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- PDB-8k0y: Crystal structure of a medaka mascRNA U23G -

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Basic information

Entry
Database: PDB / ID: 8k0y
TitleCrystal structure of a medaka mascRNA U23G
ComponentsRNA (56-MER)
KeywordsRNA / MascRNA / tRNA-like / MALAT1
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesOryzias latipes (Japanese medaka)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsHe, Y. / Deng, J. / Lin, X. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Cell Discov / Year: 2025
Title: Structural basis for tRNA mimicry by mascRNA and menRNA.
Authors: He, Y. / Deng, J. / Lin, X. / Lu, Z. / Wang, L. / Xu, L. / Zhang, Y. / Wang, J. / Huang, L.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (56-MER)
B: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,65422
Polymers36,0092
Non-polymers1,64420
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.360, 29.250, 98.080
Angle α, β, γ (deg.)90.000, 118.560, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 11 or resid 13 through 56))
d_2ens_1(chain "B" and (resid 1 through 22 or resid 29 through 56))

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Auth seq-ID: 1 - 3 / Label seq-ID: 1 - 3

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999187717128, 0.0399312903662, 0.00542199129745), (-0.039817234732, -0.999012241863, 0.019726338368), (0.00620433382666, 0.019494426301, 0.999790714892)Vector: 65. ...NCS oper: (Code: given
Matrix: (-0.999187717128, 0.0399312903662, 0.00542199129745), (-0.039817234732, -0.999012241863, 0.019726338368), (0.00620433382666, 0.019494426301, 0.999790714892)
Vector: 65.4770424131, 57.9083369761, 0.501926491904)

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Components

#1: RNA chain RNA (56-MER)


Mass: 18004.605 Da / Num. of mol.: 2 / Mutation: U23G / Source method: obtained synthetically / Source: (synth.) Oryzias latipes (Japanese medaka)
#2: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ir
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 18% v/v (+ / -)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.28→28.72 Å / Num. obs: 17707 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 63.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.4
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.174 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1336 / CC1/2: 0.618 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→28.08 Å / SU ML: 0.3618 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1786
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2854 946 5.09 %
Rwork0.2486 32731 -
obs-17707 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2141 20 14 2175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492387
X-RAY DIFFRACTIONf_angle_d0.9613713
X-RAY DIFFRACTIONf_chiral_restr0.0408500
X-RAY DIFFRACTIONf_plane_restr0.0076100
X-RAY DIFFRACTIONf_dihedral_angle_d11.71071185
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.947020664154 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.45271450.42352489X-RAY DIFFRACTION98.21
2.34-2.410.41881530.38532577X-RAY DIFFRACTION98.73
2.41-2.490.40831390.34292535X-RAY DIFFRACTION98.64
2.49-2.580.35081280.33282593X-RAY DIFFRACTION99.63
2.58-2.680.36321320.32022634X-RAY DIFFRACTION99.46
2.68-2.80.3221200.31282494X-RAY DIFFRACTION98.75
2.8-2.950.32961300.30022534X-RAY DIFFRACTION95.79
2.95-3.130.27731470.22732381X-RAY DIFFRACTION93.91
3.13-3.380.30021530.19822438X-RAY DIFFRACTION94.67
3.38-3.710.23331290.2052494X-RAY DIFFRACTION95.83
3.72-4.250.21171350.17942543X-RAY DIFFRACTION97.49
4.25-5.350.25351040.20492519X-RAY DIFFRACTION97.26
5.35-28.080.2721420.26312500X-RAY DIFFRACTION96.39
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)
10.388776373972-0.4141539897050.1328334007380.4328732066260.1714375728760.3756351049530.2315502814220.494604846465-0.4876533207860.273020408557-0.3075998113540.4233362550450.1392035132050.291629329959.91357397486E-50.5810131583770.0144842695691-0.0895583715270.5397706375410.001070580808610.80461397481555.8203560122.377679351154.8068546322
21.444738022010.3728902953120.02851488554120.09448570423410.02270469530040.1661465584080.330337511974-1.15008471755-1.256635115420.435199463079-0.231745793841-0.602499468508-0.05706991978380.1915080077670.009950628414651.03497134831-0.10106414549-0.3273311933540.9440588096280.215115364460.51059154550558.015508382414.076972923168.2263399994
31.220534205460.517532299908-0.5678232084380.240893283752-0.1109289059150.32885644177-0.3725180466740.0195292389569-0.2918713271910.5580311210230.134132635110.2042589469480.007144955024530.2380435908110.0007058943934310.5921612885290.0780597490368-0.01065720394690.6084175979180.04154994236290.52134740580852.452226223416.425533174152.4879253259
40.7964877517610.4912025297240.4718563014610.2825857806680.4305137828620.5404544346840.4256011908460.989051687108-0.1193802457870.4010155507660.0526659088581-0.3781902443820.0454777582013-0.4595196803280.03533261028630.6554279792660.07141029199810.06137546661710.654097175191-0.1576359465530.69689028060310.597563682934.584669805357.0908330335
50.0709875002973-0.0463655384590.04166227556220.612172341250.0980593702870.05093349406070.494469553365-1.271425064870.9468393261460.5643971419360.746616999810.330039231991-0.8419249484510.3952375712810.03371183775841.73857415733-0.1118496089890.2857627091181.48449276036-0.237379771890.804540642615.8307005799942.513480826976.4582617034
60.408778867010.00178265175071-0.2133271670260.135037933750.1640479463530.280989836268-0.2471240420250.05981534085650.2318321699390.4719185632870.2281117974410.495339828738-0.16525571356-0.540916727736-0.0006359241633270.7598902634730.09027447356850.05720876899470.760982532970.04111467000420.7632825325049.0828777489548.608575479255.1679054288
70.5422295710170.5396094139230.1187731178070.5155688092260.147289528707-0.0122242940837-0.23439105850.393004702501-0.6797730238530.3317553113020.26847809324-0.875006229397-0.0334401587061-0.1466129760190.003053283074180.6087247537340.0545625502586-0.03217701548610.630759906504-0.1654912963650.99222403183917.915157416836.697450474654.5609057293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )AA1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 36 )AA16 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 56 )AA37 - 56
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 16 )BB1 - 16
5X-RAY DIFFRACTION5chain 'B' and (resid 17 through 31 )BB17 - 31
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 41 )BB32 - 41
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 56 )BB42 - 56

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