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- PDB-5l6d: Crystal structure of the human METTL3-METTL14 complex bound to SAH -

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Basic information

Entry
Database: PDB / ID: 5l6d
TitleCrystal structure of the human METTL3-METTL14 complex bound to SAH
Components(N6-adenosine-methyltransferase ...) x 2
KeywordsTRANSFERASE / RNA methyltransferase N6-adenine methylation Rossmann fold
Function / homology
Function and homology information


negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing ...negative regulation of hematopoietic progenitor cell differentiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / positive regulation of cap-independent translational initiation / endothelial to hematopoietic transition / RNA methylation / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing / forebrain radial glial cell differentiation / oxidoreductase complex / dosage compensation by inactivation of X chromosome / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / mRNA modification / regulation of hematopoietic stem cell differentiation / regulation of neuron differentiation / regulation of T cell differentiation / negative regulation of type I interferon-mediated signaling pathway / oogenesis / stem cell population maintenance / mRNA destabilization / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of Notch signaling pathway / positive regulation of translation / response to nutrient levels / mRNA splicing, via spliceosome / circadian rhythm / mRNA processing / cellular response to UV / spermatogenesis / nuclear speck / nuclear body / protein heterodimerization activity / innate immune response / mRNA binding / DNA damage response / Golgi apparatus / nucleoplasm / nucleus / cytosol
Similarity search - Function
N6-adenosine-methyltransferase non-catalytic subunit METTL14-like / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase-like (MT-A70-like) family profile. / N6-adenosine-methyltransferase MT-A70-like / mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase (EC 2.1.1.62) family profile. / MT-A70-like / MT-A70 / MT-A70-like family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / N(6)-adenosine-methyltransferase catalytic subunit METTL3 / N(6)-adenosine-methyltransferase non-catalytic subunit METTL14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.852 Å
AuthorsSledz, P. / Jinek, M.
CitationJournal: Elife / Year: 2016
Title: Structural insights into the molecular mechanism of the m(6)A writer complex.
Authors: Sledz, P. / Jinek, M.
History
DepositionMay 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 2.0Nov 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N6-adenosine-methyltransferase 70 kDa subunit
B: N6-adenosine-methyltransferase subunit METTL14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8445
Polymers59,3772
Non-polymers4683
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-24 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.822, 63.822, 225.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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N6-adenosine-methyltransferase ... , 2 types, 2 molecules AB

#1: Protein N6-adenosine-methyltransferase 70 kDa subunit / MT-A70 / Methyltransferase-like protein 3


Mass: 25886.646 Da / Num. of mol.: 1 / Fragment: UNP residues 354-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL3, MTA70 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86U44, mRNA (2'-O-methyladenosine-N6-)-methyltransferase
#2: Protein N6-adenosine-methyltransferase subunit METTL14 / Methyltransferase-like protein 14


Mass: 33490.051 Da / Num. of mol.: 1 / Fragment: UNP residues 107-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL14, KIAA1627 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9HCE5, mRNA (2'-O-methyladenosine-N6-)-methyltransferase

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Non-polymers , 4 types, 402 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 300 mM Mg acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03965 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03965 Å / Relative weight: 1
ReflectionResolution: 1.85→49.65 Å / Num. all: 87473 / Num. obs: 46603 / % possible obs: 99.9 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 34.19
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 4.91 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.852→49.634 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 4330 4.95 %
Rwork0.157 --
obs0.1588 87392 99.89 %
all-46510 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.852→49.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 31 399 3992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113693
X-RAY DIFFRACTIONf_angle_d1.1125010
X-RAY DIFFRACTIONf_dihedral_angle_d15.7972199
X-RAY DIFFRACTIONf_chiral_restr0.06539
X-RAY DIFFRACTIONf_plane_restr0.008643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8522-1.87320.27241500.23252788X-RAY DIFFRACTION97
1.8732-1.89530.21251380.2122681X-RAY DIFFRACTION100
1.8953-1.91840.26631450.20992810X-RAY DIFFRACTION100
1.9184-1.94270.24311460.21322789X-RAY DIFFRACTION100
1.9427-1.96820.23971360.19142700X-RAY DIFFRACTION100
1.9682-1.99520.22991500.18412824X-RAY DIFFRACTION100
1.9952-2.02370.23751400.17872712X-RAY DIFFRACTION100
2.0237-2.05390.19441440.17862846X-RAY DIFFRACTION100
2.0539-2.0860.22071380.18222734X-RAY DIFFRACTION100
2.086-2.12020.21681490.16812794X-RAY DIFFRACTION100
2.1202-2.15670.21751440.16322738X-RAY DIFFRACTION100
2.1567-2.1960.19271450.17022791X-RAY DIFFRACTION100
2.196-2.23820.22441460.16542722X-RAY DIFFRACTION100
2.2382-2.28390.25441450.16822812X-RAY DIFFRACTION100
2.2839-2.33350.21171460.15192727X-RAY DIFFRACTION100
2.3335-2.38780.17481460.15872803X-RAY DIFFRACTION100
2.3878-2.44750.19181500.15122794X-RAY DIFFRACTION100
2.4475-2.51370.19371480.15142712X-RAY DIFFRACTION100
2.5137-2.58770.18311450.14742785X-RAY DIFFRACTION100
2.5877-2.67120.2061420.15022790X-RAY DIFFRACTION100
2.6712-2.76670.22721420.15842794X-RAY DIFFRACTION100
2.7667-2.87740.23611420.15292739X-RAY DIFFRACTION100
2.8774-3.00840.16151460.15692775X-RAY DIFFRACTION100
3.0084-3.16690.19991470.14372787X-RAY DIFFRACTION100
3.1669-3.36530.16271410.14262771X-RAY DIFFRACTION100
3.3653-3.62510.18261420.14122743X-RAY DIFFRACTION100
3.6251-3.98980.15441450.13482805X-RAY DIFFRACTION100
3.9898-4.56670.11911480.12462777X-RAY DIFFRACTION100
4.5667-5.75220.15541470.14322763X-RAY DIFFRACTION100
5.7522-49.65230.26641370.20152756X-RAY DIFFRACTION100

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