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- PDB-8fzb: Crystal structure of human FAM86A -

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Basic information

Entry
Database: PDB / ID: 8fzb
TitleCrystal structure of human FAM86A
ComponentsProtein-lysine N-methyltransferase EEF2KMT
KeywordsTRANSFERASE / Protein Lysine methyltransferase
Function / homology
Function and homology information


peptidyl-lysine trimethylation / protein methylation / protein-lysine N-methyltransferase activity / histone methyltransferase activity / Protein methylation / Transferases; Transferring one-carbon groups; Methyltransferases / protein-containing complex / cytoplasm / cytosol
Similarity search - Function
FAM86, N-terminal / Family of unknown function / Lysine methyltransferase / Lysine methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein-lysine N-methyltransferase EEF2KMT
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsShao, Z. / Lu, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The FAM86 domain of FAM86A confers substrate specificity to promote EEF2-Lys525 methylation.
Authors: Francis, J.W. / Shao, Z. / Narkhede, P. / Trinh, A.T. / Lu, J. / Song, J. / Gozani, O.
History
DepositionJan 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 22, 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-lysine N-methyltransferase EEF2KMT
B: Protein-lysine N-methyltransferase EEF2KMT
C: Protein-lysine N-methyltransferase EEF2KMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5516
Polymers111,3973
Non-polymers1,1533
Water00
1
A: Protein-lysine N-methyltransferase EEF2KMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5172
Polymers37,1321
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-lysine N-methyltransferase EEF2KMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5172
Polymers37,1321
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein-lysine N-methyltransferase EEF2KMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5172
Polymers37,1321
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.701, 160.701, 351.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Protein-lysine N-methyltransferase EEF2KMT / eEF2-lysine methyltransferase / eEF2-KMT


Mass: 37132.445 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF2KMT, FAM86A, SB153 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96G04, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
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: 5.1 Å3/Da / Density % sol: 75.87 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Ammonium citrate tribasic (pH 7.0), 10% w/v Polyethylene glycol 3,350 and 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 64154 / % possible obs: 100 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.998 / Χ2: 0.033 / Net I/σ(I): 4.5 / Num. measured all: 1324884
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.35-3.4717.71.61864030.3811100
3.47-3.6117.81.29264420.3911100
3.61-3.77170.95763800.4191100
3.77-3.9718.80.67564580.4781100
3.97-4.2221.50.44263810.5841100
4.22-4.5521.80.30263950.7741100
4.55-521.90.21864410.9731100
5-5.7320.40.17364021.0371100
5.73-7.2124.70.12464251.1691100
7.21-5024.70.06564271.3441100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.20.1-4487refinement
HKL-3000data reduction
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→48.82 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 2000 5.96 %
Rwork0.2306 --
obs0.2319 33574 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7300 0 78 0 7378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037540
X-RAY DIFFRACTIONf_angle_d0.6510274
X-RAY DIFFRACTIONf_dihedral_angle_d5.1061066
X-RAY DIFFRACTIONf_chiral_restr0.0411201
X-RAY DIFFRACTIONf_plane_restr0.0051300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.420.39151360.35432147X-RAY DIFFRACTION96
3.42-3.510.36631400.352217X-RAY DIFFRACTION98
3.51-3.610.3881390.32792195X-RAY DIFFRACTION98
3.61-3.730.3841410.30862230X-RAY DIFFRACTION98
3.73-3.860.28711410.27282225X-RAY DIFFRACTION99
3.86-4.020.281430.2542260X-RAY DIFFRACTION100
4.02-4.20.32021430.25582240X-RAY DIFFRACTION100
4.2-4.420.28621420.26032260X-RAY DIFFRACTION100
4.42-4.70.30161440.23372262X-RAY DIFFRACTION99
4.7-5.060.24791450.22772285X-RAY DIFFRACTION100
5.06-5.570.24531450.22842279X-RAY DIFFRACTION100
5.57-6.370.24261460.22462310X-RAY DIFFRACTION100
6.37-8.020.23651460.22192298X-RAY DIFFRACTION98
8.02-48.820.17851490.17612366X-RAY DIFFRACTION96

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