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- PDB-6q55: Crystal structure of Cryptosporidium hominis CPSF3 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6q55
TitleCrystal structure of Cryptosporidium hominis CPSF3 in complex with Compound 61
ComponentsCleavage and Polyadenylation Specificity Factor 3 (CPSF3)
KeywordsRNA BINDING PROTEIN / mRNA processing factor / metallo-beta-lactamase / beta-CASP / oxaborole-inhibitor
Function / homology
Function and homology information


mRNA processing / nucleus
Similarity search - Function
Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily ...Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HJB / ISOPROPYL ALCOHOL / Cleavage and polyadenylation specificity factor
Similarity search - Component
Biological speciesCryptosporidium hominis TU502 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPalencia, A. / Swale, C.
Funding support France, 2items
OrganizationGrant numberCountry
European CommissioniNEXT Grant 653706 France
French National Research AgencyANR-11-LABX- 0024 Parafrap France
CitationJournal: Sci Transl Med / Year: 2019
Title: Metal-captured inhibition of pre-mRNA processing activity by CPSF3 controls Cryptosporidium infection.
Authors: Swale, C. / Bougdour, A. / Gnahoui-David, A. / Tottey, J. / Georgeault, S. / Laurent, F. / Palencia, A. / Hakimi, M.A.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cleavage and Polyadenylation Specificity Factor 3 (CPSF3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,11315
Polymers54,0101
Non-polymers1,10314
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-16 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 90.670, 237.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cleavage and Polyadenylation Specificity Factor 3 (CPSF3)


Mass: 54010.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis TU502 (eukaryote)
Gene: CHUDEA8_460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL Codon plus / References: UniProt: A0A0S4TJL4

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HJB / 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-5-yl]propanoic acid


Mass: 223.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12BO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.9 % / Description: 3D needles
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% (v/v) Poly Ethylene Glycol 4000, 10% (v/v) Isopropanol, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2018
RadiationMonochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 39853 / % possible obs: 99.6 % / Redundancy: 7.8 % / CC1/2: 0.99 / Rrim(I) all: 0.13 / Rsym value: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2893 / CC1/2: 0.26 / Rrim(I) all: 0.25 / Rsym value: 0.24 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model based on 2I7V

2i7v


Resolution: 2→47.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.374 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22244 1979 5 %RANDOM
Rwork0.18131 ---
obs0.18335 37874 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 2→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 66 214 3893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0143788
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173476
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6675131
X-RAY DIFFRACTIONr_angle_other_deg0.8831.6548155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76321.789190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.215652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9891526
X-RAY DIFFRACTIONr_chiral_restr0.1250.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9994.7981861
X-RAY DIFFRACTIONr_mcbond_other3.9814.7961860
X-RAY DIFFRACTIONr_mcangle_it5.9677.1892329
X-RAY DIFFRACTIONr_mcangle_other5.9767.1922330
X-RAY DIFFRACTIONr_scbond_it5.1255.291927
X-RAY DIFFRACTIONr_scbond_other5.1065.291927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6927.6992794
X-RAY DIFFRACTIONr_long_range_B_refined10.82657.1114179
X-RAY DIFFRACTIONr_long_range_B_other10.82657.1224180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 119 -
Rwork0.353 2772 -
obs--99.62 %

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