9CSN | pdb_00009csn

Crystal structure of human ribonuclease 7 (RNase 7) in complex with 5'-adenosine monophosphate (5'-AMP)

PDB DOI: https://doi.org/10.2210/pdb9CSN/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-24 Released: 2025-07-30
Deposition Author(s): Tran, T.T.Q., Pham, N.T.H., Calmettes, C., Doucet, N.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Fonds de Recherche du Quebec - Sante (FRQS), Canada Foundation for Innovation, Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Engineering human RNase 7 with an eosinophil RNase segment reveals determinants of cytotoxic and antimicrobial activity.

Tran, T.T.Q., Larda, S.T., Nieves, C., Veyrier, F.J., Calmettes, C., Doucet, N.

(2026) J Biol Chem 302: 113189-113189

PubMed: 42203172 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2026.113189
Primary Citation Related Structures:
9CSM, 9CSN

PubMed Abstract:
Human ribonuclease 7 is a potent antimicrobial member of the RNase A superfamily with little cytotoxic activity, in contrast to the closely related eosinophil cationic protein (HsR3). To determine which structural elements underlie these divergent functions, we engineered a chimeric RNase 7 variant in which loop 4 to 5 residues 61 to 77 were replaced by the corresponding segment from HsR3. This chimera acquired cytotoxicity toward HeLa cells while retaining antibacterial activity against Escherichia coli and Mycobacterium smegmatis, identifying this segment as a key transferable determinant of RNase function. Consistent with this result, a peptide spanning HsR3 residues 61 to 77 also displayed antibacterial activity, supporting a direct contribution of this region to host-defense activity and functional modulation within the RNase scaffold. To define the structural basis of RNase 7 activity, we determined crystal structures of RNase 7 in apo and 5'-AMP-bound forms and combined these with NMR titrations and molecular docking. These analyses revealed a canonical RNase fold together with an unexpected adenine-binding pose in the B ₁ subsite. Complementary binding analyses showed that RNase 7 preferentially recognizes pyrimidines, yet can also accommodate purine-containing ligands such as UpA in more than one binding mode. Together, these findings establish loop 4 to 5 as a portable functional module that can reprogram biological activity within the human RNase scaffold and provide a structural framework for engineering multifunctional RNases with tailored properties.

Organizational Affiliation

Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Quebec, Canada.

Macromolecule Content

Total Structure Weight: 30.54 kDa
Atom Count: 2,199
Modeled Residue Count: 256
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 7	A, B	129	Homo sapiens	Mutation(s): 0 Gene Names: RNASE7, UNQ2516/PRO6006 EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1E1 (Homo sapiens) Explore Q9H1E1 Go to UniProtKB: Q9H1E1
PHAROS: Q9H1E1 GTEx: ENSG00000165799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H1E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A]	G [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], K [auth A], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
BO3 Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] I [auth A] J [auth A] C [auth A], D [auth A], E [auth A], I [auth A], J [auth A], O [auth B]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.262 (Depositor), 0.263 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.11	α = 90
b = 48.17	β = 97.28
c = 62.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2022-04368
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2017-06091
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	CREATE APRENTICE
Fonds de Recherche du Quebec - Sante (FRQS)	Canada	281993
Canada Foundation for Innovation	Canada	MSI - GlycoNet Integrated Services
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)	Canada	PROTEO