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- PDB-8hl6: Crystal structure of human valosin-containing protein methyltrans... -

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Basic information

Entry
Database: PDB / ID: 8hl6
TitleCrystal structure of human valosin-containing protein methyltransferase
ComponentsProtein N-lysine methyltransferase METTL21D
KeywordsPROTEIN BINDING / VCPKMT / methyltransferase / ASPL / ASPSCR1 / UBXD9 / TUG
Function / homology
Function and homology information


peptidyl-lysine methylation / peptidyl-lysine trimethylation / negative regulation of ATP-dependent activity / protein-lysine N-methyltransferase activity / Protein methylation / Transferases; Transferring one-carbon groups; Methyltransferases / ATPase binding / protein-containing complex / cytoplasm / cytosol
Similarity search - Function
Lysine methyltransferase / Lysine methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Protein N-lysine methyltransferase METTL21D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKang, W. / Yang, J.K.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A6A1A10044154 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1C1C1004221 Korea, Republic Of
CitationJournal: Iscience / Year: 2023
Title: Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase.
Authors: Nguyen, T.Q. / Koh, S. / Kwon, J. / Jang, S. / Kang, W. / Yang, J.K.
History
DepositionNov 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein N-lysine methyltransferase METTL21D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0642
Polymers26,6651
Non-polymers3981
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10060 Å2
Unit cell
Length a, b, c (Å)58.170, 58.170, 129.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein N-lysine methyltransferase METTL21D / Methyltransferase-like protein 21D


Mass: 26665.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21D / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H867, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 1000, 0.1 M Na/K phosphate (pH 6.2), and 0.2M sodium chloride
PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→64.6 Å / Num. obs: 23428 / % possible obs: 93.2 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 17.2
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 2011 / CC1/2: 0.405 / Rpim(I) all: 0.683

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
MOSFLMdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.748 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 1146 4.91 %
Rwork0.1918 --
obs0.1935 23334 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→32.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 0 96 1761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071698
X-RAY DIFFRACTIONf_angle_d0.9232297
X-RAY DIFFRACTIONf_dihedral_angle_d3.6261020
X-RAY DIFFRACTIONf_chiral_restr0.057260
X-RAY DIFFRACTIONf_plane_restr0.005290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.36641340.3352260X-RAY DIFFRACTION81
1.8819-1.98110.34891280.29242551X-RAY DIFFRACTION91
1.9811-2.10530.3011430.24282810X-RAY DIFFRACTION99
2.1053-2.26780.2811240.22472855X-RAY DIFFRACTION100
2.2678-2.49590.24541350.20482883X-RAY DIFFRACTION100
2.4959-2.85690.25131650.2052857X-RAY DIFFRACTION100
2.8569-3.59870.22011640.19272916X-RAY DIFFRACTION100
3.5987-32.7480.18671530.16053056X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.701 Å / Origin y: 6.4623 Å / Origin z: 8.3012 Å
111213212223313233
T0.27 Å20.0163 Å20.0608 Å2-0.2341 Å20.0057 Å2--0.2798 Å2
L2.9456 °20.7419 °2-1.2475 °2-3.9825 °2-1.4537 °2--3.499 °2
S-0.0194 Å °0.0387 Å °-0.0129 Å °-0.2619 Å °-0.1278 Å °-0.306 Å °0.1384 Å °0.0959 Å °0.1081 Å °
Refinement TLS groupSelection details: all

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