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- PDB-5nxq: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bo... -

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Basic information

Entry
Database: PDB / ID: 5nxq
TitleCrystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP
Components
  • DNA polymerase alpha-binding protein
  • MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU
KeywordsREPLICATION / DNA replication / adaptor protein / beta-propeller domain
Function / homology
Function and homology information


establishment of sister chromatid cohesion / Unwinding of DNA / Cul8-RING ubiquitin ligase complex / GINS complex / CMG complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork ...establishment of sister chromatid cohesion / Unwinding of DNA / Cul8-RING ubiquitin ligase complex / GINS complex / CMG complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / mitotic cell cycle / nucleosome assembly / DNA repair / chromatin binding / identical protein binding / nucleus
Similarity search - Function
: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA replication complex GINS protein SLD5, C-terminal / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain ...: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / DNA replication complex GINS protein SLD5, C-terminal / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain / GINS, helical bundle-like domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA polymerase alpha-binding protein / DNA replication complex GINS protein SLD5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 Å
AuthorsWu, Y. / Pellegrini, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
Citation
Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Targeting the Genome-Stability Hub Ctf4 by Stapled-Peptide Design.
Authors: Wu, Y. / Villa, F. / Maman, J. / Lau, Y.H. / Dobnikar, L. / Simon, A.C. / Labib, K. / Spring, D.R. / Pellegrini, L.
#1: Journal: Nature / Year: 2014
Title: A Ctf4 trimer couples the CMG helicase to DNA polymerase alpha in the eukaryotic replisome.
Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / van Deursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase alpha-binding protein
B: DNA polymerase alpha-binding protein
C: DNA polymerase alpha-binding protein
D: MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU
E: MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3156
Polymers168,2235
Non-polymers921
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-35 kcal/mol
Surface area50530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.679, 100.287, 219.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-1004-

HOH

21C-1065-

HOH

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Components

#1: Protein DNA polymerase alpha-binding protein / Chromosome replication protein CHL15 / Chromosome transmission fidelity protein 4 / Protein POB1


Mass: 54534.562 Da / Num. of mol.: 3 / Fragment: UNP residues 471-927
Source method: isolated from a genetically manipulated source
Details: Ctf4-CTD (amino acids 427 to 971; C-end) was expressed and purified with an N-terminal Histag followed by a TEV protease cleavage site.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTF4, CHL15, POB1, YPR135W, P9659.7 / Plasmid: pRSF-Duet1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01454
#2: Protein/peptide MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU


Mass: 2309.615 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The molecule is a stapled version of the wild-type Sld5 CIP. it was produced by replacing amino acids 4 and 11 with two unnatural amino acids (UA1 and UA2) containing azide moieties in their ...Details: The molecule is a stapled version of the wild-type Sld5 CIP. it was produced by replacing amino acids 4 and 11 with two unnatural amino acids (UA1 and UA2) containing azide moieties in their side chains, and reacting the resulting diazido peptide with a bis-triazole dialkynyl linker, via a Cu(I)-catalysed click chemistry reaction.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03406*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M tri-sodium citrate pH 6.2 7.5-9% (w/v) PEG 8000 0.40-0.65 M NaCI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.413→49.21 Å / Num. obs: 76177 / % possible obs: 99.96 % / Redundancy: 13.2 % / Biso Wilson estimate: 58.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1424 / Rpim(I) all: 0.04074 / Net I/σ(I): 14.8
Reflection shellResolution: 2.413→2.499 Å / Redundancy: 12.1 % / Rmerge(I) obs: 2.453 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 7499 / CC1/2: 0.329 / Rpim(I) all: 0.7354 / % possible all: 99.83

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c8s

4c8s


Resolution: 2.413→49.209 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 25.42
RfactorNum. reflection% reflection
Rfree0.2114 7290 5.01 %
Rwork0.1844 --
obs0.1858 145636 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.413→49.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9537 0 6 336 9879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029853
X-RAY DIFFRACTIONf_angle_d0.56413360
X-RAY DIFFRACTIONf_dihedral_angle_d8.9095885
X-RAY DIFFRACTIONf_chiral_restr0.0411434
X-RAY DIFFRACTIONf_plane_restr0.0031715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4127-2.44010.38512450.35824542X-RAY DIFFRACTION99
2.4401-2.46880.37262180.3434637X-RAY DIFFRACTION100
2.4688-2.49890.37022460.34524632X-RAY DIFFRACTION100
2.4989-2.53060.3572410.3274620X-RAY DIFFRACTION100
2.5306-2.56380.37882260.32934591X-RAY DIFFRACTION100
2.5638-2.5990.35122440.32154596X-RAY DIFFRACTION100
2.599-2.63610.31932450.30144622X-RAY DIFFRACTION100
2.6361-2.67540.3322470.2944667X-RAY DIFFRACTION100
2.6754-2.71720.34111970.28924625X-RAY DIFFRACTION100
2.7172-2.76180.30832550.2844548X-RAY DIFFRACTION100
2.7618-2.80940.27592550.27414623X-RAY DIFFRACTION100
2.8094-2.86050.28642540.26244674X-RAY DIFFRACTION100
2.8605-2.91550.26572180.24484575X-RAY DIFFRACTION100
2.9155-2.9750.28982330.24264659X-RAY DIFFRACTION100
2.975-3.03970.26582560.22264617X-RAY DIFFRACTION100
3.0397-3.11040.2942450.22574565X-RAY DIFFRACTION100
3.1104-3.18820.252240.21424664X-RAY DIFFRACTION100
3.1882-3.27430.24692320.20714625X-RAY DIFFRACTION100
3.2743-3.37070.22192170.20484603X-RAY DIFFRACTION100
3.3707-3.47940.17642600.18574615X-RAY DIFFRACTION100
3.4794-3.60380.21432390.17864638X-RAY DIFFRACTION100
3.6038-3.7480.17992200.17194616X-RAY DIFFRACTION100
3.748-3.91850.19012350.16584639X-RAY DIFFRACTION100
3.9185-4.1250.20892490.15634582X-RAY DIFFRACTION100
4.125-4.38330.17052900.13554602X-RAY DIFFRACTION100
4.3833-4.72150.19072670.13254589X-RAY DIFFRACTION100
4.7215-5.19620.1572680.1294555X-RAY DIFFRACTION100
5.1962-5.94690.1722420.14744635X-RAY DIFFRACTION100
5.9469-7.48830.19162480.15594612X-RAY DIFFRACTION100
7.4883-49.2190.1552740.14854578X-RAY DIFFRACTION100

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