, B AND C) AND ENDS OF THEIR CLEAVED PRODUCTS (BETA AND GAMMA) AND THE ORDERED PEPTIDE_ARM MIGHT HAVE UNACCEPTABLE STEREOCHEMISTRY. THESE RESIDUES ARE A 56, A 363, D 364, D 379, B 56, B 363, E 364, E 379, C 20, C 31, C 55, C 363, F 364, AND F 379.
RfactorNum. reflection% reflection
Rwork0.221 --
obs0.221 112000 67.5 %
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7403 201 5 208 7817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.81
X-RAY DIFFRACTIONx_mcangle_it1.31.5
X-RAY DIFFRACTIONx_scbond_it1.91.5
X-RAY DIFFRACTIONx_scangle_it2.72
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / σ(F): 4 / Rfactor obs: 0.221 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0140.02
X-RAY DIFFRACTIONx_angle_d0.030.03
X-RAY DIFFRACTIONx_planar_d0.0460.05
X-RAY DIFFRACTIONx_plane_restr0.0180.02
X-RAY DIFFRACTIONx_chiral_restr0.2080.15

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