Protein arginine N-methyltransferase 5
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count | Chain A； UniProt 1–637 | Not recorded | Methylosome protein 50 × 4 （Q9BQA1） ADN ADENOSINE × 4 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；286 K；Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods. 2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol | Resolution 2.41 Å R-free 0.303 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 7MXC | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4GQB Crystal Structure of the human PRMT5:MEP50 Complex Deposited 2012-08-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–637（637 aa）
|
Not recorded | 0XU (2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20-30% PEG3350, 100-250 mM ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.06 Å R-free 0.222 |
| 4X60 Crystal structure of PRMT5:MEP50 with EPZ015666 and sinefungin Deposited 2014-12-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | SFG SINEFUNGIN × 1 3XV N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]-6-(oxetan-3-ylamino)pyrimidine-4-carboxamide × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.35 Å R-free 0.254 |
| 4X61 Crystal structure of PRMT5:MEP50 with EPZ015666 and SAM Deposited 2014-12-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 3XV N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]-6-(oxetan-3-ylamino)pyrimidine-4-carboxamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.85 Å R-free 0.260 |
| 4X63 Crystal structure of PRMT5:MEP50 with EPZ015666 and SAH Deposited 2014-12-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 3XV N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]-6-(oxetan-3-ylamino)pyrimidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 3.05 Å R-free 0.274 |
| 5C9Z Crystal structure of PRMT5:MEP50 with EPZ015866 and sinefungin Deposited 2015-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Mutation：N-terminal FLAG tag | SFG SINEFUNGIN × 1 4Z2 2-(cyclobutylamino)-N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]pyridine-4-carboxamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.36 Å R-free 0.288 |
| 5EMJ Crystal structure of PRMT5:MEP50 with Compound 8 and sinefungin Deposited 2015-11-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
|
Not recorded | SFG SINEFUNGIN × 4 5QJ (2~{S})-1-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-3-[[4-(3-methylbenzimidazol-5-yl)pyridin-2-yl]amino]propan-2-ol × 4 GOL GLYCEROL × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.27 Å R-free 0.266 |
| 5EMK Crystal structure of PRMT5:MEP50 with Compound 9 and sinefungin Deposited 2015-11-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
|
Not recorded | SFG SINEFUNGIN × 4 5QH ~{N}-[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-3-pyridin-2-yl-benzamide × 4 GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.52 Å R-free 0.262 |
| 5EML Crystal structure of PRMT5:MEP50 with Compound 10 and SAM Deposited 2015-11-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 4 5QK ~{N}-[(2~{R})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-2-quinolin-8-yloxy-ethanamide × 4 GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.39 Å R-free 0.282 |
| 5EMM Crystal structure of PRMT5:MEP50 with Compound 15 and sinefungin Deposited 2015-11-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
|
Not recorded | SFG SINEFUNGIN × 4 5QL ~{N}-[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-3-(oxan-4-ylamino)benzamide × 4 GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
|
Resolution 2.37 Å R-free 0.293 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–637（637 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–637（637 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–637（637 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–637（637 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 6CKC Structure of PRMT5:MEP50 in complex with LLY-283, a potent and selective inhibitor of PRMT5, with antitumor activity Deposited 2018-02-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | F5J 7-[(5R)-5-C-phenyl-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；16% PEG 3350, 200mM Magnesium Chloride, 100mM Bis-Tris pH 5.5
|
Resolution 2.80 Å R-free 0.214 |
| 6K1S Discovery of Potent and Selective Covalent Protein Arginine Methyltransferase (PRMT5) Inhibitors Deposited 2019-05-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | CUX 2-[[7-[(2~{R},3~{R},4~{S},5~{R})-5-[(~{R})-(4-chlorophenyl)-oxidanyl-methyl]-3,4-bis(oxidanyl)oxolan-2-yl]pyrrolo[2,3-d]pyrimidin-4-yl]amino]ethanal × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Na-Citrate, pH6.0
0.2M NaAc
12% PEG4000
|
Resolution 2.60 Å R-free 0.275 |
| 6RLL CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146 Deposited 2019-05-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | K8H (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-5-(1,8-diazaspiro[4.5]decan-1-ylmethyl)oxolane-3,4-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20-30% PEG3350; 150mM Ammonium Sulfate
|
Resolution 2.22 Å R-free 0.291 |
| 6RLQ CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ45031882 Deposited 2019-05-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–637（636 aa）
|
Not recorded | K8N (1~{S},2~{R},3~{S},5~{R})-3-[2-(2-azanyl-3-bromanyl-quinolin-7-yl)ethyl]-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)cyclop entane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；30-50% PEG3350, 150mM Ammonium Sulphate
|
Resolution 2.53 Å R-free 0.299 |
| 6UGH Cryo-EM structure of the apo form of human PRMT5:MEP50 complex at a resolution of 3.4 angstrom Deposited 2019-09-26 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–637（637 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 6UXX PRMT5:MEP50 Complexed with Allosteric Inhibitor Compound 1a Deposited 2019-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | QL1 (5R)-2-amino-5-(4-methoxyphenyl)-3-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-yl]-3,5-dihydro-4H-imidazol-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.69 Å R-free 0.277 |
| 6UXY PRMT5:MEP50 Complexed with Allosteric Inhibitor Compound 8 Deposited 2019-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | QKY (5R)-2-amino-5-(2-cyclohexylethyl)-3-methyl-5-phenyl-3,5-dihydro-4H-imidazol-4-one × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.57 Å R-free 0.275 |
| 6V0N PRMT5 bound to PBM peptide from Riok1 Deposited 2019-11-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | SFG SINEFUNGIN × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；281 K；30% PEG 3350
200 mM ammonium sulfate
0.05% w/v dodecyl-maltoside
|
Resolution 2.11 Å R-free 0.235 |
| 6V0N PRMT5 bound to PBM peptide from Riok1 Deposited 2019-11-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–637（637 aa）
|
Not recorded | SFG SINEFUNGIN × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；281 K；30% PEG 3350
200 mM ammonium sulfate
0.05% w/v dodecyl-maltoside
|
Resolution 2.11 Å R-free 0.235 |
| 6V0O PRMT5 bound to the PBM peptide from pICln Deposited 2019-11-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | SFG SINEFUNGIN × 4 ACE ACETYL GROUP × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；281 K；30% PEG 3350
200 mM ammonium sulfate
0.05% w/v dodecyl-maltoside
|
Resolution 2.86 Å R-free 0.247 |
| 6V0O PRMT5 bound to the PBM peptide from pICln Deposited 2019-11-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–637（637 aa）
|
Not recorded | SFG SINEFUNGIN × 4 ACE ACETYL GROUP × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；281 K；30% PEG 3350
200 mM ammonium sulfate
0.05% w/v dodecyl-maltoside
|
Resolution 2.86 Å R-free 0.247 |
| 6V0P PRMT5 complex bound to covalent PBM inhibitor BRD6711 Deposited 2019-11-19 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | QN4 2-(5-chloro-6-oxopyridazin-1(6H)-yl)-N-(4-methyl-3-sulfamoylphenyl)acetamide × 4 CL CHLORIDE ION × 8 SFG SINEFUNGIN × 4 GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；281 K；26% PEG3350
200 mM ammonium sulfate
0.05% w/v DDM
|
Resolution 1.88 Å R-free 0.230 |
| 7BO7 CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437 Deposited 2021-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–637（636 aa）
|
Not recorded | U6K (2~{R},3~{R},4~{S},5~{R})-2-[(4~{a}~{S},7~{a}~{S})-4-azanyl-1,4,4~{a},7~{a}-tetrahydropyrrolo[2,3-d]pyrimidin-7-yl]-5-(quinolin-7-yloxymethyl)oxolane-3,4-diol × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG3350, 150mM ammonium sulfate
|
Resolution 2.83 Å R-free 0.250 |
| 7BOC Crystal structure of the PRMT5 TIM barrel domain in complex with RioK1 peptide Deposited 2021-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–292（292 aa）
Fragment：TIM barrel domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1M NaAcetate, 30% w/v PEG400, 0.2M CaAcetate
|
Resolution 2.55 Å R-free 0.251 |
| 7KIB PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 Deposited 2020-10-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | WFM (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol × 1 EDO 1,2-ETHANEDIOL × 10 CL CHLORIDE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.52 Å R-free 0.245 |
| 7KIC PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 34 Deposited 2020-10-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 WFS (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.43 Å R-free 0.263 |
| 7KID PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72 Deposited 2020-10-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 WFV (1S,2R,3aR,4S,6aR)-4-[(2-amino-3,5-difluoroquinolin-7-yl)methyl]-2-(4-amino-5-fluoro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydropentalene-1,6a(1H)-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.50 Å R-free 0.279 |
| 7L1G PRMT5-MEP50 Complexed with SAM Deposited 2020-12-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 15 CL CHLORIDE ION × 2 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.47 Å R-free 0.255 |
| 7M05 CryoEM structure of PRMT5 bound to covalent PBM-site inhibitor BRD-6988 Deposited 2021-03-10 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
Chain C
1–637（637 aa）
Chain E
1–637（637 aa）
Chain G
1–637（637 aa）
|
Not recorded | YJG 2-(5-chloro-6-oxopyridazin-1(6H)-yl)-N-(4-methyl-3-{[2-(pyridin-2-yl)ethyl]sulfamoyl}phenyl)acetamide × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.39 Å |
| 7MX7 PRMT5:MEP50 complexed with inhibitor PF-06939999 Deposited 2021-05-18 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | ZR1 (1S,2S,3S,5R)-3-{[6-(difluoromethyl)-5-fluoro-1,2,3,4-tetrahydroisoquinolin-8-yl]oxy}-5-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；286.15 K；Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods. 2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol. Microseeding from initial crystals produced crystals suitable for data collection. Crystals for data collection were flash-frozen in liquid N2 using 25% (v/v) ethylene glycol in the mother liquor as a cryoprotectant
|
Resolution 2.49 Å R-free 0.279 |
| 7MXA PRMT5:MEP50 complexed with inhibitor PF-06855800 Deposited 2021-05-18 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | ZR4 7-[(5R)-5-C-(4-chloro-3-fluorophenyl)-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；286 K；Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods. 2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol
|
Resolution 2.71 Å R-free 0.307 |
| 7MXG PRMT5(M420T mutant):MEP50 complexed with inhibitor PF-06855800 Deposited 2021-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
Chain C
1–637（637 aa）
|
Mutation：M420T Mutation：M420T | ZR4 7-[(5R)-5-C-(4-chloro-3-fluorophenyl)-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；286 K；Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods. 2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol.
|
Resolution 2.40 Å R-free 0.282 |
| 7MXN PRMT5(M420T mutant):MEP50 complexed with inhibitor PF-06939999 Deposited 2021-05-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–637（637 aa）
|
Not recorded | ZR1 (1S,2S,3S,5R)-3-{[6-(difluoromethyl)-5-fluoro-1,2,3,4-tetrahydroisoquinolin-8-yl]oxy}-5-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；286 K；Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods. 2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol. Microseeding from initial crystals produced crystals suitable for data collection.
|
Resolution 2.55 Å R-free 0.277 |
| 7S0U PRMT5/MEP50 crystal structure with MTA and phthalazinone fragment bound Deposited 2021-08-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | CL CHLORIDE ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 81X 4-(aminomethyl)phthalazin-1(2H)-one × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；281 K；100 mM Sodium Citrate pH 5.4, 15% PEG3350, 4% Tascimate pH 5.0
|
Resolution 2.01 Å R-free 0.265 |
| 7S1P PRMT5/MEP50 crystal structure with sinefungin bound Deposited 2021-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | SFG SINEFUNGIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；281 K；100 mM Sodium Citrate pH 5.4, 15% PEG 3350, 4% Tacsimate pH 5
|
Resolution 2.21 Å R-free 0.250 |
| 7S1Q PRMT5/MEP50 crystal structure with MTA and a phthalazinone inhibitor bound (Compound 9) Deposited 2021-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 84W [7-(1-methyl-1H-pyrazol-4-yl)-4-oxo-3,4-dihydrophthalazin-1-yl]methanaminium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；281 K；100 mM Sodium Citrate pH 5, 18% PEG 4000, 150 mM Sodium Acetate
|
Resolution 2.78 Å R-free 0.248 |
| 7S1R PRMT5/MEP50 crystal structure with MTA and a phthalazinone inhibitor bound (compound (M)-31) Deposited 2021-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 85E {7-[(5M)-5-(1-cyano-3-fluoronaphthalen-2-yl)-1-methyl-1H-pyrazol-4-yl]-4-oxo-3,4-dihydrophthalazin-1-yl}methanaminium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；281 K；100 mM Sodium Citrate pH 5, 9% PEG 4000, 150 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.223 |
| 7S1S PRMT5/MEP50 crystal structure with MTA and MRTX-1719 bound Deposited 2021-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 85K (7-{(5M)-5-[3-chloro-6-cyano-5-(cyclopropyloxy)-2-fluorophenyl]-1-methyl-1H-pyrazol-4-yl}-4-oxo-3,4-dihydrophthalazin-1-yl)methanaminium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；281 K；100 mM Sodium Citrate pH 5.4, 11% PEG 4000, 50 mM Sodium Acetate
|
Resolution 2.62 Å R-free 0.233 |
| 7SER PRMT5/MEP50 with compound 30 bound Deposited 2021-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | 97L (2M)-2-{4-[4-(aminomethyl)-1-oxo-1,2-dihydrophthalazin-6-yl]-1-methyl-1H-pyrazol-5-yl}-1-benzothiophene-3-carbonitrile × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；100 mM Sodium Citrate pH 5.4, 12% PEG 3350, 4% Tascimate pH 5
|
Resolution 2.14 Å R-free 0.253 |
| 7SES PRMT5/MEP50 with compound 29 bound Deposited 2021-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | 97X (2P)-2-{4-[4-(aminomethyl)-1-oxo-1,2-dihydrophthalazin-6-yl]-1-methyl-1H-pyrazol-5-yl}naphthalene-1-carbonitrile × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；100 mM Sodium Citrate pH 5, 10% PEG 4K, 50 mM Sodium Acetate (pH 7)
|
Resolution 2.50 Å R-free 0.245 |
| 7U30 PRMT5:MEP50 Complexed with Cyclonucleoside Compound 1 Deposited 2022-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 8 LB3 (9R,10R,11S,12R,13R,14R)-4-amino-9-(3,4-difluorophenyl)-6,7,8,9,10,11,12,13-octahydro-10,13-epoxy[1,3]diazecino[1,2-e]purine-11,12-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
|
Resolution 2.60 Å R-free 0.208 |
| 7UOH PRMT5/MEP50 crystal structure with MTA and an achiral, class 1, non-atropisomeric inhibitor bound Deposited 2022-04-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | NXF (2M)-2-[(4M)-4-{4-(aminomethyl)-1-oxo-8-[(2R)-oxolan-2-yl]-1,2-dihydrophthalazin-6-yl}-1-methyl-1H-pyrazol-5-yl]-1-benzothiophene-3-carbonitrile × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；11 %w/v PEG 4K
0.1 M Na3 Cititrate 5 pH
0.05 M Na Acetate
|
Resolution 2.70 Å R-free 0.232 |
| 7UY1 HUMAN PRMT5:MEP50 COMPLEX WITH MTA and Fragment 5 Bound Deposited 2022-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | PJ0 3-methyl-1,5-naphthyridin-2-amine × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；PEG/Buffer/Salt
|
Resolution 2.66 Å R-free 0.300 |
| 7UYF Human PRMT5:MEP50 structure with Fragment 4 and MTA Bound Deposited 2022-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | PUI 4-methyl-1,5-naphthyridin-2-amine × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 PEG DI(HYDROXYETHYL)ETHER × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；281 K；10% PEG 4000, 100 mM Sodium Acetate, 100 mM Sodium Citrate pH 5.4
|
Resolution 2.82 Å R-free 0.315 |
| 7ZUP Human PRMT5:MEP50 structure with Fragment (Example 18) and MTA Bound Deposited 2022-05-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 JYX 3-ethylimidazo[4,5-b]pyridin-2-amine × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；15% PEG3350, 100 mM Na citrate, pH 5.4, 100mM Carboxylic acids
|
Resolution 2.01 Å R-free 0.271 |
| 7ZUQ HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 GOL GLYCEROL × 2 UNL UNKNOWN LIGAND × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；12.5% PEG3350, 100 mM Na citrate pH 5.4, 120 mM Ethylene glycols
|
Resolution 2.48 Å R-free 0.279 |
| 7ZUU HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 UNL UNKNOWN LIGAND × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；13% PEG3350, 100 mM Na citrate, pH 5.4, 100mM Carboxylic acids
|
Resolution 2.09 Å R-free 0.280 |
| 7ZUY HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 UNL UNKNOWN LIGAND × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；13 % PEG3350, 100 mM Na citrate, pH 5.4, 4% Tacsimate pH 7.0
|
Resolution 2.00 Å R-free 0.270 |
| 7ZV2 HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 UNL UNKNOWN LIGAND × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；16% PEG3350, 100 mM Na citrate pH 5.4, 100mM Carboxylic acids
|
Resolution 2.01 Å R-free 0.275 |
| 7ZVL HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound Deposited 2022-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 UNL UNKNOWN LIGAND × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；16% PEG3350, 100 mM Na citrate pH 5.4, 100mM Carboxylic acids
|
Resolution 2.39 Å R-free 0.286 |
| 7ZVU HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound Deposited 2022-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 UNL UNKNOWN LIGAND × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；14% PEG3350, 100 mM Na citrate pH 5.4, 100mM Carboxylic acids
|
Resolution 1.95 Å R-free 0.266 |
| 8CSG Human PRMT5:MEP50 structure with Fragment 1 and MTA Bound Deposited 2022-05-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | PWL 6-bromo-1H-pyrrolo[3,2-b]pyridin-5-amine × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；13% PEG 4000, 100 mM Sodium Acetate pH 5.0
|
Resolution 2.48 Å R-free 0.292 |
| 8CTB Human PRMT5:MEP50 structure with Fragment 3 and MTA Bound Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | PWX 7-chloro-1-methyl-1H-benzimidazol-2-amine × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；10% PEG 8000, 100 mM Sodium Citrate 5.4, 100 mM Sodium Acetate
|
Resolution 2.61 Å R-free 0.288 |
| 8CYI Cryo-EM structures and computational analysis for enhanced potency in MTA-synergic inhibition of human protein arginine methyltransferase 5 Deposited 2022-05-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–637（637 aa）
|
Not recorded | P2R N-[(2-aminoquinolin-7-yl)methyl]-9-(2-hydroxyethyl)-2,3,4,9-tetrahydro-1H-carbazole-6-carboxamide × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 8G1U Structure of the methylosome-Lsm10/11 complex Deposited 2023-02-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric |
Chain A
1–637（637 aa）
Chain E
1–637（637 aa）
Chain I
1–637（637 aa）
Chain M
1–637（637 aa）
|
Not recorded | ADN ADENOSINE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 8VEO Crystal structure of PRMT5:MEP50 in complex with MTA Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 EDO 1,2-ETHANEDIOL × 10 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
|
Resolution 2.03 Å R-free 0.278 |
| 8VET Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 1 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 A1AAS N-(5-methylpyridin-3-yl)-2-[(2R)-2-(1-methyl-1H-pyrrol-2-yl)piperidin-1-yl]-2-oxoacetamide × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；291 K；10% PEG 4000, 0.2M magnesium chloride, 0.1M MES (pH 6.5)
|
Resolution 2.63 Å R-free 0.277 |
| 8VEU Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 23 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 A1AAT N-(6-amino-5-methylpyridin-3-yl)-2-[(2R,5S)-5-methyl-2-phenylpiperidin-1-yl]-2-oxoacetamide × 1 EDO 1,2-ETHANEDIOL × 20 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
|
Resolution 2.46 Å R-free 0.250 |
| 8VEW Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 24 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 A1AAU 5-{2-[(2R,5S)-5-methyl-2-phenylpiperidin-1-yl](oxo)acetamido}pyridine-3-carboxamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
|
Resolution 2.69 Å R-free 0.269 |
| 8VEX Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 28 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 A1AAR N-(6-amino-5-methylpyridin-3-yl)-2-[(2R,5S)-2-(4-hydroxyphenyl)-5-methylpiperidin-1-yl]-2-oxoacetamide × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
|
Resolution 2.79 Å R-free 0.270 |
| 8VEY Crystal structure of PRMT5:MEP50 in complex with MTA and TNG908 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 A1AAV N-(6-amino-5-methylpyridin-3-yl)-2-[(2R,5S)-2-(1,3-benzothiazol-5-yl)-5-methylpiperidin-1-yl]-2-oxoacetamide × 1 PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.2M magnesium chloride, 0.1M sodium citrate (pH 6.0)
|
Resolution 2.44 Å R-free 0.261 |
| 8X6L PRMT5:MEP50 WITH SCR-6920 AND SAM Deposited 2023-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
Chain C
1–637（637 aa）
Chain E
1–637（637 aa）
Chain F
1–637（637 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 4 GOL GLYCEROL × 4 YFU 1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-oxidanylidene-2-[(3~{S})-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl]-2,3-dihydro-1,4-benzodiazepin-5-one × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9C10 AMG 193, a clinical stage MTA-cooperative PRMT5 inhibitor, drives anti-tumor activity preclinically and in patients with MTAP-deleted cancers Deposited 2024-05-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–637（637 aa）
|
Not recorded | GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1 A1ATH (4-amino-1,3-dihydrofuro[3,4-c][1,7]naphthyridin-8-yl){(3S)-3-[4-(trifluoromethyl)phenyl]morpholin-4-yl}methanone × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.1M Na citrate tribasic dihydrate pH 5.6 2% Tascimate pH 5.0, 16% PEG 3350
|
Resolution 2.85 Å R-free 0.299 |
| 9DOD Crystal structure of PRMT5:MEP50 in complex with PRT543 Deposited 2024-09-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | A1A79 7-[(3xi,5R)-5-C-(3,4-dichlorophenyl)-3-C-methyl-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M Na-Cit,0.2M NaAc,11% PEG4000,pH6.0
|
Resolution 2.50 Å R-free 0.259 |
| 9E3A Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICln PBM local refinement) Deposited 2024-10-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
1–637（637 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；30 mM HEPES pH 7.4, 150 mM NaCl, 3 mM TCEP, 3.33 mM sinefungin
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 9E3B Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric |
Chain A
1–637（637 aa）
Chain C
1–637（637 aa）
Chain G
1–637（637 aa）
Chain J
1–637（637 aa）
|
Not recorded | SFG SINEFUNGIN × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；30 mM HEPES pH 7.4, 150 mM NaCl, 3 mM TCEP, 3.33 mM sinefungin
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 9E3C Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (GRG local refine) Deposited 2024-10-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
1–637（637 aa）
|
Not recorded | SFG SINEFUNGIN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；30 mM HEPES pH 7.4, 150 mM NaCl, 3 mM TCEP, 3.33 mM sinefungin
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.19 Å |
| 9EYU Human PRMT5 in complex with AZ compound 1 Deposited 2024-04-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | A1H8A (1~{S})-2-[(2-carbamimidamido-1,3-thiazol-5-yl)methyl]-~{N}-[(4-fluorophenyl)methyl]-3-oxidanylidene-1~{H}-isoindole-1-carboxamide × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14-16 w/v % PEG3350, 24-25 v/v % 2-methyl-2,4-pentanediol and 0.1 M tri-sodium-citrate buffer at pH 5.4
|
Resolution 2.35 Å R-free 0.305 |
| 9EYV Human PRMT5 in complex with AZ compound 12 Deposited 2024-04-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | A1H76 (1~{S})-~{N}-[(4-fluorophenyl)methyl]-3-oxidanylidene-2-(1~{H}-pyrrolo[3,2-b]pyridin-2-ylmethyl)-1~{H}-isoindole-1-carboxamide × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14-16 w/v % PEG3350, 24-25 v/v % 2-methyl-2,4-pentanediol and 0.1 M tri-sodium-citrate buffer at pH 5.4
|
Resolution 2.15 Å R-free 0.279 |
| 9EYW Human PRMT5 in complex with AZ compound 21 Deposited 2024-04-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | A1H8B (3~{S})-2-[(5-azanyl-1~{H}-pyrrolo[3,2-b]pyridin-2-yl)methyl]-6-fluoranyl-1'-[(4-fluorophenyl)methyl]spiro[isoindole-3,3'-pyrrolidine]-1,2'-dione × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14-16 w/v % PEG3350, 24-25 v/v % 2-methyl-2,4-pentanediol and 0.1 M tri-sodium-citrate buffer at pH 5.4
|
Resolution 2.30 Å R-free 0.296 |
| 9EYX Human PRMT5 in complex with AZ compound 28 Deposited 2024-04-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | A1H73 (3~{S})-2-[(5-azanyl-6-fluoranyl-1~{H}-pyrrolo[3,2-b]pyridin-2-yl)methyl]-6-fluoranyl-1'-[(4-fluorophenyl)methyl]spiro[isoindole-3,3'-pyrrolidine]-1,2'-dione × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14-16 w/v % PEG3350, 24-25 v/v % 2-methyl-2,4-pentanediol and 0.1 M tri-sodium-citrate buffer at pH 5.4
|
Resolution 2.20 Å R-free 0.288 |
| 9MGL Crystal structure of PRMT5:MEP50 in complex with MTA and GSK3326595 Deposited 2024-12-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | A1BLM pemrametostat × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 SO4 SULFATE ION × 12 EDO 1,2-ETHANEDIOL × 40 PEG DI(HYDROXYETHYL)ETHER × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；35% PEG 3350, 327 mM ammonium sulfate
|
Resolution 2.25 Å R-free 0.268 |
| 9MGM Crystal structure of PRMT5:MEP50 in complex with MTA and compound 24 Deposited 2024-12-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BLL 2-(cyclobutylamino)-N-[(2S)-2-hydroxy-3-{6-[(1-methyl-1H-pyrazol-5-yl)methoxy]-3,4-dihydroisoquinolin-2(1H)-yl}propyl]pyridine-4-carboxamide × 4 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；283 K；25% PEG 3350, 0.1 M HEPES (pH 7.5), 0.2 M ammonium sulfate
|
Resolution 2.25 Å R-free 0.289 |
| 9MGN Crystal structure of PRMT5:MEP50 in complex with MTA and compound 41 Deposited 2024-12-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | A1BLK 2-(cyclobutylamino)-N-[(2S)-2-hydroxy-3-{6-[(1H-pyrazol-4-yl)methoxy]-3,4-dihydroisoquinolin-2(1H)-yl}propyl]pyridine-4-carboxamide × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
|
Resolution 2.82 Å R-free 0.281 |
| 9MGP Crystal structure of PRMT5:MEP50 in complex with MTA and compound 46a Deposited 2024-12-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BLI [2-(cyclobutylamino)pyridin-4-yl][(3R,4R)-3-hydroxy-4-{6-[(1-methyl-1H-pyrazol-5-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl}piperidin-1-yl]methanone × 4 EDO 1,2-ETHANEDIOL × 64 NA SODIUM ION × 16 GOL GLYCEROL × 4 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
|
Resolution 2.67 Å R-free 0.271 |
| 9MGQ Crystal structure of PRMT5:MEP50 in complex with sinefungin and compound 47 Deposited 2024-12-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | SFG SINEFUNGIN × 4 A1BLG 2-(cyclobutylamino)-N-{(2R)-2-hydroxy-2-[(3S)-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl}pyridine-4-carboxamide × 4 EDO 1,2-ETHANEDIOL × 76 SO4 SULFATE ION × 32 PEG DI(HYDROXYETHYL)ETHER × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；25% PEG 3350, 0.1 M Bis-Tris (pH 5.5), 0.2 M ammonium sulfate
|
Resolution 1.85 Å R-free 0.242 |
| 9MGR Crystal structure of PRMT5:MEP50 in complex with MTA and compound 51 Deposited 2024-12-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | A1BLF 6-[(1-acetylazetidin-3-yl)amino]-N-[(2R)-2-hydroxy-2-{(3S)-7-[(4-methyl-1,3-oxazol-5-yl)methoxy]-1,2,3,4-tetrahydroisoquinolin-3-yl}ethyl]-2-(4-methylpiperidin-1-yl)pyrimidine-4-carboxamide × 4 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 EDO 1,2-ETHANEDIOL × 60 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
|
Resolution 2.07 Å R-free 0.273 |
| 9MRE From DNA-Encoded Library Screening to AM-9747 - an MTA-Cooperative PRMT5 Inhibitor with Potent Oral in vivo Efficacy Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–637（637 aa）
|
Not recorded | A1BQW 2-amino-3-methyl-N-[(1R)-1-(pyrimidin-2-yl)ethyl]-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}quinoline-6-carboxamide × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 3 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；2% Tascimate pH 5.0, 16% PEG 3350
|
Resolution 2.25 Å R-free 0.241 |
| 9N3N Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 3 Deposited 2025-01-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BV5 N-(6-amino-5-cyclopropylpyridin-3-yl)-2-[(2R,5S)-2-(1,3-benzothiazol-5-yl)-5-methylpiperidin-1-yl]-2-oxoacetamide × 4 CL CHLORIDE ION × 16 EDO 1,2-ETHANEDIOL × 56 PEG DI(HYDROXYETHYL)ETHER × 12 PGE TRIETHYLENE GLYCOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine
|
Resolution 2.75 Å R-free 0.264 |
| 9N3O Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 14 Deposited 2025-01-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BV4 N-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-2-[(2R,5S)-2-(1,3-benzothiazol-5-yl)-5-methylpiperidin-1-yl]-2-oxoacetamide × 4 CL CHLORIDE ION × 8 EDO 1,2-ETHANEDIOL × 40 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000. 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine
|
Resolution 2.37 Å R-free 0.227 |
| 9N3P Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 30 Deposited 2025-01-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BV3 N-(6-amino-5-methylpyridin-3-yl)-2-[(2S,5R)-2-(4-fluorophenyl)-5-methyl-4-(2-methylpropanoyl)piperazin-1-yl]-2-oxoacetamide × 8 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 28 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine
|
Resolution 2.51 Å R-free 0.223 |
| 9N3Q Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 51 Deposited 2025-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
Chain C
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BV2 N-(6-amino-5-methylpyridin-3-yl)-2-{(2R,5S)-5-methyl-2-[2-(1-methylpiperidin-4-yl)-1,3-benzothiazol-5-yl]piperidin-1-yl}-2-oxoacetamide × 4 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenonsine
|
Resolution 2.54 Å R-free 0.267 |
| 9N3R Crystal structure of PRMT5:MEP50 in complex with MTA and TNG462 Deposited 2025-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
Chain C
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1BV0 N-(6-amino-5-ethylpyridin-3-yl)-2-{(2R,5S)-5-methyl-2-[2-(1-methylpiperidin-4-yl)-1,3-benzothiazol-5-yl]piperidin-1-yl}-2-oxoacetamide × 4 CL CHLORIDE ION × 10 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine
|
Resolution 2.47 Å R-free 0.243 |
| 9NWY Discovery of MTA-cooperative PRMT5 Inhibitors from Co-factor directed DNA-Encoded Library Screens Deposited 2025-03-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–637（637 aa）
|
Not recorded | A1B6Y 2-amino-3-methyl-N-(2-methylpropyl)-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}quinoline-6-carboxamide × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；281 K；1M Bis-Tris at pH 5.5, 10% - 25% PEG3350, 100 - 250mM MgCl2
|
Resolution 3.10 Å R-free 0.272 |
| 9OVY Cryo-EM structure of human PRMT5:MEP50 in complex with SAH and compounds 16-19F and HJL-1 Deposited 2025-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–637（637 aa）
Chain C
1–637（637 aa）
Chain E
1–637（637 aa）
Chain G
1–637（637 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.10 Å |
| 9PCA HUMAN PRMT5:MEP50 COMPLEX IN COMPLEX WITH LIGAND 18 Deposited 2025-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | A1CHO (1S,2R,3S,5R)-3-{2-[2-amino-6-(2-hydroxyethyl)quinolin-7-yl]ethyl}-5-(7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol × 1 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.27 M (NH4)2SO4; 0.05 M MES pH 6.75; 23.0% w/v PEG 3350
PROTEIN SOLUTION : 2 mM DTT, 10 % Glycerol, 10 mM HEPES-NaOH pH 7.5, 150 mM NaCl
|
Resolution 2.20 Å R-free 0.266 |
| 9PXZ PRMT5 Bound to Compound 6 and MTA Deposited 2025-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | A1CMW 4-amino-1-methyl-N-[(1R)-1-(pyrimidin-2-yl)ethyl]-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}-1H-pyrazolo[4,3-c]quinoline-8-carboxamide × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；11-22% PEG 3350, 200 mM ammonium sulfate
|
Resolution 2.47 Å R-free 0.269 |
| 9PY0 PRMT5 Bound to Compound 12 and MTA Deposited 2025-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | A1CMZ 4-amino-N'-(cyclopropanecarbonyl)-N',1-dimethyl-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}-1H-pyrazolo[4,3-c]quinoline-8-carbohydrazide × 1 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；11-22% PEG 3350, 200 mM ammonium sulfate
|
Resolution 2.36 Å R-free 0.283 |
| 9PY1 PRMT5 Bound to Compound 8 and MTA Deposited 2025-08-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–637（636 aa）
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 A1CM0 4-amino-1-methyl-N-(2-oxopiperidin-1-yl)-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}-1H-pyrazolo[4,3-c]quinoline-8-carboxamide × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；11-22% PEG 3350, 200 mM ammonium sulfate
|
Resolution 3.04 Å R-free 0.260 |
| 9T43 Human PRMT5:MEP50 in complex with AZD3470 Deposited 2025-10-30 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–637（637 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.18 Å R-free 0.268 |
| 9ZL2 Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 8 Deposited 2025-12-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1C3Y N~1~,N~1~-dibenzyl-N~2~-(5-carbamoylpyridin-3-yl)ethanediamide × 4 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
|
Resolution 3.18 Å R-free 0.293 |
| 9ZL3 Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 18 Deposited 2025-12-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 A1C37 N~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-{(1R)-1-[2-fluoro-4-(trifluoromethyl)phenyl]ethyl}-N~1~-methylethanediamide × 4 PEG DI(HYDROXYETHYL)ETHER × 32 EDO 1,2-ETHANEDIOL × 136 CL CHLORIDE ION × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
|
Resolution 1.71 Å R-free 0.239 |
| 9ZL4 Crystal structure of PRMT5:MEP50 in complex with MTA and TNG456 Deposited 2025-12-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
2–637（636 aa）
Fragment：FULL LENGTH
|
Not recorded | A1C4I N~2~-(4-amino-1H-pyrazolo[4,3-c]pyridin-7-yl)-N~1~-methyl-N~1~-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}ethanediamide × 8 MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 PEG DI(HYDROXYETHYL)ETHER × 4 CL CHLORIDE ION × 16 EDO 1,2-ETHANEDIOL × 156 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% PEG 4000, 0.1 M sodium citrate (pH 6.), 0.2 M magnesium chloride
|
Resolution 1.95 Å R-free 0.236 |
91 other PDB entries and 96 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | ANM5_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–637； UniProt 1–637 |
