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- PDB-5l6e: Crystal structure of the human METTL3-METTL14 complex bound to SAM -

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Basic information

Entry
Database: PDB / ID: 5l6e
TitleCrystal structure of the human METTL3-METTL14 complex bound to SAM
Components(N6-adenosine-methyltransferase ...) x 2
KeywordsTRANSFERASE / methyltransferase N6-adenine methylation m6A Rossmann fold
Function / homology
Function and homology information


negative regulation of hematopoietic progenitor cell differentiation / positive regulation of cap-independent translational initiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / RNA methylation / endothelial to hematopoietic transition / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing ...negative regulation of hematopoietic progenitor cell differentiation / positive regulation of cap-independent translational initiation / mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / RNA methylation / endothelial to hematopoietic transition / regulation of meiotic cell cycle / RNA methyltransferase activity / primary miRNA processing / forebrain radial glial cell differentiation / dosage compensation by inactivation of X chromosome / oxidoreductase complex / S-adenosyl-L-methionine binding / gliogenesis / mRNA stabilization / regulation of hematopoietic stem cell differentiation / mRNA modification / 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 / circadian rhythm / mRNA splicing, via spliceosome / 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-ADENOSYLMETHIONINE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.901 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 1.1Apr 25, 2018Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)59,8585
Polymers59,3772
Non-polymers4823
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-24 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.949, 63.949, 225.858
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 90-580
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, 361 molecules

#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#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.: 358 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
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: 1.9→44.62 Å / Num. obs: 43352 / % possible obs: 99.9 % / Redundancy: 19.5 % / CC1/2: 1 / Rsym value: 0.089 / Net I/σ(I): 29.93
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 4.71 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L6D

5l6d


Resolution: 1.901→44.611 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 4031 4.97 %
Rwork0.1572 --
obs0.1585 43273 99.85 %
all-43271 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→44.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 32 358 3930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113664
X-RAY DIFFRACTIONf_angle_d1.0814970
X-RAY DIFFRACTIONf_dihedral_angle_d16.1922176
X-RAY DIFFRACTIONf_chiral_restr0.06535
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9014-1.92380.32081380.2492604X-RAY DIFFRACTION96
1.9238-1.94730.28031400.22042673X-RAY DIFFRACTION100
1.9473-1.97190.22661350.20812620X-RAY DIFFRACTION100
1.9719-1.99790.22441320.18962712X-RAY DIFFRACTION100
1.9979-2.02520.21891420.18122603X-RAY DIFFRACTION100
2.0252-2.05420.20961380.17722742X-RAY DIFFRACTION100
2.0542-2.08480.23431360.17632586X-RAY DIFFRACTION100
2.0848-2.11740.21941420.17662702X-RAY DIFFRACTION100
2.1174-2.15210.2091400.17112672X-RAY DIFFRACTION100
2.1521-2.18920.18941410.16652613X-RAY DIFFRACTION100
2.1892-2.2290.21931400.16972674X-RAY DIFFRACTION100
2.229-2.27190.21951410.16262678X-RAY DIFFRACTION100
2.2719-2.31830.20941390.15672661X-RAY DIFFRACTION100
2.3183-2.36870.1961430.15272698X-RAY DIFFRACTION100
2.3687-2.42380.17841400.15162623X-RAY DIFFRACTION100
2.4238-2.48440.1571410.14992644X-RAY DIFFRACTION100
2.4844-2.55160.191420.15622676X-RAY DIFFRACTION100
2.5516-2.62660.21951400.15292643X-RAY DIFFRACTION100
2.6266-2.71140.18041340.15532684X-RAY DIFFRACTION100
2.7114-2.80830.22541330.15712649X-RAY DIFFRACTION100
2.8083-2.92070.21681460.15832704X-RAY DIFFRACTION100
2.9207-3.05360.14991370.15272640X-RAY DIFFRACTION100
3.0536-3.21460.18721410.14222671X-RAY DIFFRACTION100
3.2146-3.41590.13761350.14532611X-RAY DIFFRACTION100
3.4159-3.67950.16791380.13642687X-RAY DIFFRACTION100
3.6795-4.04960.15351390.14022689X-RAY DIFFRACTION100
4.0496-4.63510.11211420.12422654X-RAY DIFFRACTION100
4.6351-5.83760.15781420.14482674X-RAY DIFFRACTION100
5.8376-44.62360.241340.20832651X-RAY DIFFRACTION100

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