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- PDB-9go4: Structural characterization of citrate-binding site in human RNase2 -

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Basic information

Entry
Database: PDB / ID: 9go4
TitleStructural characterization of citrate-binding site in human RNase2
ComponentsNon-secretory ribonuclease
KeywordsPROTEIN BINDING / Tricarboxylate / citrate / RNase / Immune system
Function / homology
Function and homology information


RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / innate immune response in mucosa / chemotaxis / azurophil granule lumen / defense response to virus / nucleic acid binding / hydrolase activity ...RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / innate immune response in mucosa / chemotaxis / azurophil granule lumen / defense response to virus / nucleic acid binding / hydrolase activity / Neutrophil degranulation / : / extracellular exosome / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Non-secretory ribonuclease
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsXincheng, K. / Jiarui, L. / Prats-Ejarque, G. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2022-137872NB-I00 Spain
CitationJournal: Biorxiv / Year: 2026
Title: Structural basis for saccharide binding by human RNase 2/EDN, a protein combining enzymatic and lectin properties
Authors: Kang, X. / Prats-Ejarque, G. / Boix, E. / Li, J.
History
DepositionSep 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-secretory ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,51411
Polymers15,6121
Non-polymers90310
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-11 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.678, 52.418, 56.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Non-secretory ribonuclease / Eosinophil-derived neurotoxin / RNase UpI-2 / Ribonuclease 2 / RNase 2 / Ribonuclease US


Mass: 15611.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Gene: RNASE2, EDN, RNS2 / Production host: Expression vector pET-mod (others) / References: UniProt: P10153, pancreatic ribonuclease

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Non-polymers , 6 types, 220 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3,350, pH 5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.17→38.41 Å / Num. obs: 32960 / % possible obs: 88.5 % / Redundancy: 4 % / CC1/2: 0.998 / Net I/σ(I): 1.98
Reflection shellResolution: 1.175→1.217 Å / Redundancy: 1.3 % / Num. unique obs: 470 / CC1/2: 0.794 / % possible all: 42.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→33.53 Å / SU ML: 0.098 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 1676 5.09 %
Rwork0.1515 31279 -
obs0.1533 32955 78.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.76 Å2
Refinement stepCycle: LAST / Resolution: 1.17→33.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 59 210 1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621242
X-RAY DIFFRACTIONf_angle_d0.93851699
X-RAY DIFFRACTIONf_chiral_restr0.0833175
X-RAY DIFFRACTIONf_plane_restr0.009235
X-RAY DIFFRACTIONf_dihedral_angle_d23.444180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.210.3205140.2545292X-RAY DIFFRACTION8.98
1.21-1.250.3154480.24811036X-RAY DIFFRACTION31.28
1.25-1.290.2452960.22541669X-RAY DIFFRACTION51.53
1.29-1.340.20361220.21272242X-RAY DIFFRACTION68.26
1.34-1.410.211630.16782790X-RAY DIFFRACTION86.07
1.41-1.480.22371580.14833229X-RAY DIFFRACTION97.58
1.48-1.570.17871920.13823271X-RAY DIFFRACTION99.8
1.57-1.690.19021600.14023304X-RAY DIFFRACTION99.77
1.69-1.860.18521900.14643317X-RAY DIFFRACTION99.89
1.86-2.130.18611700.14073336X-RAY DIFFRACTION99.86
2.13-2.690.17721800.14873278X-RAY DIFFRACTION97.16
2.69-33.530.1781830.14973515X-RAY DIFFRACTION99.62

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