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- PDB-3p22: Crystal structure of the ENE, a viral RNA stability element, in c... -

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Basic information

Entry
Database: PDB / ID: 3p22
TitleCrystal structure of the ENE, a viral RNA stability element, in complex with A9 RNA
Components
  • Core ENE hairpin from KSHV PAN RNA
  • oligo(A)9 RNA
KeywordsRNA / Major groove triple helix / viral non-coding RNA / stability element / Nucleus
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.501 Å
AuthorsMitton-Fry, R.M. / DeGregorio, S.J. / Wang, J. / Steitz, T.A. / Steitz, J.A.
CitationJournal: Science / Year: 2010
Title: Poly(A) tail recognition by a viral RNA element through assembly of a triple helix.
Authors: Mitton-Fry, R.M. / DeGregorio, S.J. / Wang, J. / Steitz, T.A. / Steitz, J.A.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core ENE hairpin from KSHV PAN RNA
B: oligo(A)9 RNA
C: Core ENE hairpin from KSHV PAN RNA
D: oligo(A)9 RNA
E: Core ENE hairpin from KSHV PAN RNA
F: oligo(A)9 RNA
G: Core ENE hairpin from KSHV PAN RNA
H: oligo(A)9 RNA


Theoretical massNumber of molelcules
Total (without water)63,2938
Polymers63,2938
Non-polymers00
Water32418
1
A: Core ENE hairpin from KSHV PAN RNA
B: oligo(A)9 RNA


Theoretical massNumber of molelcules
Total (without water)15,8232
Polymers15,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area8280 Å2
MethodPISA
2
C: Core ENE hairpin from KSHV PAN RNA
D: oligo(A)9 RNA


Theoretical massNumber of molelcules
Total (without water)15,8232
Polymers15,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-13 kcal/mol
Surface area8010 Å2
MethodPISA
3
E: Core ENE hairpin from KSHV PAN RNA
F: oligo(A)9 RNA


Theoretical massNumber of molelcules
Total (without water)15,8232
Polymers15,8232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-12 kcal/mol
Surface area8300 Å2
MethodPISA
4
G: Core ENE hairpin from KSHV PAN RNA
H: oligo(A)9 RNA


Theoretical massNumber of molelcules
Total (without water)15,8232
Polymers15,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-13 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.746, 50.869, 91.380
Angle α, β, γ (deg.)90.00, 125.06, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12C
22G
13B
23F
14D
24H

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GTPGTPCCAA1 - 401 - 40
21GTPGTPCCEE1 - 401 - 40
12GTPGTPCCCC1 - 401 - 40
22GTPGTPCCGG1 - 401 - 40
13AAAABB1 - 91 - 9
23AAAAFF1 - 91 - 9
14AAHOHHOHDD - L1 - 92
24AAHOHHOHHH - O1 - 92

NCS ensembles :
ID
1
2
3
4

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Components

#1: RNA chain
Core ENE hairpin from KSHV PAN RNA


Mass: 12905.439 Da / Num. of mol.: 4 / Fragment: hairpin from KSHV PAN RNA / Source method: obtained synthetically
Details: In vitro transcribed from plasmid template DNA using T7 RNA polymerase
#2: RNA chain
oligo(A)9 RNA


Mass: 2917.895 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1662
2
3
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 17% MPD, 0.09 M magnesium acetate, 0.05 M MES, pH 5.6 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X29A21.1048, 1.1052, 1.0858
SYNCHROTRONNSLS X29A31.1051, 1.1054
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 11, 2009
ADSC QUANTUM 3152CCDOct 10, 2009
ADSC QUANTUM 3153CCDOct 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray2
3SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.08091
21.10481
31.10521
41.08581
51.10511
61.10541
ReflectionResolution: 2.5→50 Å / Num. all: 19113 / Num. obs: 18693 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 83.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.977 / Mean I/σ(I) obs: 1 / % possible all: 85.3

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Processing

Software
NameClassification
CBASSdata collection
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.501→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.95 / SU B: 26.367 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.112 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23343 965 5.2 %RANDOM
Rwork0.21834 ---
all0.21913 18147 --
obs0.21913 17722 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.938 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å2-1.36 Å2
2--2.04 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.501→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4148 0 18 4166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214630
X-RAY DIFFRACTIONr_angle_refined_deg1.3182.9947210
X-RAY DIFFRACTIONr_chiral_restr0.060.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021990
X-RAY DIFFRACTIONr_scbond_it1.08334630
X-RAY DIFFRACTIONr_scangle_it1.7414.57206
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A853TIGHT POSITIONAL0.050.05
1A853TIGHT THERMAL0.10.5
2C853TIGHT POSITIONAL0.040.05
2C853TIGHT THERMAL0.080.5
3B195TIGHT POSITIONAL0.030.05
3B195TIGHT THERMAL0.10.5
4D173TIGHT POSITIONAL0.020.05
4D173TIGHT THERMAL0.040.5
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 62 -
Rwork0.445 1105 -
obs--81.89 %
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)
17.29320.09390.55212.50710.23620.52460.115-0.3370.2348-0.0374-0.00580.0304-0.1325-0.087-0.10920.05960.00860.04490.13220.00480.0446-4.4184.7423.104
22.055-0.4547-0.57485.844-1.28625.50220.04880.20350.0053-0.2590.06280.37440.15670.0935-0.11160.0461-0.02550.02820.1144-0.03340.08736.9518.21710.446
35.0099-1.74950.31243.37680.79430.4221-0.0404-0.065-0.05950.04880.09940.14310.0301-0.0819-0.05890.0984-0.09130.04250.16970.0450.117323.07915.9634.906
42.65541.63493.83374.15580.44496.79880.1211-0.22970.00590.0454-0.1086-0.13580.2048-0.1925-0.01250.09010.0080.03540.2852-0.16320.12928.01114.11744.657
59.3442-0.96590.3188.41473.09092.7859-0.2174-0.31840.5621-0.08190.4488-0.4697-0.02530.3037-0.23140.155-0.07270.02120.0999-0.06290.066537.12212.94229.697
62.3685-1.21480.58920.6802-0.4744.6792-0.1425-0.0479-0.0120.09870.0876-0.02590.15940.01680.05490.1503-0.02440.02280.1184-0.05940.031735.3288.64611.069
74.8624-1.9373-0.29422.2586-0.62681.47880.20.24220.38850.0051-0.01020.2702-0.11480.0005-0.18980.05470.01140.03340.09260.04630.154949.28-17.20714.744
81.8977-1.9851-1.04518.59532.20979.20660.1003-0.24890.10040.65080.272-0.23610.22730.6326-0.37230.11320.00670.0550.13420.03990.314638.241-16.06828.403
93.08270.2425-0.55821.63960.88573.23380.1278-0.06460.2814-0.07420.1846-0.2128-0.17280.1083-0.31240.07860.03860.06110.10150.00690.116620.251-11.49333.009
103.0027-0.72232.52071.0078-2.91688.747-0.09440.1574-0.0029-0.19320.0966-0.02130.4858-0.0716-0.00210.0971-0.03980.03980.1586-0.02910.039718.307-7.906-8.56
115.12110.9676-2.04266.5148-0.83632.4366-0.0307-0.01170.3371-0.1320.00060.6465-0.0504-0.33330.03010.06060.0539-0.00770.147-0.02980.10710.124-11.2576.286
122.1092-0.69830.74521.8791.88873.9443-0.0940.1358-0.0103-0.0480.0505-0.07310.1117-0.05540.04350.15320.00960.10170.17120.03040.077610.379-18.7423.531
133.1666-3.0366-3.2943.25122.87313.6672-0.1042-0.03140.14240.21270.0385-0.38470.01890.02860.06560.11180.0372-0.02090.17220.02610.249129.594-7.9883.91
143.4734-0.06392.93961.84413.52059.42160.06830.2687-0.06160.03590.1517-0.08630.12760.5291-0.220.1338-0.0689-0.01290.1617-0.01530.017211.15.2529.697
1511.5798-1.336-7.10999.79710.76424.36690.40890.54820.6460.4065-0.02980.5436-0.248-0.3312-0.37910.1461-0.05470.0550.12320.09280.211520.39618.06732.682
160.0884-0.94680.917116.1665-2.86317.59660.0486-0.0519-0.0207-0.27470.35590.02130.5903-0.7732-0.40450.025-0.01990.00010.10630.05080.068235.551-20.76811.457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION1A34 - 40
3X-RAY DIFFRACTION2A8 - 12
4X-RAY DIFFRACTION2A27 - 33
5X-RAY DIFFRACTION2B5 - 9
6X-RAY DIFFRACTION3A13 - 26
7X-RAY DIFFRACTION4C1 - 7
8X-RAY DIFFRACTION4C34 - 40
9X-RAY DIFFRACTION5C8 - 12
10X-RAY DIFFRACTION5C27 - 33
11X-RAY DIFFRACTION5D4 - 9
12X-RAY DIFFRACTION6C13 - 26
13X-RAY DIFFRACTION7G1 - 7
14X-RAY DIFFRACTION7G34 - 40
15X-RAY DIFFRACTION8G8 - 12
16X-RAY DIFFRACTION8G27 - 33
17X-RAY DIFFRACTION8H4 - 9
18X-RAY DIFFRACTION9G13 - 26
19X-RAY DIFFRACTION10E1 - 7
20X-RAY DIFFRACTION10E34 - 40
21X-RAY DIFFRACTION11E8 - 12
22X-RAY DIFFRACTION11E27 - 33
23X-RAY DIFFRACTION11F5 - 9
24X-RAY DIFFRACTION12E13 - 26
25X-RAY DIFFRACTION13F1 - 4
26X-RAY DIFFRACTION14B1 - 4
27X-RAY DIFFRACTION15D1 - 3
28X-RAY DIFFRACTION16H1 - 3

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