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- PDB-5lyu: The native crystal structure of 7SK 5'-hairpin -

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Basic information

Entry
Database: PDB / ID: 5lyu
TitleThe native crystal structure of 7SK 5'-hairpin
Components7SK RNA
KeywordsRNA / non-coding RNA major groove base triple transcription
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.2 Å
AuthorsMartinez-Zapien, D. / Legrand, P. / McEwen, A.C. / Pasquali, S. / Dock-Bregeon, A.-C.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-06-BLAN-0072 France
French National Research AgencyANR-12-BSV5-0018 France
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The crystal structure of the 5 functional domain of the transcription riboregulator 7SK.
Authors: Martinez-Zapien, D. / Legrand, P. / McEwen, A.G. / Proux, F. / Cragnolini, T. / Pasquali, S. / Dock-Bregeon, A.C.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 18, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.4Jan 17, 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7SK RNA
B: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4706
Polymers37,3522
Non-polymers1184
Water4,125229
1
A: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7343
Polymers18,6761
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7363
Polymers18,6761
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.790, 47.780, 68.670
Angle α, β, γ (deg.)90.000, 99.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 7SK RNA /


Mass: 18675.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 1000, 50 mM Tris pH 7.5, 50 to 75 mM NaCl, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 13144 / % possible obs: 87.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 59.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 18.57
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 2.38 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 0.97 / CC1/2: 0.425 / % possible all: 52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LYS

5lys


Resolution: 2.2→28.32 Å / Cor.coef. Fo:Fc: 0.9587 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.606 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.275 / SU Rfree Cruickshank DPI: 0.254
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 553 4.21 %RANDOM
Rwork0.1913 ---
obs0.1935 13139 87.17 %-
Displacement parametersBiso max: 113.74 Å2 / Biso mean: 58.65 Å2 / Biso min: 24.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.6653 Å20 Å25.0623 Å2
2---0.555 Å20 Å2
3----2.1103 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: final / Resolution: 2.2→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2472 4 230 2706
Biso mean--63.04 55.62 -
Num. residues----116
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d634SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes126HARMONIC5
X-RAY DIFFRACTIONt_it2994HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion504SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3246SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2994HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4668HARMONIC20.81
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion23.65
LS refinement shellResolution: 2.2→2.38 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3018 72 4.34 %
Rwork0.2356 1586 -
all0.2383 1658 -
obs--54.15 %
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)
12.39350.29290.47780.74390.32583.91880.06380.33180.013-0.05780.1261-0.0692-0.1170.3811-0.19-0.1501-0.01610.0115-0.17340.0457-0.08710.2009-0.065230.7894
22.3973-0.0134-0.63510.60.53691.70110.0714-0.027-0.16680.04820.00570.0296-0.0004-0.2024-0.0771-0.10330.009-0.018-0.1614-0.0252-0.1253-13.62490.321133.772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|23 - A|87 }A23 - 87
2X-RAY DIFFRACTION2{ B|23 - B|87 }B23 - 87

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