8G91

LaM domain of human LARP1 in complex with Rp phosphorothioate isomer of AAAAA(SRA) RNA

PDB DOI: https://doi.org/10.2210/pdb8G91/pdb
NAKB: 8G91

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

Deposited: 2023-02-20 Released: 2024-04-17
Deposition Author(s): Kozlov, G., Jiang, J., Gehring, K.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.189
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into RNA binding by the LaM domain of LARP1

Kozlov, G., Jiang, J., Noronha, A.M., Wilds, C.J., Gehring, K.

To be published.

Macromolecule Content

Total Structure Weight: 13.84 kDa
Atom Count: 936
Modelled Residue Count: 93
Deposited Residue Count: 105
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of La-related protein 1	A	99	Homo sapiens	Mutation(s): 0 Gene Names: LARP1, KIAA0731, LARP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PKG0-3 (Homo sapiens) Explore Q6PKG0-3 Go to UniProtKB: Q6PKG0-3
GTEx: ENSG00000155506
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PKG0-3
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(APAPAPAPAP(SRA))-3')	B	6	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.189
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.781	α = 90
b = 53.781	β = 90
c = 90.452	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

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 R01GM133198.