7DWH | pdb_00007dwh

Complex structure of SAM-dependent methyltransferase ribozyme

PDB DOI: https://doi.org/10.2210/pdb7DWH/pdb
NAKB: 7DWH

Classification: TRANSFERASE/RNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-17 Released: 2021-10-27
Deposition Author(s): Jiang, H.Y., Gao, Y.Q., Chen, D.R., Murchie, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.258 (Depositor), 0.252 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences

Jiang, H.Y., Gao, Y.Q., Zhang, L., Chen, D.R., Gan, J.H., Murchie, A.I.H.

(2021) Nat Catal 4: 872-881

DOI: https://doi.org/10.1038/s41929-021-00685-z

Macromolecule Content

Total Structure Weight: 76.81 kDa
Atom Count: 4,902
Modeled Residue Count: 464
Deposited Residue Count: 498
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	A, B, C, D	102	Homo sapiens	Mutation(s): 0 Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012 Go to UniProtKB: P09012
PHAROS: P09012 GTEx: ENSG00000077312
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09012
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (45-MER)	E [auth X], F [auth Y]	45	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain J [auth Y] SDF format, chain H [auth X] MOL2 format, chain J [auth Y] MOL2 format, chain H [auth X] mmCIF format, chain J [auth Y] mmCIF format, chain H [auth X]	H [auth X], J [auth Y]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain H [auth X] Focus chain J [auth Y] Interactions & Density Focus chain H [auth X] Focus chain J [auth Y]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain I [auth Y] SDF format, chain G [auth X] MOL2 format, chain I [auth Y] MOL2 format, chain G [auth X] mmCIF format, chain I [auth Y] mmCIF format, chain G [auth X]	G [auth X], I [auth Y]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth X] Focus chain I [auth Y] Interactions & Density Focus chain G [auth X] Focus chain I [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.258 (Depositor), 0.252 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.923	α = 90
b = 77.305	β = 93.24
c = 101.469	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-10-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-10-27
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.