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- PDB-8k30: Crystal structure of a medaka mascRNA U23G -

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Basic information

Entry
Database: PDB / ID: 8k30
TitleCrystal structure of a medaka mascRNA U23G
ComponentsRNA (56-MER)
KeywordsRNA / MascRNA / tRNA-like / MALAT1
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciesOryzias latipes (Japanese medaka)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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: To Be Published
Title: Crystal structure of mascRNA and menRNA
Authors: He, Y. / Deng, J. / Lin, X. / Huang, L.
History
DepositionJul 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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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)36,43715
Polymers36,0092
Non-polymers42813
Water19811
1
A: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,27610
Polymers18,0051
Non-polymers2729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-30 kcal/mol
Surface area8880 Å2
MethodPISA
2
B: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1615
Polymers18,0051
Non-polymers1574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-41 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.940, 29.147, 99.179
Angle α, β, γ (deg.)90.000, 118.002, 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_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 - 3 / Label seq-ID: 1 - 3

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999741795881, 0.0210335301749, -0.00859838221335), (-0.0211431755227, -0.999693665263, 0.0128663033307), (-0.00832512445085, 0.0130447783025, 0.999880255862)Vector: ...NCS oper: (Code: given
Matrix: (-0.999741795881, 0.0210335301749, -0.00859838221335), (-0.0211431755227, -0.999693665263, 0.0128663033307), (-0.00832512445085, 0.0130447783025, 0.999880255862)
Vector: 66.0174055476, 57.0835659588, 0.98212493983)

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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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 56.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6
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: Jan 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.43→37.02 Å / Num. obs: 15588 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 57.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.5
Reflection shellResolution: 2.43→2.49 Å / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1097 / CC1/2: 0.817 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→34.86 Å / SU ML: 0.3975 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.5877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2838 798 5.18 %
Rwork0.2638 14608 -
obs0.2648 15406 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.98 Å2
Refinement stepCycle: LAST / Resolution: 2.43→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2204 13 11 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542457
X-RAY DIFFRACTIONf_angle_d1.07083822
X-RAY DIFFRACTIONf_chiral_restr0.0494515
X-RAY DIFFRACTIONf_plane_restr0.0078103
X-RAY DIFFRACTIONf_dihedral_angle_d14.07681221
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.757096990727 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.580.4591340.42512367X-RAY DIFFRACTION98.58
2.58-2.780.39441500.37472396X-RAY DIFFRACTION99.49
2.78-3.060.35361260.28392414X-RAY DIFFRACTION98.64
3.06-3.50.26851360.23382364X-RAY DIFFRACTION96.71
3.5-4.410.2251190.21542482X-RAY DIFFRACTION99.05
4.41-34.860.2681330.26662585X-RAY DIFFRACTION99.34
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)
15.38478379041-0.9922687735050.3389731873523.45653420264-1.344585943691.818647974550.5901885650330.262497413959-1.250834484730.18953941422-0.2662403086140.6951224295860.560475228023-0.162769742927-0.1209025055990.61206335690.0388861289373-0.01595175021360.53619596851-0.07654964286440.47134901923849.157118241424.845161635155.4189251323
20.0788562209205-0.258806726021-0.1703023104332.893330443441.157642332020.4883533476190.5051694019291.12300967021-0.0924267127488-0.0750550070733-0.2702499444990.121492357015-1.409261358910.5376457127730.2359905334091.17864434862-0.0479761304573-0.3610957161150.9379024939290.04819597944470.79061240557867.337161947717.776541095958.0615012432
33.61778192903-1.398325055620.6112438489160.9127523920630.6806313565974.07978645725-0.144082756898-1.3752596877-0.6803642230991.68642195034-0.502995227199-0.920412363459-0.289986020902-0.123729113283-0.8567804803231.57905528763-0.168128312858-0.5431035503030.9498814657660.2918708982440.81960512835258.135459686113.22332047471.0889956149
43.16228781055-0.885225327130.9138748753140.866546514426-1.149762567662.79223236345-0.381363732105-0.3272653874970.5164862025510.67988349388-0.306803741364-0.3962023946210.0182368334270.2187593384530.6006371183950.7111137485150.162448814081-0.1603379748970.961804273889-0.1160320900360.55940570221361.24052684799.7356445631652.5827991285
50.331274945413-0.6954699045270.376713797012.66180232586-0.2253719333040.426198743197-0.1551334985920.1209795989240.1297792639510.579342461322-0.08907912362370.547537748795-0.090699638888-0.1099922624440.2601687492960.6198524571210.0480836323360.04016230707410.5453376140260.02733093908350.4178206723943.037214322423.202515305654.3414195348
60.9609305795250.475654047867-0.2042067425720.539581086079-0.0823817704402-0.04583714529110.2357380062351.32090593264-0.478777458229-0.352825475221-0.4017066411180.7288362263320.08786814378260.07248989519030.1810228103610.6397092535210.154812455007-0.001187223257410.991376525884-0.2990231721860.72244629120723.93784494131.316406252349.6497044472
72.03195530241-1.064922356530.4715805311420.5937472249-0.6455686310040.9462847174620.7672689613090.689166930536-0.987032097991-0.91843476628-0.2076812848520.6487667687330.806887658778-0.175730779965-0.2957280518750.831946155823-0.06413249883680.2752828127090.580040273758-0.06351373275390.8616025725863.7345774509836.052136344462.1024417389
80.525107402162-0.2743886558380.1999524093850.241684933182-0.06380542184270.451121697706-0.22630067796-1.28468395493-0.4713020971781.65189000106-0.5072011271291.339111612720.237211138479-0.4944644572480.2022490659481.74421302276-0.07679895278980.5774272387421.29457640808-0.08717655201741.01846480288.1608994528444.095747457271.9213595145
92.244975557170.602058928319-0.1052665463052.129324446580.3538835453171.37793404167-0.1274300237050.675800199607-0.7914839580920.1448958095760.194956974258-0.081252271766-0.0513679173076-0.320822815514-0.07482280482020.5952816649920.0774747392387-0.004532721250790.652634318733-0.09380452875730.54207899955114.014505760739.945794585554.2101976884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 15 )AA11 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 36 )AA16 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 46 )AA37 - 46
5X-RAY DIFFRACTION5chain 'A' and (resid 47 through 56 )AA47 - 56
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 5 )BB1 - 5
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 16 )BB6 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 36 )BB17 - 36
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 56 )BB37 - 56

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