8RR3

Human mitochondrial RNase Z complex with ELAC2-D550N catalytic mutant and tRNA-Gln precursor (Composite model)

• PDB DOI: https://doi.org/10.2210/pdb8RR3/pdb
• EM Map EMD-19455: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2024-01-22 Released: 2025-01-08 
• Deposition Author(s): Bhatta, A., Yu, R.D., Kuhle, B., Hillen, H.S.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Structural basis of human mitochondrial and nuclear tRNA 3'-end processing

Bhatta, A., Kuhle, B., Yu, R.D., Ditter, K., Hillen, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 265.7 kDa 
• Atom Count: 16,294 
• Modelled Residue Count: 1,995 
• Deposited Residue Count: 2,253 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase type-2	A, B, C, D	261	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B10, ERAB, HADH2, MRPP2, SCHAD, SDR5C1, XH98G2 EC: 1.1.1.35 (PDB Primary Data), 1.1.1.62 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.178 (PDB Primary Data), 1.1.1.53 (PDB Primary Data), 1.1.1.159 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99714 (Homo sapiens) Explore Q99714  Go to UniProtKB:  Q99714
PHAROS:  Q99714 GTEx:  ENSG00000072506

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc phosphodiesterase ELAC protein 2	E	798	Homo sapiens	Mutation(s): 1  Gene Names: ELAC2, HPC2 EC: 3.1.26.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ52 (Homo sapiens) Explore Q9BQ52  Go to UniProtKB:  Q9BQ52
PHAROS:  Q9BQ52 GTEx:  ENSG00000006744

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA methyltransferase 10 homolog C	F	315	Homo sapiens	Mutation(s): 0  Gene Names: TRMT10C, MRPP1, RG9MTD1 EC: 2.1.1 (PDB Primary Data), 2.1.1.218 (PDB Primary Data), 2.1.1.221 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L0Y3 (Homo sapiens) Explore Q7L0Y3  Go to UniProtKB:  Q7L0Y3
PHAROS:  Q7L0Y3 GTEx:  ENSG00000174173

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Human mitochondrial tRNA-Gln precursor with 3' trailer RNA	G [auth T]	96	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	J [auth F]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN (Subject of Investigation/LOI)	H [auth E], I [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX	1.20.1-4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Bhatta, A., Yu, R.D., Kuhle, B., Hillen, H.S.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB1190
German Research Foundation (DFG)	Germany	FOR2848
German Research Foundation (DFG)	Germany	SFB1565
German Research Foundation (DFG)	Germany	EXC 2067/1 390729940
European Research Council (ERC)	European Union	101116869

Revision History  

• Version 1.0: 2025-01-08
  Type: Initial release