9DPI | pdb_00009dpi

Cryo-EM structure of SerRS dimer in complex with two SIRT2

PDB DOI: https://doi.org/10.2210/pdb9DPI/pdb
EM Map EMD-47105: EMDB EMDataResource

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

Deposited: 2024-09-21 Released: 2026-03-18
Deposition Author(s): Yang, J., Zhang, Q., Zhang, H., Lander, G., Yang, X.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9DPI

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

Literature

Cryo-EM structure of SerRS dimer in complex with two SIRT2

Yang, J., Zhang, Q., Yang, X., Lander, G.

To be published.

Macromolecule Content

Total Structure Weight: 205.31 kDa
Atom Count: 7,651
Modeled Residue Count: 959
Deposited Residue Count: 1,806
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine--tRNA ligase, cytoplasmic	A [auth D], C [auth F]	514	Homo sapiens	Mutation(s): 0 Gene Names: SARS1, SARS, SERS EC: 6.1.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P49591 (Homo sapiens) Explore P49591 Go to UniProtKB: P49591
PHAROS: P49591 GTEx: ENSG00000031698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49591
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	B [auth C], D [auth E]	389	Homo sapiens	Mutation(s): 0 Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6 Go to UniProtKB: Q8IXJ6
PHAROS: Q8IXJ6 GTEx: ENSG00000068903
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IXJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 (Subject of Investigation/LOI) Query on AR6 Download:Ideal Coordinates CCD File SDF format, chain F [auth E] SDF format, chain E [auth C] MOL2 format, chain F [auth E] MOL2 format, chain E [auth C] mmCIF format, chain F [auth E] mmCIF format, chain E [auth C]	E [auth C], F [auth E]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain E [auth C] Focus chain F [auth E] Interactions & Density Focus chain E [auth C] Focus chain F [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	cryoSPARC
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-03-18
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.