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Yorodumi- PDB-1sxj: Crystal Structure of the Eukaryotic Clamp Loader (Replication Fac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sxj | ||||||
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Title | Crystal Structure of the Eukaryotic Clamp Loader (Replication Factor C, RFC) Bound to the DNA Sliding Clamp (Proliferating Cell Nuclear Antigen, PCNA) | ||||||
Components |
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Keywords | REPLICATION / CLAMP LOADER / PROCESSIVITY CLAMP / DNA SLIDING CLAMP / AAA+ ATPASE / DNA POLYMERASE / DNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA replication factor C complex / Ctf18 RFC-like complex / meiotic mismatch repair / DNA clamp loader activity / Processive synthesis on the lagging strand / Removal of the Flap Intermediate ...DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA replication factor C complex / Ctf18 RFC-like complex / meiotic mismatch repair / DNA clamp loader activity / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / PCNA complex / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / lagging strand elongation / postreplication repair / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / leading strand elongation / DNA polymerase processivity factor activity / error-free translesion synthesis / Gap-filling DNA repair synthesis and ligation in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA replication / positive regulation of DNA repair / replication fork / DNA damage checkpoint signaling / nucleotide-excision repair / DNA-templated DNA replication / mitotic cell cycle / chromosome, telomeric region / cell division / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å | ||||||
Authors | Bowman, G.D. / O'Donnell, M. / Kuriyan, J. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Authors: Bowman, G.D. / O'Donnell, M. / Kuriyan, J. | ||||||
History |
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Remark 999 | SEQUENCE The actual sequence of the region 697-747 (shown as UNK in SEQRES) is ...SEQUENCE The actual sequence of the region 697-747 (shown as UNK in SEQRES) is DKIGLRLDYLPTFRKRLLDPFLKQGADAISSVIEVMDDYYLTKEDWDSIME |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sxj.cif.gz | 464.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sxj.ent.gz | 375.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/1sxj ftp://data.pdbj.org/pub/pdb/validation_reports/sx/1sxj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 6 molecules ABDFGH
#1: Protein | Mass: 56377.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC1, CDC44, YOR217W, YOR50-7 / Plasmid: pLANT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38630 |
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#2: Protein | Mass: 36171.977 Da / Num. of mol.: 1 / Mutation: R162Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC4, YOL094C, O0923 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40339 |
#4: Protein | Mass: 39765.410 Da / Num. of mol.: 1 / Mutation: R160Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC2, YJR068W, J1808 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40348 |
#6: Protein | Mass: 32053.217 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL30, YBR088C, YBR0811 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15873 |
-Activator 1 40 kDa ... , 2 types, 2 molecules CE
#3: Protein | Mass: 38225.480 Da / Num. of mol.: 1 / Mutation: R165Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC3, YNL290W, N0533 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38629 |
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#5: Protein | Mass: 39964.520 Da / Num. of mol.: 1 / Mutation: R184Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC5, YBR087W, YBR0810 / Plasmid: pLANT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38251 |
-Non-polymers , 3 types, 9 molecules
#7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-AGS / #9: Chemical | ChemComp-ADP / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 3350, sodium chloride, CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.85→100 Å / Num. all: 139719 / Num. obs: 132895 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 41.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 22.7 | ||||||||||||||||||
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 7230 / Rsym value: 0.481 / % possible all: 100 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 100 Å / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: 1PLQ, 1JR3, 1NJF, 1IQP Resolution: 2.85→48.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 122662.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: IN CHAIN A, IT WAS NOT POSSIBLE TO UNAMBIGUOUSLY DETERMINE THE SEQUENCE REGISTER FOR RESIDUES 697 TO 747. THESE RESIDUES ARE THEREFORE DESIGNATED UNK TO INDICATE THIS AMBIGUITY. IN CHAIN E, ...Details: IN CHAIN A, IT WAS NOT POSSIBLE TO UNAMBIGUOUSLY DETERMINE THE SEQUENCE REGISTER FOR RESIDUES 697 TO 747. THESE RESIDUES ARE THEREFORE DESIGNATED UNK TO INDICATE THIS AMBIGUITY. IN CHAIN E, RESIDUES 86 TO 121 ARE GIVEN THE AMINO ACID TYPES THAT CORRESPOND TO THE GENE NUMBERING, HOWEVER THE SEQUENCE REGISTER MAY BE INCORRECT DUE TO A LACK OF DENSITY FOR FLANKING LOOPS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1289 Å2 / ksol: 0.280894 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→48.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.6 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 91.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.429 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.398 |