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- PDB-8k2z: Crystal structure of a human mascRNA A2G -

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Basic information

Entry
Database: PDB / ID: 8k2z
TitleCrystal structure of a human mascRNA A2G
ComponentsRNA (57-MER)
KeywordsRNA / MascRNA / tRNA-like / MALAT1
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 14, 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 (57-MER)
B: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,97614
Polymers36,7002
Non-polymers27612
Water43224
1
A: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5118
Polymers18,3501
Non-polymers1617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4656
Polymers18,3501
Non-polymers1155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.365, 30.111, 89.353
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 24 or (resid 30...
d_2ens_1chain "B"

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 - 5 / Label seq-ID: 1 - 5

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.997484263136, 0.0464510229926, 0.0535485504923), (-0.0433234327538, -0.997366903553, 0.0581578874386), (0.0561090453609, 0.0556916704708, 0.996870208637)Vector: -1. ...NCS oper: (Code: given
Matrix: (-0.997484263136, 0.0464510229926, 0.0535485504923), (-0.0433234327538, -0.997366903553, 0.0581578874386), (0.0561090453609, 0.0556916704708, 0.996870208637)
Vector: -1.03398972801, 10.3633177375, 1.24004614781)

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Components

#1: RNA chain RNA (57-MER)


Mass: 18349.811 Da / Num. of mol.: 2 / Mutation: A2G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 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: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→66.76 Å / Num. obs: 16486 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 61.47 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1215 / CC1/2: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→28.67 Å / SU ML: 0.4185 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 37.01
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2922 789 4.81 %
Rwork0.2769 15614 -
obs0.2775 16403 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2320 12 24 2356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522587
X-RAY DIFFRACTIONf_angle_d1.14934029
X-RAY DIFFRACTIONf_chiral_restr0.0453544
X-RAY DIFFRACTIONf_plane_restr0.0066108
X-RAY DIFFRACTIONf_dihedral_angle_d14.31621298
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.55368713387 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.43241340.40992560X-RAY DIFFRACTION99.19
2.55-2.750.40951440.3952572X-RAY DIFFRACTION99.78
2.75-3.020.34761220.31672569X-RAY DIFFRACTION98.86
3.02-3.460.28341340.25112564X-RAY DIFFRACTION99.37
3.46-4.350.24631270.23542622X-RAY DIFFRACTION99.42
4.36-28.670.28021280.27422727X-RAY DIFFRACTION99.2
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)
11.0911161549-0.814734567754-0.2193829861931.492391665040.5803159164860.239486017953-0.04829684849810.01944580700540.1983859331190.18944529633-0.1795272425810.08756425212180.0990747908006-0.5799120219780.215748230410.7867483207770.557840819110.06938491270771.55371819890.02917411269120.789263779034-24.21675147627.03402761847-28.2870940431
20.1276422619790.1957877515130.7514573989472.251465864520.3651465085134.742123145990.816306422451-0.7385823067150.6618321186581.55573412086-0.5724461122221.44886253025-0.282355146806-1.92381210425-0.1865814626871.854863788510.4729958171780.3872073269222.55957487138-0.4891011449931.09643111087-28.393484145418.0652597786-10.3746628093
31.28618559698-1.234518242620.1638117938541.29634330212-0.001776654040350.4841717908440.0550239154734-0.0150326208075-0.231755007987-0.0263190807032-0.0795164655470.2894001559720.0812624822486-0.01098484599730.007076098575870.5016650900090.683967802792-0.002122921302181.371501956580.08061868195950.67470868309-19.500356135615.1760152377-33.4655147557
44.71994575329-1.142628635480.5041507234142.3127786610.4662420685120.215384043051-0.291318451639-1.029980033090.03227076515440.7147954671940.7608198803840.0191873418793-0.449426067898-0.339841612064-0.4389849069080.8738097638920.369719535195-0.1230425098521.03104481640.02952464855140.6808568288722.15111848712.43052466539-27.5335903869
50.1314705557250.2397259427320.3552487850520.4419654040630.6453767097490.9373825004170.358285783348-0.862448373891-0.3262971585130.913499345486-0.326443821533-0.8328132940390.3311412513520.119087550879-0.06184309123281.638402995410.521121277648-0.5109073322982.184558542590.4679497766460.99341614452723.331156179-8.26463208962-12.5008398847
62.93488977999-1.57621410764-0.7672390866062.216080211120.4597383052073.55613677996-0.175633894561-0.767321901787-0.003228960077070.6438403083060.5884832218340.653239400454-0.006212723079320.630977482372-0.3448626295960.5822149133580.1833868791380.02064568171870.479164904350.03570318384770.82414823016917.0724872478-5.53616121497-32.7848689476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )AA1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 35 )AA21 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 57 )AA36 - 57
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 20 )BB1 - 20
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 35 )BB21 - 35
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 57 )BB36 - 57

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