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- PDB-9imb: The crystal structure of human m5C methyltransferase NSUN6 bound ... -

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Basic information

Entry
Database: PDB / ID: 9imb
TitleThe crystal structure of human m5C methyltransferase NSUN6 bound to its S-adenosyl-L-methionine analog and a NECTIN-2 3'-UTR RNA substrate
Components
  • RNA (5'-R(*GP*CP*CP*CP*UP*CP*UP*UP*CP*AP*UP*CP*UP*CP*CP*AP*AP*AP*GP*AP*GP*GP*GP*C)-3')
  • tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
KeywordsRNA BINDING PROTEIN/RNA / m5C methyltransferase / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / RNA methylation / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / cytoplasm / cytosol
Similarity search - Function
Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / : / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / PUA domain superfamily / PUA domain profile. / PUA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / RNA / RNA (> 10) / tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLv, M.Q. / Zhong, F.M. / Pu, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32293213,32100958,32090040 China
CitationJournal: Structure / Year: 2025
Title: NSUN6 inhibitor discovery guided by its mRNA substrate bound crystal structure.
Authors: Zhong, F. / Pu, T. / Hu, Q. / Li, M. / Wang, L. / Wang, S. / Ruan, K. / Shi, Y. / Sun, B. / Jiang, Y. / Lv, M.
History
DepositionJul 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
D: RNA (5'-R(*GP*CP*CP*CP*UP*CP*UP*UP*CP*AP*UP*CP*UP*CP*CP*AP*AP*AP*GP*AP*GP*GP*GP*C)-3')
A: tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
C: RNA (5'-R(*GP*CP*CP*CP*UP*CP*UP*UP*CP*AP*UP*CP*UP*CP*CP*AP*AP*AP*GP*AP*GP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6406
Polymers118,8774
Non-polymers7632
Water1267
1
B: tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
D: RNA (5'-R(*GP*CP*CP*CP*UP*CP*UP*UP*CP*AP*UP*CP*UP*CP*CP*AP*AP*AP*GP*AP*GP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8203
Polymers59,4392
Non-polymers3811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-20 kcal/mol
Surface area21250 Å2
MethodPISA
2
A: tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
C: RNA (5'-R(*GP*CP*CP*CP*UP*CP*UP*UP*CP*AP*UP*CP*UP*CP*CP*AP*AP*AP*GP*AP*GP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8203
Polymers59,4392
Non-polymers3811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-17 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.814, 72.441, 77.150
Angle α, β, γ (deg.)62.48, 83.38, 69.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 / m5C methyltransferase NSUN6 / NOL1/NOP2/Sun and PUA domain-containing protein 1 / NOL1/NOP2/Sun ...m5C methyltransferase NSUN6 / NOL1/NOP2/Sun and PUA domain-containing protein 1 / NOL1/NOP2/Sun domain family member 6


Mass: 51834.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSUN6, NOPD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TEA1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (5'-R(*GP*CP*CP*CP*UP*CP*UP*UP*CP*AP*UP*CP*UP*CP*CP*AP*AP*AP*GP*AP*GP*GP*GP*C)-3')


Mass: 7604.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 1% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium (pH 7.0)

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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 PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.9→43.003 Å / Num. obs: 24167 / % possible obs: 98.22 % / Redundancy: 3.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.124 / Net I/σ(I): 5.7
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2643 / CC1/2: 0.839 / % possible all: 97.74

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WWQ

5wwq


Resolution: 2.9→43 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1258 5.21 %
Rwork0.2068 --
obs0.2101 24167 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 1007 54 7 7873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038119
X-RAY DIFFRACTIONf_angle_d0.59611252
X-RAY DIFFRACTIONf_dihedral_angle_d17.3983093
X-RAY DIFFRACTIONf_chiral_restr0.0421355
X-RAY DIFFRACTIONf_plane_restr0.0041279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.020.33911340.27492509X-RAY DIFFRACTION98
3.02-3.150.35051420.26912544X-RAY DIFFRACTION98
3.15-3.320.29971590.25772527X-RAY DIFFRACTION98
3.32-3.530.31821290.23842548X-RAY DIFFRACTION98
3.53-3.80.29641290.21282551X-RAY DIFFRACTION98
3.8-4.180.26571180.19052565X-RAY DIFFRACTION98
4.18-4.790.21491420.16982575X-RAY DIFFRACTION99
4.79-6.030.22451400.1912557X-RAY DIFFRACTION99
6.03-430.21511650.17312533X-RAY DIFFRACTION98
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)
11.2331-0.03760.04432.1056-0.9012.19960.1432-0.4163-0.03550.41410.20750.59570.1768-0.4986-0.31170.2914-0.06540.06850.42140.10560.39672.0773-18.524-20.9607
22.4058-0.0140.2334.0979-0.04272.430.0336-0.1759-0.8085-0.05570.34080.14250.9868-0.3501-0.27710.509-0.1044-0.0490.34460.14110.48544.9896-39.3294-20.2989
30.9377-0.04680.3122.0932-0.81032.6622-0.0261-0.0006-0.3962-0.63180.18550.69721.1788-0.5246-0.13840.6338-0.1623-0.15150.3860.10570.64661.0486-37.4925-26.9251
42.2927-0.78760.71033.1041-0.78742.39990.06190.1103-0.1323-0.42560.0141-0.37660.37620.2678-0.0820.18380.03960.07870.1568-0.01340.249123.2417-14.1326-34.7751
52.38610.32521.26531.9948-0.46132.2548-0.0743-0.4924-0.21330.4138-0.0883-0.15880.09010.07020.11190.2360.07760.00890.25620.02190.220523.1648-12.3698-17.3653
62.44340.65560.28962.8568-0.31142.09390.0597-0.42620.43790.315-0.08870.635-0.1443-0.34780.03520.25140.11680.060.3953-0.02540.26728.9374-5.354-18.8806
74.6203-1.32564.05291.5318-0.08074.4790.73660.38460.093-0.0896-0.61760.23330.08290.8869-0.16570.84890.0049-0.19180.49120.12930.631721.1562-38.2953-10.2101
82.9682-0.6081-0.63053.71160.78494.24170.0621-0.80020.08331.64680.8089-0.83060.02591.1692-0.39530.89920.2509-0.14120.44420.08210.58511.6703-25.9599-26.7935
97.5351-4.34128.96983.1694-5.47942.06020.78440.77290.02060.8561-1.2696-0.67761.61950.92850.28110.93590.169-0.33280.60190.01090.896720.9937-39.6486-19.4969
104.5204-0.43612.73892.4385-3.05756.89930.7792-0.40980.0812-0.4214-0.42250.24020.8915-0.1833-0.06941.016-0.1296-0.30930.34970.01660.780923.7119-47.7684-2.2507
111.86240.771-0.28133.8268-0.06842.11780.0610.11430.1485-0.34060.03991.2217-0.3037-0.8897-0.14860.4670.0001-0.12610.45730.09781.080924.2949-14.823715.9474
120.9969-1.0021-0.11464.214-1.04860.4892-0.2007-0.29670.32760.78180.32790.0163-0.4605-0.2968-0.10580.44870.08340.03450.2803-0.00780.277250.7937-17.376630.4831
131.9523-0.8442-0.54825.3255-0.21551.8252-0.00190.04140.8942-0.36410.1491-0.2814-0.4184-0.0132-0.18110.41060.0257-0.01840.22380.02340.518450.81941.25916.5345
141.2542-0.74490.44553.1772-0.86891.3543-0.00280.2670.225-0.44310.0234-0.14750.0479-0.03850.01890.2813-0.01670.03510.17930.04630.227351.7349-29.406316.7557
152.39640.01291.70142.3298-0.6832.482-0.08890.5950.9861-1.633-0.416-0.73660.27030.51070.06340.7497-0.04470.21220.4320.0623-0.153255.3751-30.38463.6325
161.61650.82380.38122.4099-0.11591.732-0.04830.34790.2794-1.11810.25280.60850.1655-0.2026-0.14670.5766-0.0941-0.26040.34960.17130.40840.0695-30.12985.397
171.27920.02630.01683.73550.09921.853-0.0484-0.09220.1564-0.04080.07811.24530.1572-0.4069-0.07440.29660.0102-0.06460.35870.12360.629633.1667-29.938219.7361
183.389-2.07362.4166.4451-1.54492.048-0.619-0.24410.3822-0.1901-0.5342-0.7153-0.82270.79131.06880.7445-0.0771-0.1650.43540.11230.637.37225.7305-1.7006
191.9093-2.25791.84752.6895-2.54953.93880.17010.2744-0.5224-0.6647-0.30060.15751.6183-0.0003-0.09611.44840.1278-0.16040.44970.18470.735843.4305-11.9499-3.0692
202.85650.1616-1.82814.3486-5.71578.49990.09211.1842-0.501-1.15370.6146-0.5110.6255-1.3704-0.39120.61950.18210.01360.47470.04250.440949.2646-15.503314.8557
215.1904-2.97265.92791.6529-3.16468.12980.32720.75441.0237-1.27370.15090.29031.32280.3618-0.55910.7681-0.029-0.14880.62240.15850.555149.3782-5.2986-0.0627
222.9069-2.8652.2712.9797-2.25127.262-1.04220.15270.91420.2593-0.0974-0.1588-0.19780.49370.87840.6447-0.1235-0.32950.36140.13390.925937.89216.0271-10.2807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 112 )
2X-RAY DIFFRACTION2chain 'B' and (resid 113 through 168 )
3X-RAY DIFFRACTION3chain 'B' and (resid 169 through 209 )
4X-RAY DIFFRACTION4chain 'B' and (resid 210 through 317 )
5X-RAY DIFFRACTION5chain 'B' and (resid 318 through 390 )
6X-RAY DIFFRACTION6chain 'B' and (resid 391 through 469 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 10 )
8X-RAY DIFFRACTION8chain 'D' and (resid 11 through 15 )
9X-RAY DIFFRACTION9chain 'D' and (resid 16 through 20 )
10X-RAY DIFFRACTION10chain 'D' and (resid 21 through 24 )
11X-RAY DIFFRACTION11chain 'A' and (resid 2 through 45 )
12X-RAY DIFFRACTION12chain 'A' and (resid 46 through 112 )
13X-RAY DIFFRACTION13chain 'A' and (resid 113 through 201 )
14X-RAY DIFFRACTION14chain 'A' and (resid 202 through 268 )
15X-RAY DIFFRACTION15chain 'A' and (resid 269 through 301 )
16X-RAY DIFFRACTION16chain 'A' and (resid 302 through 372 )
17X-RAY DIFFRACTION17chain 'A' and (resid 373 through 469 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 5 )
19X-RAY DIFFRACTION19chain 'C' and (resid 6 through 10 )
20X-RAY DIFFRACTION20chain 'C' and (resid 11 through 15 )
21X-RAY DIFFRACTION21chain 'C' and (resid 16 through 20 )
22X-RAY DIFFRACTION22chain 'C' and (resid 21 through 24 )

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