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- PDB-5ew4: Crystal structure of C9ORF72 Antisense CCCCGG repeat RNA associat... -

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Basic information

Entry
Database: PDB / ID: 5ew4
TitleCrystal structure of C9ORF72 Antisense CCCCGG repeat RNA associated with Lou Gehrig's disease and frontotemporal dementia, crystallized with Sr2+
ComponentsRNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')
KeywordsRNA / REPEAT EXPANSION DISORDER / GENETIC DISEASE
Function / homology: / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.47 Å
AuthorsTomchick, D.R. / Dodd, D.W. / Gagnon, K.T. / Corey, D.R.
CitationJournal: Biochemistry / Year: 2016
Title: Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches.
Authors: Dodd, D.W. / Tomchick, D.R. / Corey, D.R. / Gagnon, K.T.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')
B: RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,34215
Polymers13,8182
Non-polymers52413
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-79 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.020, 47.615, 58.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')


Mass: 6909.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.04 M sodium cacodylate, 50 mM KCl, 0.04 M LiCl, 0.012 M spermine, 0.08 M strontium chloride, 10% (v/v) (+/-)-2-methyl-2,4-pentanediol, equilibrated against 35% (v/v) (+/-)-2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2014 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 20000 / % possible obs: 98.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 13.58 Å2 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.016 / Rrim(I) all: 0.036 / Χ2: 0.839 / Net I/av σ(I): 36.407 / Net I/σ(I): 14.1 / Num. measured all: 90931
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.47-1.52.90.5428880.7130.3430.6480.81189.4
1.5-1.523.50.4549770.8180.2690.5320.85498.8
1.52-1.554.30.39710000.9090.2110.4510.87699.9
1.55-1.584.60.3359970.950.1710.3780.927100
1.58-1.624.70.2469830.9770.1230.2760.908100
1.62-1.664.70.1810100.9880.0890.2020.899100
1.66-1.74.80.1369920.9960.0680.1530.8999.9
1.7-1.744.80.1179930.9950.0580.1310.921100
1.74-1.794.70.10710170.9910.0540.120.921100
1.79-1.854.80.0889930.9930.0440.0990.87399.9
1.85-1.924.80.0689960.9960.0340.0760.874100
1.92-24.80.05410130.9970.0270.0610.86499.9
2-2.094.80.0429900.9980.020.0470.78999.7
2.09-2.24.70.03410170.9980.0170.0380.70799.7
2.2-2.334.80.0310090.9980.0140.0330.6599.6
2.33-2.514.70.0310170.9980.0150.0340.73899.6
2.51-2.774.70.03310220.9970.0160.0371.01699
2.77-3.174.70.03210300.9950.0160.0361.11198.7
3.17-3.994.60.02310240.9990.0110.0250.6197.3
3.99-504.40.01910320.9980.010.0220.52591.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
ACORNphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.47→23.923 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1928 10.01 %throughout
Rwork0.2155 17341 --
obs0.2179 19269 95.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.31 Å2 / Biso mean: 23.1584 Å2 / Biso min: 8.88 Å2
Refinement stepCycle: final / Resolution: 1.47→23.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 818 13 162 993
Biso mean--22.92 28.05 -
Num. residues----41
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024954
X-RAY DIFFRACTIONf_angle_d0.5081408
X-RAY DIFFRACTIONf_chiral_restr0.025195
X-RAY DIFFRACTIONf_plane_restr0.00339
X-RAY DIFFRACTIONf_dihedral_angle_d6.489462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.50730.3309870.269478186861
1.5073-1.54810.28161190.26731079119885
1.5481-1.59360.21881410.25221269141099
1.5936-1.6450.27061440.226512861430100
1.645-1.70380.24741400.226612591399100
1.7038-1.7720.24591410.216912751416100
1.772-1.85260.26191450.218612981443100
1.8526-1.95030.23361420.226312831425100
1.9503-2.07240.2461430.206912851428100
2.0724-2.23230.25021450.202713001445100
2.2323-2.45680.2121440.207812951439100
2.4568-2.81180.23021450.23221307145299
2.8118-3.54070.22971440.19581296144098
3.5407-23.92620.23421480.21181328147694
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)
15.8985-0.9968-0.89111.22791.67232.3652-0.2317-0.1520.2422-0.0094-0.00560.5378-0.1973-0.08930.07510.1363-0.00120.0140.1204-0.04440.355117.663535.168459.5573
21.7376-1.8031.08291.9598-1.38462.08670.30490.29910.0211-0.5025-0.0620.12030.25030.3447-0.18680.1775-0.0086-0.02990.1040.00530.075618.6727.375443.7451
34.10650.2043-1.11791.9849-0.71861.99030.09930.2577-0.4567-0.2451-0.088-0.08160.1068-0.1173-0.02550.1705-0.0115-0.02060.1276-0.00630.1120.121734.988826.0809
43.26870.6626-0.93373.00580.50330.9594-0.12680.1414-0.28650.02930.00790.34010.3691-0.33780.11520.2895-0.0312-0.06260.19-0.0160.513617.176428.048725.3666
51.1944-0.37950.54431.6386-0.83141.63680.009-0.07870.1063-0.05830.1156-0.102-0.0150.0123-0.12220.144-0.0050.0060.0899-0.01320.092620.053432.101951.7152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:8 )A3 - 8
2X-RAY DIFFRACTION2( CHAIN A AND RESID 9:14 )A9 - 14
3X-RAY DIFFRACTION3( CHAIN A AND RESID 15:21 )A15 - 21
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:8 )B2 - 8
5X-RAY DIFFRACTION5( CHAIN B AND RESID 9:21 )B9 - 21

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