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- PDB-4fzv: Crystal structure of the human MTERF4:NSUN4:SAM ternary complex -

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Basic information

Entry
Database: PDB / ID: 4fzv
TitleCrystal structure of the human MTERF4:NSUN4:SAM ternary complex
Components
  • Putative methyltransferase NSUN4
  • mTERF domain-containing protein 2
KeywordsTRANSFERASE / MTERF fold / methyltransferase fold / rRNA methyltransferase / mitochondria
Function / homology
Function and homology information


tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / rRNA (cytosine-C5-)-methyltransferase activity / rRNA methyltransferase activity / mitochondrial transcription / mitochondrial ribosome assembly / protein targeting to mitochondrion / camera-type eye development / mitochondrial large ribosomal subunit / rRNA methylation ...tRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / rRNA (cytosine-C5-)-methyltransferase activity / rRNA methyltransferase activity / mitochondrial transcription / mitochondrial ribosome assembly / protein targeting to mitochondrion / camera-type eye development / mitochondrial large ribosomal subunit / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / rRNA processing / heart development / double-stranded DNA binding / rRNA binding / mitochondrial matrix / regulation of DNA-templated transcription / mitochondrion / cytosol
Similarity search - Function
Alpha-Beta Plaits - #40 / Alpha-Beta Plaits / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F ...Alpha-Beta Plaits - #40 / Alpha-Beta Plaits / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Other non-globular / Vaccinia Virus protein VP39 / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / S-ADENOSYLMETHIONINE / Transcription termination factor 4, mitochondrial / 5-methylcytosine rRNA methyltransferase NSUN4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9996 Å
AuthorsGuja, K.E. / Yakubovskaya, E. / Mejia, E. / Castano, S. / Hambardjieva, E. / Choi, W.S. / Garcia-Diaz, M.
CitationJournal: Structure / Year: 2012
Title: Structure of the Essential MTERF4:NSUN4 Protein Complex Reveals How an MTERF Protein Collaborates to Facilitate rRNA Modification.
Authors: Yakubovskaya, E. / Guja, K.E. / Mejia, E. / Castano, S. / Hambardjieva, E. / Choi, W.S. / Garcia-Diaz, M.
History
DepositionJul 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative methyltransferase NSUN4
B: mTERF domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1605
Polymers67,6532
Non-polymers5073
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-3 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)298.667, 53.226, 52.963
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Putative methyltransferase NSUN4 / NOL1/NOP2/Sun domain family member 4


Mass: 40607.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSUN4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96CB9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein mTERF domain-containing protein 2


Mass: 27045.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTERFD2, HSPC096 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6M4

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Non-polymers , 4 types, 304 molecules

#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIN CHAIN B, THE UNK RESIDUES ARE PART OF THE SEQUENCE ...IN CHAIN B, THE UNK RESIDUES ARE PART OF THE SEQUENCE EPECRRNLVQCLLEKQGTPVVQGSLELERVMSSLLDMGFSNAHINELLSVRRGASL BUT WHOSE REGISTRATION IS UNKNOWN DUE TO LACK OF ELECTRON DENSITY

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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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M magnesium formate, 50 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9790, 0.9795, 0.9500
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2012
RadiationMonochromator: Si-111 double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97951
30.951
ReflectionResolution: 1.9996→46.815 Å / Num. obs: 55979

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9996→46.815 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 2840 5.07 %
Rwork0.1647 --
obs0.166 55972 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9996→46.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 34 301 4573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124432
X-RAY DIFFRACTIONf_angle_d1.3166058
X-RAY DIFFRACTIONf_dihedral_angle_d13.4691574
X-RAY DIFFRACTIONf_chiral_restr0.11703
X-RAY DIFFRACTIONf_plane_restr0.006793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9996-2.03410.32541450.25282672X-RAY DIFFRACTION100
2.0341-2.07110.26661330.22262591X-RAY DIFFRACTION99
2.0711-2.11090.18991250.19292666X-RAY DIFFRACTION100
2.1109-2.1540.25251390.18082664X-RAY DIFFRACTION100
2.154-2.20080.2251410.17812642X-RAY DIFFRACTION100
2.2008-2.2520.19361370.16672599X-RAY DIFFRACTION100
2.252-2.30830.1821330.14652666X-RAY DIFFRACTION100
2.3083-2.37080.15581490.14252618X-RAY DIFFRACTION100
2.3708-2.44050.15931240.1482661X-RAY DIFFRACTION100
2.4405-2.51930.21261440.14412675X-RAY DIFFRACTION100
2.5193-2.60930.19881550.14992582X-RAY DIFFRACTION100
2.6093-2.71380.17521650.15522636X-RAY DIFFRACTION100
2.7138-2.83730.18011560.15812654X-RAY DIFFRACTION100
2.8373-2.98680.23381460.16692659X-RAY DIFFRACTION100
2.9868-3.17390.20871400.1652654X-RAY DIFFRACTION100
3.1739-3.41890.1851550.16152647X-RAY DIFFRACTION100
3.4189-3.76290.15591440.15312682X-RAY DIFFRACTION100
3.7629-4.3070.17391280.14422671X-RAY DIFFRACTION100
4.307-5.42510.19571540.15942701X-RAY DIFFRACTION100
5.4251-46.82830.19371270.19862792X-RAY DIFFRACTION100
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)
13.31010.4116-0.40591.4728-0.00062.29640.0251-0.09150.11090.0952-0.0238-0.1223-0.05680.3644-0.00150.231-0.0009-0.03560.16230.01390.163190.642111.614625.5656
27.11651.95481.25663.57441.73861.17980.0853-1.0987-0.35340.7788-0.24770.40430.581-0.2856-0.24680.3996-0.00550.02080.23720.10820.292977.4862-1.51932.4755
34.89130.8836-0.36371.6725-0.00652.7719-0.00610.64160.0421-0.27670.04830.03510.02050.1347-0.0490.24780.0024-0.02430.20650.02950.125184.67019.143711.9202
44.31330.93584.62410.20441.00464.9599-0.03290.09310.0784-0.2320.18180.414-0.0908-0.2439-0.15512.1785-0.58140.38322.14090.41252.0804164.671738.038813.4236
58.1129-2.17545.43240.5927-1.41123.84370.19811.4881-0.4248-0.9576-1.4485-2.1806-1.26121.71191.23931.1637-0.43310.15741.681-0.07282.0509158.856436.760922.7175
67.3208-2.234-1.25642.53230.13390.248-0.04190.3581.137-0.2514-0.2362-0.57380.0029-0.11350.22370.9518-0.53030.39982.02750.0892.262155.361728.545513.1521
73.3248-0.46890.03612.94331.00511.67530.1833-0.50340.67570.1372-0.2096-1.3001-0.24620.59820.06380.6211-0.41210.04412.1842-0.03511.8265156.980919.857920.0778
83.5397-0.85410.18242.79810.34080.5823-0.0103-0.0210.16230.1447-0.1647-0.8549-0.07340.94590.10.5308-0.1315-0.02451.93990.00681.2477147.23513.905216.8581
93.697-0.8359-0.31361.6912-0.1190.52670.09780.0965-0.3086-0.0442-0.2576-0.5615-0.08380.85880.03360.22830.02480.13391.9433-0.0131.0306134.95559.338811.0884
108.7904-0.6777-1.4515.1668-0.09491.6337-0.03970.92630.0369-0.79640.2376-0.5126-0.1420.7396-0.10330.4382-0.1810.0951.06960.04560.4477119.66615.37957.4696
119.08620.4612-1.53665.162-0.54233.7727-0.2854-0.69720.00980.10780.1952-0.36870.04191.0064-0.00690.2351-0.0826-0.03830.9098-0.01570.3818114.06414.695321.9086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 219 )
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 384 )
4X-RAY DIFFRACTION4chain 'B' and (resid 94 through 110 )
5X-RAY DIFFRACTION5chain 'B' and (resid 111 through 125 )
6X-RAY DIFFRACTION6chain 'B' and (resid 126 through 146 )
7X-RAY DIFFRACTION7chain 'B' and (resid 147 through 169 )
8X-RAY DIFFRACTION8chain 'B' and (resid 170 through 204 )
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 257 )
10X-RAY DIFFRACTION10chain 'B' and (resid 258 through 309 )
11X-RAY DIFFRACTION11chain 'B' and (resid 310 through 328 )

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