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- PDB-5lys: The crystal structure of 7SK 5'-hairpin - Gold derivative -

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Basic information

Entry
Database: PDB / ID: 5lys
TitleThe crystal structure of 7SK 5'-hairpin - Gold derivative
Components7SK RNA
KeywordsRNA / non-coding RNA major groove base triple transcription
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsMartinez-Zapien, D. / Legrand, P. / McEwen, A.G. / 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 1.4May 1, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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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)37,1036
Polymers36,6612
Non-polymers4414
Water3,315184
1
A: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5282
Polymers18,3311
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5754
Polymers18,3311
Non-polymers2443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.320, 47.830, 69.230
Angle α, β, γ (deg.)90.000, 105.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 7SK RNA


Mass: 18330.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
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, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.04014 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04014 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 23716 / % possible obs: 93.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 54.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 3.56 % / Rmerge(I) obs: 1.327 / Mean I/σ(I) obs: 1.12 / CC1/2: 0.469 / % possible all: 61.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Theoretical model of RNA generated with RNAcomposer

Resolution: 2.32→40 Å / Cor.coef. Fo:Fc: 0.9576 / Cor.coef. Fo:Fc free: 0.9436 / SU R Cruickshank DPI: 0.99 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.276 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 491 3.99 %RANDOM
Rwork0.1845 ---
obs0.1866 12303 93.83 %-
Displacement parametersBiso max: 138.83 Å2 / Biso mean: 59.05 Å2 / Biso min: 24.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.0225 Å20 Å25.3761 Å2
2---1.8343 Å20 Å2
3---3.8568 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: final / Resolution: 2.32→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2426 4 184 2614
Biso mean--59.44 47.86 -
Num. residues----114
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d649SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes129HARMONIC5
X-RAY DIFFRACTIONt_it3072HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion516SEMIHARMONIC5
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_contact3234SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3072HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4793HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion26.46
LS refinement shellResolution: 2.32→2.54 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2737 73 3.01 %
Rwork0.214 2352 -
all0.2158 2425 -
obs--78.31 %
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)
12.7849-0.09930.16032.3966-1.09286.08130.14610.04950.03620.0209-0.1051-0.3994-0.05990.5787-0.041-0.2835-0.0354-0.032-0.1890.0451-0.11427.02270.533133.6236
23.2522-0.3761-0.97322.5444-0.27373.09840.0676-0.176-0.31440.03350.06580.20660.1551-0.1523-0.1335-0.2431-0.0227-0.0436-0.21540.0095-0.1903-17.7189-0.27634.4312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|24 - A|87 }A24 - 87
2X-RAY DIFFRACTION2{ B|24 - B|87 }B24 - 87

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