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- PDB-4plx: Crystal structure of the triple-helical stability element at the ... -

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Basic information

Entry
Database: PDB / ID: 4plx
TitleCrystal structure of the triple-helical stability element at the 3' end of MALAT1
ComponentsCore ENE hairpin and A-rich tract from MALAT1
KeywordsRNA / Triple helix / RNA stability element / MALAT1 / long noncoding RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsBrown, J.A. / Bulkley, D. / Wang, J. / Valenstein, M.L. / Yario, T.A. / Steitz, T.A. / Steitz, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM026154 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix.
Authors: Brown, J.A. / Bulkley, D. / Wang, J. / Valenstein, M.L. / Yario, T.A. / Steitz, T.A. / Steitz, J.A.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: pdbx_audit_support / pdbx_database_status ...pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / struct_conn
Item: _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible ..._pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 and A-rich tract from MALAT1
B: Core ENE hairpin and A-rich tract from MALAT1
C: Core ENE hairpin and A-rich tract from MALAT1


Theoretical massNumber of molelcules
Total (without water)73,7203
Polymers73,7203
Non-polymers00
Water63135
1
A: Core ENE hairpin and A-rich tract from MALAT1


Theoretical massNumber of molelcules
Total (without water)24,5731
Polymers24,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Core ENE hairpin and A-rich tract from MALAT1


Theoretical massNumber of molelcules
Total (without water)24,5731
Polymers24,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Core ENE hairpin and A-rich tract from MALAT1


Theoretical massNumber of molelcules
Total (without water)24,5731
Polymers24,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.820, 162.820, 65.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: A / End label comp-ID: A / Refine code: _ / Auth seq-ID: 2 - 75 / Label seq-ID: 2 - 75

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: RNA chain Core ENE hairpin and A-rich tract from MALAT1


Mass: 24573.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: malat1 / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Folded RNA was combined with an equal volume of the reservoir solution (50 mM sodium cacodylate pH 6.5, 18 mM magnesium chloride, 2.5 mM spermine and 9% isopropanol)

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.979
SYNCHROTRONNSLS X2521.1053, 1.1060, 1.1046
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELDec 15, 2012
DECTRIS PILATUS 6M2PIXELFeb 16, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.10531
31.1061
41.10461
ReflectionResolution: 3.1→50 Å / Num. obs: 17565 / % possible obs: 99.7 % / Redundancy: 11.2 % / Net I/σ(I): 17.2
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.28 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 3.1→48.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 42.238 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 915 5 %RANDOM
Rwork0.22 ---
obs0.222 17565 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.68 Å20 Å2
2--0.68 Å20 Å2
3----2.2 Å2
Refinement stepCycle: 1 / Resolution: 3.1→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4709 0 35 4744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0115261
X-RAY DIFFRACTIONr_bond_other_d0.0070.022133
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.358183
X-RAY DIFFRACTIONr_angle_other_deg1.46235213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1420.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022547
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021101
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A46290.13
12B46290.13
21A44570.13
22C44570.13
31B44140.14
32C44140.14
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 83 -
Rwork0.329 1266 -
obs--99.78 %
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)
10.106-0.1905-0.00140.50240.08760.1085-0.0877-0.0103-0.01970.17640.04560.0520.09380.0140.04210.18070.04930.04380.19230.01640.76872.539865.925465.8105
20.30720.18950.05430.1416-0.05760.7919-0.01980.07790.1637-0.03360.08560.0398-0.0673-0.2296-0.06580.16090.0245-0.00590.23810.03570.7126-20.29890.945351.8973
31.7314-0.8652-0.53711.0370.20910.18380.25750.0961-0.26460.0118-0.21620.3297-0.124-0.0534-0.04120.27410.28190.01410.5198-0.04680.987-77.8346111.178430.4334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION2B1 - 76
3X-RAY DIFFRACTION3C1 - 76

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