7QRD | pdb_00007qrd

Crystal structure of mouse CARM1 in complex with histone H3_10-25

PDB DOI: https://doi.org/10.2210/pdb7QRD/pdb

Classification: TRANSCRIPTION
Organism(s): Mus musculus
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No

Deposited: 2022-01-11 Released: 2022-12-28
Deposition Author(s): Marechal, N., Cura, V., Troffer-Charlier, N., Bonnefond, L., Cavarelli, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.222 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

CARM1 Transition State Mimics

Marechal, N., Cura, V., Troffer-Charlier, N., Bonnefond, L., Cavarelli, J.

To be published.

Macromolecule Content

Total Structure Weight: 176.09 kDa
Atom Count: 12,176
Modeled Residue Count: 1,437
Deposited Residue Count: 1,544
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-arginine methyltransferase CARM1	A, B, C, D	378	Mus musculus	Mutation(s): 0 Gene Names: Carm1, Prmt4 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q9WVG6 (Mus musculus) Explore Q9WVG6 Go to UniProtKB: Q9WVG6
IMPC: MGI:1913208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WVG6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-THR-GLY-GLY-LYS-ALA-PRO-URU-LYS-GLN-LEU-ALA-THR-LYS-ALA-ALA	E [auth L], F [auth M]	16	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P68433 (Mus musculus) Explore P68433 Go to UniProtKB: P68433
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68433
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D]	J [auth B], M [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain J [auth B] Focus chain M [auth D] Interactions & Density Focus chain J [auth B] Focus chain M [auth D]
QVR (Subject of Investigation/LOI) Query on QVR Download Ideal Coordinates CCD File SDF format, chain O [auth L] SDF format, chain P [auth M] MOL2 format, chain O [auth L] MOL2 format, chain P [auth M] mmCIF format, chain O [auth L] mmCIF format, chain P [auth M]	O [auth L], P [auth M]	(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol C₁₂ H₁₅ N₅ O₃ UYHMWDPUDJRZGB-JVINVVEESA-N		Interactions Focus chain O [auth L] Focus chain P [auth M] Interactions & Density Focus chain O [auth L] Focus chain P [auth M]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth L] MOL2 format, chain I [auth B] MOL2 format, chain N [auth L] mmCIF format, chain I [auth B] mmCIF format, chain N [auth L]	I [auth B], N [auth L]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain N [auth L] Interactions & Density Focus chain I [auth B] Focus chain N [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	G [auth B], H [auth B], K [auth D], L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB: 7QRD	Ki: min: 400, max: 860 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.254 (Depositor), 0.253 (DCC)
R-Value Work: 0.222 (Depositor), 0.223 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.183	α = 90
b = 99.204	β = 90
c = 208.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-12-28
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 2.0: 2024-10-09
Changes: Atomic model, Data collection, Structure summary

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Deposit Data

Help and Resources

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Crystal structure of mouse CARM1 in complex with histone H3_10-25

CARM1 Transition State Mimics

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt