8X6L | pdb_00008x6l

PRMT5:MEP50 WITH SCR-6920 AND SAM

PDB DOI: https://doi.org/10.2210/pdb8X6L/pdb
EM Map EMD-38091: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-11-21 Released: 2025-02-26
Deposition Author(s): Zhou, F., Zhou, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8X6L

This is version 1.0 of the entry. See complete history.

Literature

PRMT5:MEP50 WITH SCR-6920 AND SAM

Zhou, F., Zhou, F.

To be published.

Macromolecule Content

Total Structure Weight: 442.24 kDa
Atom Count: 29,724
Modeled Residue Count: 3,708
Deposited Residue Count: 3,916
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A, C, E, F	637	Homo sapiens	Mutation(s): 0 Gene Names: PRMT5 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744 Go to UniProtKB: O14744
PHAROS: O14744 GTEx: ENSG00000100462
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14744
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein WDR77	B, D, G, H	342	Homo sapiens	Mutation(s): 0 Gene Names: WDR77
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1 Go to UniProtKB: Q9BQA1
PHAROS: Q9BQA1 GTEx: ENSG00000116455
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BQA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YFU (Subject of Investigation/LOI) Query on YFU Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain T [auth F] SDF format, chain Q [auth E] SDF format, chain K [auth A] MOL2 format, chain N [auth C] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain K [auth A] mmCIF format, chain N [auth C] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain K [auth A]	K [auth A], N [auth C], Q [auth E], T [auth F]	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 C₃₂ H₄₀ N₄ O₄ QIAGGSLHFCTYMT-MHZLTWQESA-N		Interactions Focus chain K [auth A] Focus chain N [auth C] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain K [auth A] Focus chain N [auth C] Focus chain Q [auth E] Focus chain T [auth F]
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain O [auth E] SDF format, chain L [auth C] SDF format, chain I [auth A] MOL2 format, chain R [auth F] MOL2 format, chain O [auth E] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] mmCIF format, chain R [auth F] mmCIF format, chain O [auth E] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A]	I [auth A], L [auth C], O [auth E], R [auth F]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain P [auth E] SDF format, chain M [auth C] SDF format, chain J [auth A] MOL2 format, chain S [auth F] MOL2 format, chain P [auth E] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] mmCIF format, chain S [auth F] mmCIF format, chain P [auth E] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A]	J [auth A], M [auth C], P [auth E], S [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.