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- PDB-8v1i: Crystal structure of human mascRNA -

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Basic information

Entry
Database: PDB / ID: 8v1i
TitleCrystal structure of human mascRNA
ComponentsmascRNA
KeywordsRNA / non-coding RNAs / cancer / mascRNA
Function / homologyACETATE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSkeparnias, I. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Structural basis of MALAT1 RNA maturation and mascRNA biogenesis.
Authors: Skeparnias, I. / Bou-Nader, C. / Anastasakis, D.G. / Fan, L. / Wang, Y.X. / Hafner, M. / Zhang, J.
History
DepositionNov 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: mascRNA
A: mascRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,68717
Polymers36,9882
Non-polymers69915
Water48627
1
B: mascRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8348
Polymers18,4941
Non-polymers3407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: mascRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8529
Polymers18,4941
Non-polymers3598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.063, 137.063, 135.805
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain mascRNA


Mass: 18493.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 1108618392
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate and 20% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 29, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→31.99 Å / Num. obs: 21925 / % possible obs: 99.77 % / Redundancy: 34 % / CC1/2: 0.994 / Net I/σ(I): 19.33
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2172 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→31.99 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1067 4.87 %
Rwork0.2147 --
obs0.2154 21898 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2417 30 27 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052706
X-RAY DIFFRACTIONf_angle_d1.0794204
X-RAY DIFFRACTIONf_dihedral_angle_d12.2091367
X-RAY DIFFRACTIONf_chiral_restr0.042565
X-RAY DIFFRACTIONf_plane_restr0.007118
Refinement TLS params.Method: refined / Origin x: 0.3797 Å / Origin y: -33.4721 Å / Origin z: -9.7843 Å
111213212223313233
T0.7919 Å2-0.0281 Å2-0.1249 Å2-0.6847 Å2-0.1108 Å2--0.8778 Å2
L0.7798 °20.2244 °20.2624 °2-0.4566 °2-0.1171 °2--0.3895 °2
S0.1119 Å °0.1743 Å °-0.3185 Å °-0.066 Å °0.0931 Å °-0.1543 Å °0.2793 Å °-0.2302 Å °-0.2148 Å °
Refinement TLS groupSelection details: all

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