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- PDB-6myl: The Prp8 intein-cisplatin complex -

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Basic information

Entry
Database: PDB / ID: 6myl
TitleThe Prp8 intein-cisplatin complex
ComponentsPre-mRNA-processing-splicing factor 8
Keywordshydrolase/hydrolase inhibitor / Prp8 / intein / cisplatin / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


: / U5 snRNA binding / U6 snRNA binding / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity
Similarity search - Function
Hint domain superfamily / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core ...Hint domain superfamily / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesCryptococcus gattii serotype B (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.06 Å
AuthorsLi, Z. / Li, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM39422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM44844 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140726-01A1 United States
CitationJournal: Emerg Microbes Infect / Year: 2019
Title: Cisplatin protects mice from challenge ofCryptococcus neoformansby targeting the Prp8 intein.
Authors: Li, Z. / Fu, B. / Green, C.M. / Liu, B. / Zhang, J. / Lang, Y. / Chaturvedi, S. / Belfort, M. / Liao, G. / Li, H.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 20, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: Pre-mRNA-processing-splicing factor 8
C: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,09812
Polymers73,3423
Non-polymers1,7569
Water00
1
A: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0334
Polymers24,4471
Non-polymers5853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0334
Polymers24,4471
Non-polymers5853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pre-mRNA-processing-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0334
Polymers24,4471
Non-polymers5853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.853, 74.853, 191.886
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 22 or resid 24...
21(chain B and (resid 1 through 22 or resid 24...
31(chain C and (resid 1 through 22 or resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSGLNGLN(chain A and (resid 1 through 22 or resid 24...AA1 - 2244 - 65
12GLYGLYASPASP(chain A and (resid 1 through 22 or resid 24...AA24 - 5367 - 96
13LEULEUGLUGLU(chain A and (resid 1 through 22 or resid 24...AA55 - 7198 - 114
14GLUGLUGLUGLU(chain A and (resid 1 through 22 or resid 24...AA108 - 144151 - 187
15PROPROASNASN(chain A and (resid 1 through 22 or resid 24...AA146 - 170189 - 213
21CYSCYSGLNGLN(chain B and (resid 1 through 22 or resid 24...BB1 - 2244 - 65
22GLYGLYASPASP(chain B and (resid 1 through 22 or resid 24...BB24 - 5367 - 96
23LEULEUGLUGLU(chain B and (resid 1 through 22 or resid 24...BB55 - 7198 - 114
24GLUGLUGLUGLU(chain B and (resid 1 through 22 or resid 24...BB108 - 144151 - 187
25PROPROASNASN(chain B and (resid 1 through 22 or resid 24...BB146 - 170189 - 213
31CYSCYSGLNGLN(chain C and (resid 1 through 22 or resid 24...CC1 - 2244 - 65
32GLYGLYASPASP(chain C and (resid 1 through 22 or resid 24...CC24 - 5367 - 96
33LEULEUGLUGLU(chain C and (resid 1 through 22 or resid 24...CC55 - 7198 - 114
34GLUGLUGLUGLU(chain C and (resid 1 through 22 or resid 24...CC108 - 144151 - 187
35PROPROASNASN(chain C and (resid 1 through 22 or resid 24...CC146 - 170189 - 213

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Components

#1: Protein Pre-mRNA-processing-splicing factor 8


Mass: 24447.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus gattii serotype B (fungus)
Strain: R265 / Gene: CNBG_0411 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A095EAP2
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION

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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: 1.83 Å3/Da / Density % sol: 32.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M SODIUM CITRATE, 0.1M HEPES, PH 7.5, 10 MM DTT, 2% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.07147 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07147 Å / Relative weight: 1
ReflectionResolution: 3.05→100 Å / Num. obs: 18509 / % possible obs: 97.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 4.229 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.125.60.9546020.7020.4251.0481.39593.8
3.12-3.25.60.6886380.7810.3060.7561.44494.7
3.2-3.295.60.5476170.8760.2440.6011.51193.3
3.29-3.385.50.4556280.9070.2020.51.72795.3
3.38-3.495.50.3486450.930.1560.3831.66594.3
3.49-3.625.50.2786350.9590.1260.3061.94196.8
3.62-3.765.40.1986460.970.090.2182.48796.9
3.76-3.935.30.1626720.9820.0750.1792.57798.4
3.93-4.145.40.1236810.9890.0570.1363.03599.9
4.14-4.45.80.0996740.9910.0440.1083.20399.9
4.4-4.746.20.0816960.9950.0350.0893.359100
4.74-5.226.60.0776880.9960.0320.0843.809100
5.22-5.976.70.0867000.9950.0350.0934.839100
5.97-7.526.70.0867200.9960.0350.0938.5199.6
7.52-35.56.10.0757650.9970.0310.08115.94995.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6MWY

6mwy


Resolution: 3.06→35.545 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.28
RfactorNum. reflection% reflection
Rfree0.2975 1874 10.12 %
Rwork0.2426 --
obs0.2481 18509 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 314.69 Å2 / Biso mean: 97.4695 Å2 / Biso min: 54.69 Å2
Refinement stepCycle: final / Resolution: 3.06→35.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 9 0 3453
Biso mean--237.32 --
Num. residues----420
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1167X-RAY DIFFRACTION8.615TORSIONAL
12B1167X-RAY DIFFRACTION8.615TORSIONAL
13C1167X-RAY DIFFRACTION8.615TORSIONAL

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