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- PDB-8k1e: Crystal structure of a human menRNA -

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Basic information

Entry
Database: PDB / ID: 8k1e
TitleCrystal structure of a human menRNA
ComponentsRNA (58-MER)
KeywordsRNA / MascRNA / tRNA-like / MALAT1
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 11, 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 (58-MER)
B: RNA (58-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,02818
Polymers37,5742
Non-polymers45416
Water1,47782
1
A: RNA (58-MER)
hetero molecules

B: RNA (58-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,02818
Polymers37,5742
Non-polymers45416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556x+1/2,y+1/2,z+11
Buried area710 Å2
ΔGint-27 kcal/mol
Surface area18850 Å2
MethodPISA
2
A: RNA (58-MER)
hetero molecules

A: RNA (58-MER)
hetero molecules

B: RNA (58-MER)
hetero molecules

B: RNA (58-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,05636
Polymers75,1494
Non-polymers90732
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_556x+1/2,y+1/2,z+11
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area2900 Å2
ΔGint-92 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.589, 29.193, 99.144
Angle α, β, γ (deg.)90.000, 126.748, 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 24 or resid 28 through 58))
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: U / End label comp-ID: U / Auth seq-ID: 1 - 6 / Label seq-ID: 1 - 6

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.984298029865, -0.0834249107225, -0.155556011378), (-0.0833851126527, -0.996494246123, 0.00679267490115), (-0.155577348585, 0.00628503900984, -0.987803718808)Vector: 1. ...NCS oper: (Code: given
Matrix: (0.984298029865, -0.0834249107225, -0.155556011378), (-0.0833851126527, -0.996494246123, 0.00679267490115), (-0.155577348585, 0.00628503900984, -0.987803718808)
Vector: 1.60369151293, -19.7481210298, 45.8146286233)

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Components

#1: RNA chain RNA (58-MER)


Mass: 18787.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 28% 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: Jan 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→79.44 Å / Num. obs: 15793 / % possible obs: 99.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 44.14 Å2 / CC1/2: 0.904 / Net I/σ(I): 9.7
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1034 / CC1/2: 0.371 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→36.25 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 786 4.99 %
Rwork0.2365 14966 -
obs0.238 15752 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.49 Å2
Refinement stepCycle: LAST / Resolution: 2.23→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2385 16 82 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242660
X-RAY DIFFRACTIONf_angle_d0.59094142
X-RAY DIFFRACTIONf_chiral_restr0.0289555
X-RAY DIFFRACTIONf_plane_restr0.0046111
X-RAY DIFFRACTIONf_dihedral_angle_d9.73091317
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.38884466801 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.370.3521250.31092327X-RAY DIFFRACTION94.49
2.37-2.550.34571470.30792472X-RAY DIFFRACTION99.92
2.55-2.810.32511140.32932521X-RAY DIFFRACTION100
2.81-3.220.291420.24412504X-RAY DIFFRACTION99.89
3.22-4.050.22731290.19352515X-RAY DIFFRACTION99.55
4.05-36.250.23321290.21642627X-RAY DIFFRACTION99.46
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)
12.052071185361.07200027243-0.1792096633010.8009197227370.261997845111.701244728290.293476123859-0.627941746412-0.3199821290740.122723836999-0.273944449228-0.338654834462-0.1220883017630.0377245099442-0.02436230689850.232185199217-0.056388781326-0.04991041179210.3896995795340.0150238853940.41450977736123.3402672043-4.0618197060845.635360652
22.56842412538-0.461424070024-0.6726547428390.09755862989260.0337789585320.44202391530.195026420739-0.1202909358140.1253758192210.0369126489489-0.4424760558060.3761443643820.488179344085-0.6274078264210.2370238142720.344330019478-0.1029293117850.1006418191450.555254710479-0.09304663062050.65326200492348.79542752078.2649349110448.9682211165
32.14110988157-0.3896525324330.3467143764610.3572656726030.4583150208140.9061846683360.0317405337792-1.18487980014-0.001741110577630.06191433854220.106482419717-0.206321829850.09710404626090.06833393432040.00930211663110.316722016223-0.08061375534730.06121130642340.590879570093-0.06789874918280.49385067015935.26513858724.8214351451749.1785780021
42.542081329260.4064543022110.813442514981.410090578920.02827660007361.354525587640.197267740409-0.369852447260.1872452260020.0991272991407-0.205944401919-0.06244268162350.060903701869-0.2079305759730.02984354881140.189542656032-0.03359727633850.03504467584330.294436524174-0.04146979899450.28994067262315.21142841411.6223483954640.9407343951
51.8307345022-0.844259857811-1.026242877180.7536003305352.00298313023.361763965120.245808920020.2959822060930.462839128206-0.2473172594730.0992840275847-0.416499327145-0.483567059743-0.363205189284-0.3109590116360.7580594173120.002883991692450.04931536090290.4524620774850.005152049927050.41205022963913.1047665624-15.921808688-0.964537590848
60.844660397562-1.103586231330.5285410663853.028104628750.2448281877590.793994732044-0.659861253521-0.616420392306-0.4706421985860.8107389237431.01904275009-0.8203442142231.268865059181.92199758957-0.1841750831011.169589697010.448603375669-0.02750689528151.9640926605-0.08681961216991.0982378861432.092018389-26.907030685-9.99743843465
71.36735402385-0.179769401732-1.077494776740.5612037088730.480455795981.28399082374-0.01467898571940.250983225909-0.1133489868570.001096287599910.0519401744265-0.3022270268390.0399207372416-0.289791754815-0.01671586939390.8284816135770.00555525549437-0.0337800746390.359179647901-0.03508905082670.41098265640810.7929169021-22.8082155223.1655132872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )AA1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 26 )AA22 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 36 )AA27 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 58 )AA37 - 58
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 16 )BB1 - 16
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 34 )BB17 - 34
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 58 )BB35 - 58

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