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- PDB-9r6d: Structural characterization of a trehalose-binding site in human ... -

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Basic information

Entry
Database: PDB / ID: 9r6d
TitleStructural characterization of a trehalose-binding site in human RNase2
ComponentsNon-secretory ribonuclease
KeywordsPROTEIN BINDING / Disaccharide / RNase2 / Immune system / Trehalose
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
trehalose / ACETATE ION / FORMIC ACID / Non-secretory ribonuclease
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsXincheng, K. / Jiarui, L. / Prats-Ejarque, G. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2022-137872NB-100 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
DepositionMay 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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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)16,22010
Polymers15,6121
Non-polymers6089
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-42 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.002, 52.527, 56.800
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 / Sugars , 2 types, 2 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
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 207 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium formate, 14% PEG 3350, PH=7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 0.94→38.56 Å / Num. obs: 72600 / % possible obs: 90.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 8.71 Å2 / CC1/2: 0.995 / Net I/σ(I): 1.93
Reflection shellResolution: 0.94→0.97 Å / Num. unique obs: 1012 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.94→38.56 Å / SU ML: 0.0467 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.2426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1479 1986 2.74 %
Rwork0.1389 70613 -
obs0.1392 72599 89.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.43 Å2
Refinement stepCycle: LAST / Resolution: 0.94→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 38 199 1325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481274
X-RAY DIFFRACTIONf_angle_d0.84941760
X-RAY DIFFRACTIONf_chiral_restr0.0822195
X-RAY DIFFRACTIONf_plane_restr0.0056238
X-RAY DIFFRACTIONf_dihedral_angle_d12.2294499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.970.3222300.2235982X-RAY DIFFRACTION17.61
0.97-0.990.1838700.19472930X-RAY DIFFRACTION52.23
0.99-1.020.17611260.15474466X-RAY DIFFRACTION79.78
1.02-1.060.15271590.13295376X-RAY DIFFRACTION96.21
1.06-1.090.1131470.11675589X-RAY DIFFRACTION99.91
1.09-1.140.11911550.11265644X-RAY DIFFRACTION100
1.14-1.190.1231690.11165600X-RAY DIFFRACTION100
1.19-1.250.13881550.11645619X-RAY DIFFRACTION99.98
1.25-1.330.14111630.12495641X-RAY DIFFRACTION99.95
1.33-1.430.13551660.12915658X-RAY DIFFRACTION100
1.43-1.580.14391480.13095691X-RAY DIFFRACTION100
1.58-1.80.15411660.14045701X-RAY DIFFRACTION99.98
1.8-2.270.16091630.14965755X-RAY DIFFRACTION100
2.27-38.560.151690.14845961X-RAY DIFFRACTION99.8

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