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- PDB-1a34: SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a34
TitleSATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • SATELLITE TOBACCO MOSAIC VIRUS
KeywordsVirus/RNA / WATER STRUCTURE / RNA / VIRUS ASSEMBLY / MACROMOLECULAR INTERACTIONS / SATELLITE TOBACCO MOSAIC VIRUS / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Satellite virus coat domain / Satellite virus coat domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / RNA / Coat protein
Similarity search - Component
Biological speciesSatellite Tobacco Mosaic Virus
MethodX-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLarson, S.B. / Day, J. / Greenwood, A.J. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Refined structure of satellite tobacco mosaic virus at 1.8 A resolution.
Authors: Larson, S.B. / Day, J. / Greenwood, A. / McPherson, A.
#1: Journal: Nature / Year: 1993
Title: Double-Helical RNA in Satellite Tobacco Mosaic Virus
Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of Satellite Tobacco Mosaic Virus at 2.9 A Resolution
Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A.
#3: Journal: Protein Sci. / Year: 1992
Title: Macromolecular Crystal Growth Experiments on International Microgravity Laboratory--1
Authors: Day, J. / McPherson, A.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Analysis of Crystals of Satellite Tobacco Mosaic Virus
Authors: Koszelak, S. / Dodds, J.A. / McPherson, A.
History
DepositionJan 28, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other / Source and taxonomy
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 7, 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 / 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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SATELLITE TOBACCO MOSAIC VIRUS
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2185
Polymers23,7983
Non-polymers4202
Water3,027168
1
A: SATELLITE TOBACCO MOSAIC VIRUS
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,453,080300
Polymers1,427,865180
Non-polymers25,215120
Water3,243180
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: SATELLITE TOBACCO MOSAIC VIRUS
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 5


  • icosahedral pentamer
  • 121 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)121,09025
Polymers118,98915
Non-polymers2,10110
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: SATELLITE TOBACCO MOSAIC VIRUS
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 145 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)145,30830
Polymers142,78618
Non-polymers2,52112
Water32418
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: SATELLITE TOBACCO MOSAIC VIRUS
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 363 kDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)363,27075
Polymers356,96645
Non-polymers6,30430
Water81145
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)174.270, 191.770, 202.500
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 domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
3generate(-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699)
4generate(-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.80901699)
5generate(0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699)
6generate(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)
7generate(-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699)
8generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)
9generate(0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5)
10generate(1), (1), (1)
11generate(0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5)
12generate(0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699)
13generate(1), (1), (1)
14generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
15generate(0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5)

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SATELLITE TOBACCO MOSAIC VIRUS / STMV


Mass: 17533.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Satellite Tobacco Mosaic Virus / Production host: Nicotiana tabacum (common tobacco) / References: UniProt: P17574

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 170 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRNA CHAIN B HAS BEEN DESCRIBED BY AN ARBITRARY 10 NUCLEOTIDE CHAIN COMPOSED OF ADENINE BASES. ...RNA CHAIN B HAS BEEN DESCRIBED BY AN ARBITRARY 10 NUCLEOTIDE CHAIN COMPOSED OF ADENINE BASES. LIKEWISE CHAINS C AND D ARE URIDINES. THE TRUE SEQUENCE IS UNDOUBTEDLY DISORDERED, BUT THE GREATEST POPULATION IN THE RNA GENOME OF STMV OCCURS FOR ADENINE AND URIDINE BASES.
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 25 %
Description: 8 SPACE-GROWN CRYSTALS AND 12 EARTH-GROWN CRYSTALS
Crystal growMethod: liquid diffusion in microgravity / pH: 6.5
Details: PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT ...Details: PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2AMMONIUM SULFATE11
3WATER12
4AMMONIUM SULFATE1
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Koszelak, S., (1989) J.Mol.Biol., 209, 323. / PH range low: 7.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-8 mg/mlvirus1drop
210 mMcacodylate1dropcan be replaced by phosphate or Tris buffer
410-20 %satammonium sulfate1reservoir
540 mMcacodylate1reservoir
3reservoir1drop0.010ml

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 1, 1992 / Details: NONE
RadiationMonochromator: SUPPER GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.81→30 Å / Num. obs: 271689 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091
Reflection shellResolution: 1.81→1.94 Å / Redundancy: 2.1 % / Rsym value: 0.199 / % possible all: 63.9
Reflection
*PLUS
Lowest resolution: 9999 Å / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Num. measured all: 2239616

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
BRICOGNE'SGENERATEmodel building
INTERPOLATEmodel building
TNTrefinement
HEAVYmodel building
SDMSDETECTOR SYSTEMdata reduction
SDMSDETECTOR SYSTEMdata scaling
HEAVYphasing
BRICOGNE'SGENERATEphasing
INTERPOLATEphasing
TNTphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: MODIFIED STNV

Resolution: 1.81→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
Details: THE RMS DEVIATIONS LISTED ABOVE ARE FOR THE PROTEIN. RMS DEVIATIONS FOR THE DOUBLE HELICAL RNA ARE THE FOLLOWING: BONDS: 0.021 ANGLES: 3.06 DIHEDRAL ANGLES: 11.12 IMPROPER ANGLES: 2.05 MEAN ...Details: THE RMS DEVIATIONS LISTED ABOVE ARE FOR THE PROTEIN. RMS DEVIATIONS FOR THE DOUBLE HELICAL RNA ARE THE FOLLOWING: BONDS: 0.021 ANGLES: 3.06 DIHEDRAL ANGLES: 11.12 IMPROPER ANGLES: 2.05 MEAN B FOR RNA IS 99.1 AND FOR ALL NON- HYDROGEN ATOMS THE MEAN B IS 37.6. NCS RESTRAINTS WERE APPLIED TO THE RNA BACKBONE ONLY. THREE GROUPS WERE DEFINED: GROUP 1, NUCLEOTIDES 1002 - 1006 AND 1102 - 1106; GROUP 2, 1001, 1007 AND 1101, 1107; GROUP 3, 1000, 1008, 1009 AND 1100, 1108, 1109.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3277 1.5 %RANDOM
Rwork0.179 ---
obs-215809 71.8 %-
Displacement parametersBiso mean: 14.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 422 18 168 1745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.77
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.851.5
X-RAY DIFFRACTIONx_mcangle_it3.342
X-RAY DIFFRACTIONx_scbond_it2.782
X-RAY DIFFRACTIONx_scangle_it4.472.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION0.310.471100
22X-RAY DIFFRACTION0.30.51230
33X-RAY DIFFRACTION0.510.8735
LS refinement shellResolution: 1.81→1.9 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 199 1.4 %
Rwork0.204 13835 -
obs--71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMSBLW.PROTOPSBL.PRO
X-RAY DIFFRACTION2DNA-RNA-ALLH3NEW.PARAMDNA-RNA-ALLH.TOP
X-RAY DIFFRACTION3PARAM19.SOL
X-RAY DIFFRACTION4PARAM.HBN
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.81 Å / Lowest resolution: 30 Å / σ(F): 4 / % reflection Rfree: 1.5 % / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.77
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
X-RAY DIFFRACTIONx_mcbond_it1.851.5
X-RAY DIFFRACTIONx_scbond_it2.782
X-RAY DIFFRACTIONx_mcangle_it3.342
X-RAY DIFFRACTIONx_scangle_it4.472.5
LS refinement shell
*PLUS
% reflection Rfree: 1.4 %

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