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- PDB-1smv: PRIMARY STRUCTURE OF SESBANIA MOSAIC VIRUS COAT PROTEIN: ITS IMPL... -

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Basic information

Entry
Database: PDB / ID: 1smv
TitlePRIMARY STRUCTURE OF SESBANIA MOSAIC VIRUS COAT PROTEIN: ITS IMPLICATIONS TO THE ASSEMBLY AND ARCHITECTURE OF THE VIRUS
ComponentsSESBANIA MOSAIC VIRUS COAT PROTEIN
KeywordsVIRUS / COAT PROTEIN (VIRAL) / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBhuvaneshwari, M. / Murthy, M.R.N.
Citation
Journal: Structure / Year: 1995
Title: Structure of sesbania mosaic virus at 3 A resolution.
Authors: Bhuvaneshwari, M. / Subramanya, H.S. / Gopinath, K. / Savithri, H.S. / Nayudu, M.V. / Murthy, M.R.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of Sesbania Mosaic Virus at 4.7 Angstroms Resolution and Partial Sequence of the Coat Protein
Authors: Subramanya, H.S. / Gopinath, K. / Nayudu, M.V. / Savithri, H.S. / Murthy, M.R.N.
#2: Journal: Curr.Sci. / Year: 1982
Title: Purification and Partial Characterization of Sesbania Mosaic Virus
Authors: Sreenivasulu, P. / Nayudu, M.V.
History
DepositionJun 16, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 285THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE ...THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE FULL CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 0.209973 0.948239 0.238231 0.00000 X0 2 0.157347 -0.273260 0.948984 0.00000 X0 3 0.964962 -0.161777 -0.206580 0.00000 CRYSTAL AU = (X0) * (BIOMT 1-20) * CHAINS A,B,C

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SESBANIA MOSAIC VIRUS COAT PROTEIN
B: SESBANIA MOSAIC VIRUS COAT PROTEIN
C: SESBANIA MOSAIC VIRUS COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8967
Polymers85,7353
Non-polymers1604
Water00
1
A: SESBANIA MOSAIC VIRUS COAT PROTEIN
B: SESBANIA MOSAIC VIRUS COAT PROTEIN
C: SESBANIA MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,153,748420
Polymers5,144,129180
Non-polymers9,619240
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: SESBANIA MOSAIC VIRUS COAT PROTEIN
B: SESBANIA MOSAIC VIRUS COAT PROTEIN
C: SESBANIA MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 429 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)429,47935
Polymers428,67715
Non-polymers80220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: SESBANIA MOSAIC VIRUS COAT PROTEIN
B: SESBANIA MOSAIC VIRUS COAT PROTEIN
C: SESBANIA MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 515 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)515,37542
Polymers514,41318
Non-polymers96224
Water0
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
A: SESBANIA MOSAIC VIRUS COAT PROTEIN
B: SESBANIA MOSAIC VIRUS COAT PROTEIN
C: SESBANIA MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.72 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,717,916140
Polymers1,714,71060
Non-polymers3,20680
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
identity operation1_555x,y,z1
point symmetry operation19
Unit cell
Length a, b, c (Å)291.460, 291.460, 291.460
Angle α, β, γ (deg.)61.95, 61.95, 61.95
Int Tables number146
Space group name H-MR3
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein SESBANIA MOSAIC VIRUS COAT PROTEIN


Mass: 28578.496 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sesbania mosaic virus / Genus: Sobemovirus / References: UniProt: Q9EB06
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-35 mg/mlvirus1drop
20.1 Msodium acetate1drop
310 mMdithiothreitol1drop
45-20 %satammonium sulfate1drop
530-35 %ammonium sulfate1reservoir
60.1 Msodium acetate1reservoir
710 mMEDTA1reservoir

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Data collection

ReflectionResolution: 2.9→60 Å / Num. obs: 347170 / % possible obs: 70 % / Observed criterion σ(I): 1
Reflection
*PLUS
Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.227 --
obs0.227 322385 70 %
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 4 0 4516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.776
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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