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- PDB-5lyv: The crystal structure of 7SK 5'-hairpin - Osmium derivative -

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Basic information

Entry
Database: PDB / ID: 5lyv
TitleThe crystal structure of 7SK 5'-hairpin - Osmium derivative
Components7SK RNA
KeywordsRNA / non-coding RNA major groove base triple transcription
Function / homologyosmium (III) hexammine / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 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 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_PDB_ins_code / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_PDB_ins_code / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,0085
Polymers36,6612
Non-polymers3463
Water4,360242
1
A: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6172
Polymers18,3311
Non-polymers2861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7SK RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3903
Polymers18,3311
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.120, 47.740, 68.940
Angle α, β, γ (deg.)90.000, 105.200, 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-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H12N6Os
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
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: 1.13956 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: 1.13956 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 22741 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 67.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.083 / Χ2: 0.986 / Net I/σ(I): 7.37 / Num. measured all: 41939
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.410.4581.31943181613680.7740.64475.3
2.41-2.480.4571.642299175214360.7430.63382
2.48-2.550.3952.122752165515090.8020.52891.2
2.55-2.630.4192.213210171416580.7890.55996.7
2.63-2.710.2763.133015158715620.8920.36698.4
2.71-2.810.2024.12995159215580.9480.27197.9
2.81-2.920.174.662769147114460.9570.22698.3
2.92-3.040.1146.192680143514050.9890.15297.9
3.04-3.170.0887.512546139513390.9910.11896
3.17-3.320.0738.452425130612830.9940.09798.2
3.32-3.50.0619.662322126812190.9930.08196.1
3.5-3.720.05510.972131117411280.9880.07496.1
3.72-3.970.05511.142060114310980.9920.07496.1
3.97-4.290.04213.21183410369840.9940.05795
4.29-4.70.04213.7616629419040.9940.05696.1
4.7-5.260.03615.9115488898300.9960.04993.4
5.26-6.070.03615.6113287597230.9930.04895.3
6.07-7.430.03614.5711056385920.9980.04892.8
7.43-10.510.02718.798844904640.9970.03694.7
10.510.02822.454312802350.9960.03783.9

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Processing

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

5lys


Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.9437 / SU R Cruickshank DPI: 1.023 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.284 / SU Rfree Cruickshank DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 497 4.06 %RANDOM
Rwork0.1985 ---
obs0.2001 12231 97.75 %-
Displacement parametersBiso max: 126.56 Å2 / Biso mean: 58 Å2 / Biso min: 23.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.8347 Å20 Å23.219 Å2
2--1.1589 Å20 Å2
3---1.6757 Å2
Refine analyzeLuzzati coordinate error obs: 0.335 Å
Refinement stepCycle: final / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2380 55 242 2677
Biso mean--96.65 51.18 -
Num. residues----112
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d629SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes125HARMONIC5
X-RAY DIFFRACTIONt_it2974HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion500SEMIHARMONIC5
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_contact3226SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2974HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4642HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion23.94
LS refinement shellResolution: 2.35→2.57 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2947 89 3.14 %
Rwork0.2154 2749 -
all0.2178 2838 -
obs--96.4 %
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)
12.38510.1114-0.57982.1312-0.62784.45250.16640.0174-0.03020.0048-0.1299-0.3478-0.16250.5491-0.0365-0.2311-0.0304-0.0908-0.16590.0403-0.09077.30880.315833.583
22.8052-0.4647-0.55331.9789-0.11773.27420.1042-0.1188-0.2449-0.04760.05790.2180.1909-0.2757-0.1621-0.1982-0.031-0.0623-0.15980.0016-0.1635-17.20230.230132.9947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|24 - A|86 }A24 - 87
2X-RAY DIFFRACTION2{ B|24 - B|86 }B24 - 87

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