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- PDB-8dp3: Crystal structure of coxsackievirus B3 cloverleaf RNA replication... -

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Basic information

Entry
Database: PDB / ID: 8dp3
TitleCrystal structure of coxsackievirus B3 cloverleaf RNA replication element
Components
  • Fab BL3-6 Heavy Chain
  • Fab BL3-6 Light Chain
  • RNA (90-MER)
KeywordsIMMUNE SYSTEM/RNA / RNA / Fab / enteroviral replication / IMMUNE SYSTEM-RNA complex
Function / homologyPHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
Coxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsDas, N.K. / Koirala, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentStart-up United States
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.
Authors: Das, N.K. / Hollmann, N.M. / Vogt, J. / Sevdalis, S.E. / Banna, H.A. / Ojha, M. / Koirala, D.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab BL3-6 Heavy Chain
L: Fab BL3-6 Light Chain
R: RNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0904
Polymers81,9953
Non-polymers951
Water7,602422
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.173, 48.698, 144.653
Angle α, β, γ (deg.)90.000, 112.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab BL3-6 Heavy Chain


Mass: 27302.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab BL3-6 Light Chain


Mass: 25872.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: RNA chain RNA (90-MER)


Mass: 28819.084 Da / Num. of mol.: 1 / Fragment: 5' cloverleaf-like RNA domain / Source method: obtained synthetically / Source: (synth.) Coxsackievirus B3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Magnesium Acetate Tetrahydrate (0.01 M), MES Monohydrate (0.05 M), Ammonium Sulfate (2.5 M)
PH range: 5.0-6.5 / Temp details: At room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cold nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.9→66.64 Å / Num. obs: 60296 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.052 / Rrim(I) all: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.706 / Num. unique obs: 17592 / CC1/2: 0.743 / Rpim(I) all: 0.465 / Rrim(I) all: 0.85 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.1)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B3K

6b3k


Resolution: 1.91→66.62 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1968 3.64 %
Rwork0.209 52118 -
obs0.2108 54086 88.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.56 Å2 / Biso mean: 55.7154 Å2 / Biso min: 22.97 Å2
Refinement stepCycle: final / Resolution: 1.91→66.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 1907 5 424 5659
Biso mean--49.65 47.39 -
Num. residues----531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.91-1.960.6827690.6591202048
1.96-2.010.3964160405498
2.01-2.070.36651570.3216408097
2.07-2.140.34461550.2997399996
2.14-2.20.37571150.2984332697
2.22-2.30.5305700.4875168845
2.3-2.410.3481510.2614416099
2.41-2.530.29881570.2496421899
2.53-2.690.29641700.243413399
2.69-2.90.29471490.2492418199
2.9-3.190.26531530.2097408297
3.19-3.650.24221540.1779406495
3.65-4.60.19351490.1478398094
4.6-100.19931590.1484413394
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77480.8782-2.20210.2524-1.34025.50180.10070.34740.1164-0.0915-0.0076-0.1547-0.10540.0082-0.11030.38070.01550.05640.3541-0.00490.34-13.36613.4203-8.4408
22.4211-0.7024-0.92763.59253.98424.54680.24810.46720.1385-0.77710.1928-0.23450.68250.7564-0.34550.62790.08080.05190.6150.06750.2844-9.88667.5703-30.9991
30.44580.2911-0.70871.43571.43153.90890.23820.51190.1443-0.0294-0.062-0.0543-0.4961-0.0596-0.17330.7491-0.00370.05480.9170.00660.44642.4989-2.0893-40.4179
40.49830.6056-0.20350.9416-1.96828.3681-0.11830.8622-0.0846-0.17670.2911-0.21260.3647-0.4458-0.16250.756-0.10830.08881.0656-0.06380.458510.4115-6.0674-48.4906
53.091-0.3263-0.01522.03491.66594.16920.4871-0.7823-0.60570.7850.10390.17140.4246-0.1323-0.44440.4834-0.0597-0.08990.53560.12660.491-2.8455-16.1472-11.0399
63.5714-3.4064-2.29092.03195.10599.0655-0.1055-0.4280.22230.7289-0.22690.1811-0.16040.49190.37340.3313-0.1005-0.02670.4526-0.00860.2822-16.272310.380227.7872
73.6595-1.2921-1.41653.89661.30155.2959-0.0976-0.1453-0.08280.065-0.02550.1182-0.18930.11440.1070.177-0.0553-0.00510.20550.01520.2275-17.33029.145916.4425
83.61851.00830.03871.85480.90054.18580.1115-0.10050.1909-0.0214-0.0643-0.215-0.50780.3104-0.05580.2581-0.02590.00960.21650.03260.2403-17.878110.385317.4559
91.40730.0087-1.37172.3367-0.87387.27030.1244-0.35210.05710.60410.26420.0711-0.6841-0.1782-0.38570.43190.079-0.02130.46470.0190.292-30.285910.375846.8885
104.50861.1923-0.64045.7124-0.72886.2294-0.244-0.2099-0.2923-0.24630.28110.0524-0.1098-0.2078-0.03470.4710.02420.070.5364-0.01690.3212-31.67156.635345.1345
116.322.3174-2.35218.0338-1.23545.2269-0.0133-1.0378-0.89510.6854-0.1117-0.84580.06290.3198-0.12070.53010.0064-0.05740.76260.01450.3134-26.00193.759252.5275
123.80160.339-1.41411.3187-1.03334.36540.02540.05450.14890.09840.08470.0892-0.2006-0.3695-0.1220.19960.0271-0.01260.21720.00990.2611-38.21894.001415.5674
132.35540.6875-0.17912.41032.00435.99090.0211-0.74680.24050.37230.10110.2462-1.0904-0.8198-0.10920.80710.29920.07770.91280.02680.3722-44.628612.942150.9898
145.8682-2.08334.09227.8862-1.73629.05560.9619-0.2258-0.79930.8387-1.1609-1.07130.69031.44720.23740.5334-0.1659-0.13740.90670.16230.7414-1.4867-15.9903-14.6659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 11 through 30 )R11 - 30
2X-RAY DIFFRACTION2chain 'R' and (resid 31 through 40 )R31 - 40
3X-RAY DIFFRACTION3chain 'R' and (resid 41 through 60 )R41 - 60
4X-RAY DIFFRACTION4chain 'R' and (resid 61 through 80 )R61 - 80
5X-RAY DIFFRACTION5chain 'R' and (resid 81 through 90 )R81 - 90
6X-RAY DIFFRACTION6chain 'H' and (resid 3 through 20 )H3 - 20
7X-RAY DIFFRACTION7chain 'H' and (resid 21 through 63 )H21 - 63
8X-RAY DIFFRACTION8chain 'H' and (resid 64 through 115 )H64 - 115
9X-RAY DIFFRACTION9chain 'H' and (resid 116 through 157 )H116 - 157
10X-RAY DIFFRACTION10chain 'H' and (resid 158 through 201 )H158 - 201
11X-RAY DIFFRACTION11chain 'H' and (resid 202 through 228 )H202 - 228
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 114 )L1 - 114
13X-RAY DIFFRACTION13chain 'L' and (resid 115 through 215 )L115 - 215
14X-RAY DIFFRACTION14chain 'R' and (resid 1 through 10 )R1 - 10

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