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- PDB-1xok: crystal structure of alfalfa mosaic virus RNA 3'UTR in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1xok
Titlecrystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat protein N terminal peptide
Components
  • (alfalfa mosaic virus RNA 3' UTR) x 2
  • Coat protein
KeywordsViral protein/RNA / protein-rna complex / alpha helix / atypical rna duplex / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


T=3 icosahedral viral capsid / translational initiation / viral nucleocapsid / RNA binding
Similarity search - Function
Coat protein, Ilarvirus / Ilarvirus coat protein
Similarity search - Domain/homology
BROMIDE ION / RNA / RNA (> 10) / Capsid protein
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsGuogas, L.M. / Filman, D.J. / Hogle, J.M. / Gehrke, L.
CitationJournal: Science / Year: 2004
Title: Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication.
Authors: Guogas, L.M. / Filman, D.J. / Hogle, J.M. / Gehrke, L.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alfalfa mosaic virus RNA 3' UTR
B: alfalfa mosaic virus RNA 3' UTR
C: Coat protein
D: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0615
Polymers17,9814
Non-polymers801
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.1, 123.0, 53.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain alfalfa mosaic virus RNA 3' UTR


Mass: 9533.723 Da / Num. of mol.: 1 / Fragment: amv rna bases 843-872 / Source method: obtained synthetically / Details: rna synthesis dharmacon research
#2: RNA chain alfalfa mosaic virus RNA 3' UTR


Mass: 2934.831 Da / Num. of mol.: 1 / Fragment: amv rna bases 873-881 / Source method: obtained synthetically / Details: rna synthesis dharmacon research
#3: Protein/peptide Coat protein


Mass: 2756.170 Da / Num. of mol.: 2 / Fragment: amv coat protein residues 1-26 / Source method: obtained synthetically / Details: peptide synthesis by mit biopolymers laboratory / References: UniProt: P24264
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.45M ammonium sulfate, 0.01M magnesium acetate, 0.01M mes, 0.001M samarium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.91942, 0.91997, 0.92181
SYNCHROTRONAPS 19-ID20.91942
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDAug 10, 2003
CUSTOM-MADE2CCDAug 10, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1monochromatorMADMx-ray1
2monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.919421
20.919971
30.921811
ReflectionResolution: 3→99 Å / Num. all: 3508 / Num. obs: 3487 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rsym value: 0.085 / Net I/σ(I): 25
Reflection shellResolution: 3→3.19 Å / Mean I/σ(I) obs: 4.4 / Rsym value: 0.405 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.903 / SU B: 18.921 / SU ML: 0.332 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0.001 / ESU R Free: 0.467
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26888 326 9.2 %RANDOM
Rwork0.249 ---
all0.251 3237 --
obs0.251 3236 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.218 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å20 Å2
2--6.93 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms244 765 1 7 1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211098
X-RAY DIFFRACTIONr_angle_refined_deg2.1182.7971647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.027531
X-RAY DIFFRACTIONr_chiral_restr0.0910.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02561
X-RAY DIFFRACTIONr_nbd_refined0.2370.2472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.210
X-RAY DIFFRACTIONr_mcbond_it0.8492164
X-RAY DIFFRACTIONr_mcangle_it1.7614250
X-RAY DIFFRACTIONr_scbond_it1.3924934
X-RAY DIFFRACTIONr_scangle_it2.22961397
LS refinement shellHighest resolution: 3 Å / Num. reflection Rwork: 453 / Total num. of bins used: 10
Refinement TLS params.Method: refined / Origin x: 36.6597 Å / Origin y: 13.0441 Å / Origin z: 22.9456 Å
111213212223313233
T0.1429 Å20.008 Å2-0.0732 Å2-0.0288 Å20.0016 Å2--0.4331 Å2
L7.6947 °21.2288 °21.256 °2-2.0249 °2-2.526 °2--17.2649 °2
S0.089 Å °0.3297 Å °0.7699 Å °0.2161 Å °0.3884 Å °-0.0349 Å °-0.0891 Å °-0.1665 Å °-0.4775 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D27 - 28
2X-RAY DIFFRACTION1B8
3X-RAY DIFFRACTION1A2 - 5
4X-RAY DIFFRACTION1A1
5X-RAY DIFFRACTION1D9 - 26
6X-RAY DIFFRACTION1B873 - 881
7X-RAY DIFFRACTION1C12 - 26
8X-RAY DIFFRACTION1A843 - 872

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