PDB-9eyx: Human PRMT5 in complex with AZ compound 28

Basic information

• Entry: Database: PDB / ID: 9eyx
• Title: Human PRMT5 in complex with AZ compound 28

Components

• Methylosome protein WDR77
• Protein arginine N-methyltransferase 5, N-terminally processed

• Keywords: TRANSFERASE / methyl transferase / inhibitor

Function / homology

Function:

positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / negative regulation of gene expression via chromosomal CpG island methylation / regulation of mitotic nuclear division / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / liver regeneration / DNA-templated transcription termination / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm

Domain/homology:

Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily

Component:

: / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
• Authors: Debreczeni, J.

Funding support

1items

Organization	Grant number	Country
Not funded

• Citation: Journal: J.Med.Chem. / Year: 2024; Title: Discovery and In Vivo Efficacy of AZ-PRMT5i-1, a Novel PRMT5 Inhibitor with High MTA Cooperativity.; Authors: Smith, J.M. / Barlaam, B. / Beattie, D. / Bradshaw, L. / Chan, H.M. / Chiarparin, E. / Collingwood, O. / Cooke, S.L. / Cronin, A. / Cumming, I. / Dean, E. / Debreczeni, J.E. / Del Barco Barrantes, I. / Diene, C. / Gianni, D. / Guerot, C. / Guo, X. / Guven, S. / Hayhow, T.G. / Hong, T. / Kemmitt, P.D. / Lamont, G.M. / Lamont, S. / Lynch, J.T. / McWilliams, L. / Moore, S. / Raubo, P. / Robb, G.R. / Robinson, J. / Scott, J.S. / Srinivasan, B. / Steward, O. / Stubbs, C.J. / Syson, K. / Tan, L. / Turner, O. / Underwood, E. / Urosevic, J. / Vazquez-Chantada, M. / Whittaker, A.L. / Wilson, D.M. / Winter-Holt, J.J.

History

Deposition	Apr 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: Protein arginine N-methyltransferase 5, N-terminally processed

B: Methylosome protein WDR77

hetero molecules

Summary:

• 110 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,409	5
Polymers	109,524	2
Non-polymers	885	3
Water	1,243	69

1

A: Protein arginine N-methyltransferase 5, N-terminally processed

B: Methylosome protein WDR77

hetero molecules

A: Protein arginine N-methyltransferase 5, N-terminally processed

B: Methylosome protein WDR77

hetero molecules

A: Protein arginine N-methyltransferase 5, N-terminally processed

B: Methylosome protein WDR77

hetero molecules

A: Protein arginine N-methyltransferase 5, N-terminally processed

B: Methylosome protein WDR77

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 442 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	441,635	20
Polymers	438,096	8
Non-polymers	3,539	12
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_665	-x+1,-y+1,z	1
crystal symmetry operation	3_655	-x+1,y,-z	1
crystal symmetry operation	4_565	x,-y+1,-z	1

Calculated values:

Buried area	33430 Å2
ΔGint	-157 kcal/mol
Surface area	132630 Å2

Unit cell

Length a, b, c (Å)	102.124, 139.123, 178.145
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components

Protein , 2 types, 2 molecules A B

#1: Protein

A Protein arginine N-methyltransferase 5, N-terminally processed

Details:

Mass: 72766.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14744

#2: Protein

B Methylosome protein WDR77 / Androgen receptor cofactor p44 / Methylosome protein 50 / MEP-50 / WD repeat-containing protein 77 / p44/Mep50

Details:

Mass: 36757.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BQA1

Non-polymers , 4 types, 72 molecules

#3: Chemical

A-701 ChemComp-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

Details:

Mass: 491.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₆H₂₀F₃N₅O₂ / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

A-702 ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE

Details:

Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S

#5: Chemical

A-703 ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.89 ų/Da / Density % sol: 57.42 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop; Details: 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

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
• Detector: Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 24, 2023
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.95373 Å / Relative weight: 1
• Reflection: Resolution: 2.2→109.648 Å / Num. obs: 30190 / % possible obs: 92.7 % / Redundancy: 7 % / CC_1/2: 0.997 / Net I/σ(I): 7.9
• Reflection shell: Resolution: 2.203→2.505 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1509 / CC_1/2: 0.713

Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cor.coef. F_o:F_c: 0.886 / Cor.coef. F_o:F_c free: 0.856 / SU B: 25.06 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.28822	1579	5.3 %	RANDOM
Rwork	0.26901	-	-	-
obs	0.27002	28488	46.74 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 57.747 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.11 Å2	0 Å2	-0 Å2
2-	-	-1.05 Å2	-0 Å2
3-	-	-	0.94 Å2

Refinement step

Cycle: 1 / Resolution: 2.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7239	0	61	69	7369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	7497
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6798
X-RAY DIFFRACTION	r_angle_refined_deg	0.73	1.81	10243
X-RAY DIFFRACTION	r_angle_other_deg	0.29	1.744	15651
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.703	5	924
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.657	5	43
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.677	10	1148
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.035	0.2	1135
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	8922
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1731
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.525	3.14	3708
X-RAY DIFFRACTION	r_mcbond_other	0.525	3.14	3708
X-RAY DIFFRACTION	r_mcangle_it	0.987	5.646	4629
X-RAY DIFFRACTION	r_mcangle_other	0.987	5.646	4630
X-RAY DIFFRACTION	r_scbond_it	0.296	3.117	3789
X-RAY DIFFRACTION	r_scbond_other	0.295	3.111	3785
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.588	5.734	5609
X-RAY DIFFRACTION	r_long_range_B_refined	1.949	28.86	7823
X-RAY DIFFRACTION	r_long_range_B_other	1.944	28.87	7823
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.203→2.26 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.404	2	-
Rwork	0.406	121	-
obs	-	-	2.63 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.1867	0.1402	-0.0496	1.6774	-0.0976	1.2354	0.1081	-0.0711	0.015	0.1523	-0.03	0.3303	-0.1508	-0.5933	-0.0781	0.0722	0.0221	0.0301	0.3339	0.0316	0.0696	30.6127	77.1205	19.2346
2	1.3282	0.0701	-0.1215	1.8298	0.0208	1.8654	-0.0916	-0.0905	-0.2879	0.282	0.0853	0.3211	0.6654	-0.3261	0.0063	0.5318	-0.3798	0.0476	0.3976	0.0927	0.2521	23.0371	27.6043	37.3543

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 701
2	X-RAY DIFFRACTION	2	B	21 - 329