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- PDB-6h1d: Crystal structure of C21orf127-TRMT112 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6h1d
TitleCrystal structure of C21orf127-TRMT112 in complex with SAH
Components
  • HemK methyltransferase family member 2
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsGENE REGULATION / protein methyltransferase / histone methylation / complex / SAH
Function / homology
Function and homology information


arsonoacetate metabolic process / methylarsonite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity ...arsonoacetate metabolic process / methylarsonite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding / rRNA modification in the nucleus and cytosol / S-adenosylmethionine-dependent methyltransferase activity / rRNA methylation / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / positive regulation of cell growth / nucleic acid binding / protein heterodimerization activity / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Eukaryotic/archaeal PrmC-related / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Multifunctional methyltransferase subunit TRM112-like protein / Methyltransferase N6AMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsWang, S. / Hermann, B. / Metzger, E. / Peng, L. / Einsle, O. / Schuele, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research CouncilERC AdGrant 322844 Germany
German Research FoundationSFB 992, 850, 746, Schu688/15-1 Germany
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.
Authors: Metzger, E. / Wang, S. / Urban, S. / Willmann, D. / Schmidt, A. / Offermann, A. / Allen, A. / Sum, M. / Obier, N. / Cottard, F. / Ulferts, S. / Preca, B.T. / Hermann, B. / Maurer, J. / ...Authors: Metzger, E. / Wang, S. / Urban, S. / Willmann, D. / Schmidt, A. / Offermann, A. / Allen, A. / Sum, M. / Obier, N. / Cottard, F. / Ulferts, S. / Preca, B.T. / Hermann, B. / Maurer, J. / Greschik, H. / Hornung, V. / Einsle, O. / Perner, S. / Imhof, A. / Jung, M. / Schule, R.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HemK methyltransferase family member 2
B: Multifunctional methyltransferase subunit TRM112-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0013
Polymers36,6172
Non-polymers3841
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-13 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.841, 71.841, 131.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11B-202-

HOH

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Components

#1: Protein HemK methyltransferase family member 2 / M.HsaHemK2P / N(6)-adenine-specific DNA methyltransferase 1


Mass: 22344.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, PRED28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog


Mass: 14272.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 1.1-1.3 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.281 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281 Å / Relative weight: 1
ReflectionResolution: 1.94→65.58 Å / Num. obs: 26240 / % possible obs: 99.98 % / Redundancy: 24.8 % / Biso Wilson estimate: 23.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.036 / Net I/σ(I): 16.42
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 24.2 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 3.49 / CC1/2: 0.643 / Rpim(I) all: 0.186 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q87, 4QTT

3q87

4qtt


Resolution: 1.94→65.56 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 20.0858
RfactorNum. reflection% reflection
Rfree0.2374 1282 4.9 %
Rwork0.1868 --
obs0.1891 26185 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.2 Å2
Refinement stepCycle: LAST / Resolution: 1.94→65.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 26 48 2555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072589
X-RAY DIFFRACTIONf_angle_d0.91453523
X-RAY DIFFRACTIONf_chiral_restr0.0559405
X-RAY DIFFRACTIONf_plane_restr0.0063456
X-RAY DIFFRACTIONf_dihedral_angle_d4.86242167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.020.27171240.2622710X-RAY DIFFRACTION100
2.02-2.110.3031620.23082682X-RAY DIFFRACTION100
2.11-2.220.21761330.20562709X-RAY DIFFRACTION100
2.22-2.360.27091330.1982748X-RAY DIFFRACTION100
2.36-2.540.26641400.1932740X-RAY DIFFRACTION100
2.54-2.80.25051470.20022741X-RAY DIFFRACTION100
2.8-3.20.25381440.20322773X-RAY DIFFRACTION100
3.2-4.040.22041450.16912822X-RAY DIFFRACTION100
4.04-65.590.20221540.15412978X-RAY DIFFRACTION99.94
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)
10.0108057862105-0.01068769515240.03269591811650.457343435383-0.06283952542790.255348657824-0.1499296365260.298451919539-0.156829971468-0.070222110896-0.0900468099264-0.5444006441750.03775970113440.488491148069-0.004296342051690.1731809928270.0248607223316-0.002936652842140.4341596277570.006019242782020.257173998168-3.2821336645-10.1804706456-21.2913900334
20.2449203504760.177626626007-0.06027787594160.149645132247-0.08598730193690.1328272206440.08531337168060.239771373297-0.083453287261-0.382230946187-0.0272001740205-0.1475256109870.0307515758790.3088263515530.04773433213070.253929399694-0.02103112031560.0261254990930.41831861124-0.0478094970922-0.0324286775083-16.9335348347-7.61740728913-32.4190035352
30.1012677350630.06408570316970.06551751280450.1105785778380.005643025492840.06141226672990.0004266076413420.1468834310360.0180698757081-0.0671243601911-0.074955761711-0.03270499638710.01040080139260.0696343412465-0.0003225451012660.089109553849-0.00654048582280.0002046789792710.1259897250940.01444470452410.0646393833431-17.9058648949-3.16575011412-20.6984899193
40.05994453051110.1578292090790.1031847252180.496118274060.3829099801670.359275847719-0.0242833596515-0.03060595138520.1851817803320.1157028349290.152963869044-0.5614235760040.1032069289830.3362531329540.05972121992620.125011702249-0.04602025662030.004095591849510.227657292234-0.01999876710770.233132296072-7.00662291702-4.96424495536-14.7099995515
50.0947733449305-0.06566747083550.04656669659180.05897106486520.02853573569890.1954100013480.0657241258490.09487492175290.2078902561980.065575983630.1154892646670.0181548224269-0.0740879018626-0.0607137609720.0006437959433040.15987192294-0.03560098278120.02895224034150.1351335326740.01090387029490.159943722084-16.2457252819-5.4777464426-13.6255189706
60.2655684806440.297959618267-0.1910212770630.517395998384-0.3847882910280.8848960990780.1870972612960.128209377668-0.12143330714-0.234848967048-0.09153643582620.1893863243470.0610548401667-0.1131088160240.8308598598330.138014041575-0.0210756494474-0.03708968852250.128540251232-0.02449071534050.125037826-24.127334067-12.3412118029-18.3885457346
70.0299651769958-0.0715236145417-0.02790288532310.198001857739-0.00429506353150.0934214193266-0.03885618151510.0848186180153-0.115436881432-0.0560747565780.01702131968080.1294825227780.2574233951680.0756667531414-0.0004071114015920.2655720938430.0202579840218-0.006993365596690.217388359185-0.0581974376650.180943356805-15.0809545579-26.132992187-17.7869958981
80.457252766520.1816758003690.1967190500220.132180021387-0.05967172188220.3555852541150.1013096553580.160301436187-0.041631546429-0.0397472480598-0.04199534224340.1609116470410.0937886345397-0.1437792026870.002972177599550.186825945317-0.0171204533022-0.0321229940660.17762951121-0.03135709338320.202481833994-26.7372490889-16.0284428384-23.3562633018
90.07765607639740.088661412695-0.1373544482810.102635795381-0.156740778270.2403806555820.0938935997403-0.0918312874133-0.296363646652-0.255656017103-0.2038887161890.3252317343590.448876766168-0.188595458365-0.02532275921320.285960120045-0.0475356528749-0.08546036816650.302072328065-0.05039550656660.242048347061-32.8290855111-20.9298542768-28.9153170315
100.408111936323-0.3125141686230.2804112047470.475584457792-0.05709920455740.2977115258020.04812078120.103023842675-0.0572252412842-0.3809563289490.0292497379880.118316646669-0.02859693126070.03508409235260.3510588110.3232306224070.0429564028426-0.03209597447220.298050560642-0.1557707785460.0923116479241-23.9244146564-15.3237743908-34.981943611
110.3506826757310.414294799242-0.03944210570470.492917124892-0.06360618068180.1240135251880.09065155579290.1049805117920.025542732808-0.284639945045-0.01948441444320.1402244324780.270742047907-0.1775959237230.1017819330780.3006894350170.055595872513-0.01769268270850.284756934725-0.08316589159490.133997217759-22.084800591-16.8854755982-31.8152056604
120.015531853645-0.00294054314728-0.008803835968030.0341265858222-0.01369832235810.009644812608810.02936670488520.1485155437260.150351375921-0.01803063663360.000427875154612-0.05769599837660.09393285961430.0690138736405-0.0001749868521370.1474300914430.0161028014058-0.01261251436470.161116734999-0.01710445184060.216112210292-21.72629268631.7817801367-6.14337054564
130.007029102421830.008145313593530.0350972759060.008438060144330.04478268023710.2385298285460.127358711925-0.0835416898599-0.377393443937-0.0184950170415-0.08153189708060.2990120787980.143892960795-0.2562140737140.003535609391590.155085141949-0.057312816293-0.03511392393060.2130191576930.02887811430510.277656626039-28.8737955034-9.3975344684-0.545470709262
140.03849565058640.03224996497510.04895807568560.05817563950150.0230290819390.0626403836242-0.215460709642-0.0549144737587-0.08384961139140.06623590642070.0683579368553-0.3331190292360.02316712806730.08864565599891.52016284863E-50.1149038110110.0132074417701-0.01326498882130.123792991377-0.00292227899830.166572965032-13.61570059862.643514632992.89171354344
150.005519328316720.01115383479840.01080570585760.01920451809210.02040630177950.02021250702340.05166362423530.205851733175-0.04628570101740.008183936969950.161305287502-0.17787629854-0.07222540842780.362051314441-0.0001758290077660.1773565299040.003226310570650.0001294621590490.2869807648410.06428236422340.253913348525-13.689664279112.4979264916-14.0057155661
160.0494126831272-0.02331649146390.01084786725790.0123336970594-0.008240200767280.003657777348550.007698772767520.2338609180530.083749280373-0.0798199973337-0.0368287671346-0.02853052291340.0983497090391-0.2602713811264.96166609102E-60.212957802402-0.00477988513577-0.01235241902950.2197279376210.02814155076210.216879451275-26.20050817339.75590916997-15.8551839226
170.0762111289316-0.00735142866157-0.006574636558120.0900705918390.005117549824340.130841792544-0.148934106907-0.2182445770480.2186556992680.131620509465-0.02907162228250.259948328087-0.00602871018471-0.225265051571-0.004405106550650.1335529884120.01578109573-0.01130746941020.175219971233-0.0156887062340.179388620839-26.90895177676.801264491450.342933563915
180.945499588350.417151163332-0.6861408674620.9027173724870.03158778917270.6517274858260.1469108998440.113478694930.228651446518-0.07073793427490.03289020582430.09344918552960.04142464482930.08019644527020.305965868480.1370214426870.0212527678386-0.05920614006330.164715943726-0.03188755169940.24379495861-25.331388694115.1037301685-0.867834962803
190.191305457105-0.116791502327-0.1755087457750.08520855687360.1452589663470.293804049149-0.1382278481870.17066042390.186371450648-0.1537894490340.1617787013460.144128167077-0.05742663991850.0626049593690.08433941306540.113031162995-0.0170748001802-0.07227495592320.1204503058180.0471434719350.238051201816-23.156550897316.4978862824-10.639685567
201.151664038240.265177100479-1.101658303280.0854186990218-0.2580330396121.14298362591-0.211077669868-0.0039251372498-0.0782201976727-0.04082381685220.0667282485094-0.04887053405610.0746213997879-0.0588055069151-0.1625808338320.1087111907450.0053736266201-0.04268845361040.1354523484090.01395183816730.142224601568-14.79266809320.519648060072-0.432501050408
210.521662483639-0.1423792595230.1368899907120.218356044127-0.2088671308350.2159458473020.1273693194760.0604843387969-0.07259859508590.01122136574090.1242760996580.0663857994589-0.0768394790928-0.2471406756730.4035577677350.0977779842937-0.0005506650979650.02399369650040.1720895560750.02558545998210.195973769431-22.8290996594-9.492634830094.18198470923
220.0181389054946-0.0121718144821-0.01048642242650.02965962472190.0233843715380.01557466190410.178853748714-0.13338352918-0.132903669471-0.0892224173675-0.128141491763-0.04269938428110.110012685952-0.01297598247837.68581629903E-50.16781935316-0.0219841109457-0.006259609526020.1584629024310.001838541185130.195874722719-14.3484583275-9.08054335583-3.92125417729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 129 )
7X-RAY DIFFRACTION7chain 'A' and (resid 130 through 149 )
8X-RAY DIFFRACTION8chain 'A' and (resid 150 through 178 )
9X-RAY DIFFRACTION9chain 'A' and (resid 179 through 189 )
10X-RAY DIFFRACTION10chain 'A' and (resid 190 through 201 )
11X-RAY DIFFRACTION11chain 'A' and (resid 202 through 213 )
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 9 )
13X-RAY DIFFRACTION13chain 'B' and (resid 10 through 24 )
14X-RAY DIFFRACTION14chain 'B' and (resid 25 through 33 )
15X-RAY DIFFRACTION15chain 'B' and (resid 34 through 39 )
16X-RAY DIFFRACTION16chain 'B' and (resid 40 through 49 )
17X-RAY DIFFRACTION17chain 'B' and (resid 50 through 61 )
18X-RAY DIFFRACTION18chain 'B' and (resid 62 through 74 )
19X-RAY DIFFRACTION19chain 'B' and (resid 75 through 90 )
20X-RAY DIFFRACTION20chain 'B' and (resid 91 through 100 )
21X-RAY DIFFRACTION21chain 'B' and (resid 101 through 110 )
22X-RAY DIFFRACTION22chain 'B' and (resid 111 through 119 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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