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- PDB-9gqm: Structural characterization of glucose- and fucose-binding sites ... -

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Basic information

Entry
Database: PDB / ID: 9gqm
TitleStructural characterization of glucose- and fucose-binding sites in human RNase2
ComponentsNon-secretory ribonuclease
KeywordsPROTEIN BINDING / Monosaccharide / glucose / fucose / 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 / alpha-L-fucopyranose / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Non-secretory ribonuclease
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 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 9, 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)16,1446
Polymers15,6121
Non-polymers5325
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint1 kcal/mol
Surface area7610 Å2
Unit cell
Length a, b, c (Å)41.885, 52.829, 56.534
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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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 234 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: 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.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 40.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate trihydrate, pH 7.0, 12% w/v Polyethylene glycol 3,350

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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: Mar 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.01→38.6 Å / Num. obs: 56650 / % possible obs: 86.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 7.86 Å2 / CC1/2: 0.998 / Net I/σ(I): 1.45
Reflection shellResolution: 1.036→1.071 Å / Redundancy: 1.7 % / Num. unique obs: 2832 / CC1/2: 0.932 / % possible all: 30.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→38.6 Å / SU ML: 0.0621 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.4892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1524 2008 3.55 %
Rwork0.1353 54635 -
obs0.1359 56643 86.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.55 Å2
Refinement stepCycle: LAST / Resolution: 1.01→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 35 231 1355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561235
X-RAY DIFFRACTIONf_angle_d0.93921696
X-RAY DIFFRACTIONf_chiral_restr0.0833187
X-RAY DIFFRACTIONf_plane_restr0.0076229
X-RAY DIFFRACTIONf_dihedral_angle_d7.1028178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.040.2702210.192639X-RAY DIFFRACTION14.27
1.04-1.070.1462790.15141832X-RAY DIFFRACTION41.31
1.07-1.10.17611070.12573021X-RAY DIFFRACTION67.11
1.1-1.130.1341430.1173863X-RAY DIFFRACTION86.86
1.13-1.180.11061560.11074361X-RAY DIFFRACTION97.43
1.18-1.220.12341580.11134483X-RAY DIFFRACTION100
1.22-1.280.14041730.11664465X-RAY DIFFRACTION100
1.28-1.350.13711610.11884494X-RAY DIFFRACTION100
1.35-1.430.14121670.12334505X-RAY DIFFRACTION99.98
1.43-1.540.1461710.12624496X-RAY DIFFRACTION99.94
1.54-1.70.13231550.13254540X-RAY DIFFRACTION99.91
1.7-1.940.16821680.14314551X-RAY DIFFRACTION99.94
1.94-2.440.17191690.1484603X-RAY DIFFRACTION99.85
2.44-38.60.15871800.14474782X-RAY DIFFRACTION99.96

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