9QWN | pdb_00009qwn

Human UPF1 in complex with the histone stem loop RNA

• PDB DOI: https://doi.org/10.2210/pdb9QWN/pdb
• EM Map EMD-53417: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2025-04-14 Released: 2025-12-03 
• Deposition Author(s): Machado de Amorim, A., Loll, B., Hilal, T., Chakrabarti, S.
• Funding Organization(s): German Research Foundation (DFG), EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Human UPF1 in complex with the histone stem loop RNA

Machado de Amorim, A., Loll, B., Hilal, T., Chakrabarti, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 102.07 kDa 
• Atom Count: 6,825 
• Modeled Residue Count: 823 
• Deposited Residue Count: 838 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Regulator of nonsense transcripts 1	A	800	Homo sapiens	Mutation(s): 0  Gene Names: UPF1, KIAA0221, RENT1 EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92900 (Homo sapiens) Go to UniProtKB:  Q92900
PHAROS:  Q92900 GTEx:  ENSG00000005007

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA stem loop	B [auth D]	38	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Machado de Amorim, A., Loll, B., Hilal, T., Chakrabarti, S.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	CH1245/5-1, CH1245/6-1
German Research Foundation (DFG)	Germany	INST 335/589-1
German Research Foundation (DFG)	Germany	INST 335/590-1
German Research Foundation (DFG)	Germany	INST 335/590-1
German Research Foundation (DFG)	Germany	(INST 130/1014-1
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND	Germany	664726

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release