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- PDB-8f5x: Crystal structure of human eosinophil-derived neurotoxin (EDN, ri... -

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Basic information

Entry
Database: PDB / ID: 8f5x
TitleCrystal structure of human eosinophil-derived neurotoxin (EDN, ribonuclease 2) in complex with 5'-adenosine monophosphate (AMP)
ComponentsNon-secretory ribonuclease
KeywordsHYDROLASE / EDN / RNase 2 / ribonuclease / eosinophil-derived neurotoxin / transphosphorylase / AMP / adenosine monophosphate
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 / lyase 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 / lyase activity / Neutrophil degranulation / extracellular space / 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
ADENOSINE MONOPHOSPHATE / SUCCINIC ACID / Non-secretory ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTran, T.T.Q. / Pham, N.T.H. / Calmettes, C. / Doucet, N.
Funding support Canada, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN202204368 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN201706091 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)CREATE511956 Canada
Fonds de Recherche du Quebec - Sante (FRQS)251848 Canada
Fonds de Recherche du Quebec - Sante (FRQS)281993 Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases.
Authors: Tran, T.T.Q. / Narayanan, C. / Loes, A.N. / Click, T.H. / Pham, N.T.H. / Letourneau, M. / Harms, M.J. / Calmettes, C. / Agarwal, P.K. / Doucet, N.
History
DepositionNov 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-secretory ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5629
Polymers15,6121
Non-polymers9508
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 2D 1H-15N HSQC NMR titration experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.780, 52.450, 56.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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.) Homo sapiens (human) / Gene: RNASE2, EDN, RNS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10153
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2M succinic acid, 0.1M Hepes pH 7.0, 1% MME PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5215 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5215 Å / Relative weight: 1
ReflectionResolution: 1.7→38.41 Å / Num. obs: 13857 / % possible obs: 97.8 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.014 / Rrim(I) all: 0.048 / Net I/σ(I): 30.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7611.21.5222.213260.9450.4771.59895.4
1.76-1.83110.5695.813380.9780.1810.59896.1
1.83-1.9110.10.24611.613380.9930.0840.26196.5
1.91-2.029.40.14118.813550.9940.050.1597.3
2.02-2.1410.40.0927.813590.9960.030.09597.6
2.14-2.3111.50.06336.913800.9980.020.06697.6
2.31-2.54120.05142.813770.9980.0150.05398.7
2.54-2.9112.60.04547.214250.9990.0130.04799.2
2.91-3.6611.80.03752.414370.9990.0110.03899.7
3.66-38.4111.80.03156.115220.9990.0090.03299.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XSCALEdata scaling
PDB_EXTRACT4data extraction
PHASER2.8.3phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQV

1gqv


Resolution: 1.7→38.4 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 1376 9.94 %
Rwork0.178 --
obs0.1799 13839 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 63 111 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141191
X-RAY DIFFRACTIONf_angle_d1.6041621
X-RAY DIFFRACTIONf_dihedral_angle_d17.856451
X-RAY DIFFRACTIONf_chiral_restr0.084172
X-RAY DIFFRACTIONf_plane_restr0.009218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.64691240.69751192X-RAY DIFFRACTION95
1.76-1.830.42011390.37151197X-RAY DIFFRACTION96
1.83-1.910.27391340.25011200X-RAY DIFFRACTION96
1.91-2.020.23771300.20161224X-RAY DIFFRACTION97
2.02-2.140.20311400.1751218X-RAY DIFFRACTION98
2.14-2.310.2381390.17581241X-RAY DIFFRACTION98
2.31-2.540.19831410.15831236X-RAY DIFFRACTION99
2.54-2.910.19881390.16921286X-RAY DIFFRACTION99
2.91-3.660.15651460.14891291X-RAY DIFFRACTION100
3.66-38.40.14731440.15731378X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0861-0.054-0.05870.03860.04460.06460.01730.01810.1053-0.0250.0408-0.038-0.0512-0.0322-00.19030.01470.00490.1781-0.00080.19387.408515.08185.9271
20.1085-0.0505-0.03910.02770.01480.01590.0356-0.0440.00070.0075-0.0226-0.00950.0041-0.0125-00.2021-0.00750.00210.18730.00180.183611.81483.356412.0307
30.0050.0006-0.01080.01650.00090.0268-0.0492-0.0397-0.02410.1197-0.0658-0.0767-0.14170.057400.2112-0.0021-0.00160.18490.0190.181713.97770.782920.0336
40.05-0.0012-0.03170.00970.00090.02-0.035-0.17120.0972-0.0109-0.057-0.11960.02940.062300.2203-0.00660.00240.2378-0.00840.25620.359913.33794.1473
50.15970.0186-0.00630.02560.00470.06550.0704-0.09120.13920.0045-0.11960.0479-0.05810.006900.22030.00760.03150.19520.01260.248218.19916.03313.6499
60.04250.07080.00450.1596-0.04740.0706-0.06440.07150.2280.06520.06830.1158-0.00510.01540.00170.1495-0.01350.00540.1430.02480.17282.99274.024515.3806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:36)
2X-RAY DIFFRACTION2(chain A and resid 37:64)
3X-RAY DIFFRACTION3(chain A and resid 65:77)
4X-RAY DIFFRACTION4(chain A and resid 78:88)
5X-RAY DIFFRACTION5(chain A and resid 89:107)
6X-RAY DIFFRACTION6(chain A and resid 108:134)

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