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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 / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic mismatch repair / Rad17 RFC-like complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Ctf18 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex ...DNA clamp unloading / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic mismatch repair / Rad17 RFC-like complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Ctf18 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / PCNA complex / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / positive regulation of DNA replication / leading strand elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / subtelomeric heterochromatin formation / positive regulation of DNA repair / mismatch repair / translesion synthesis / DNA damage checkpoint signaling / replication fork / nucleotide-excision repair / DNA-templated DNA replication / mitotic cell cycle / chromosome, telomeric region / cell division / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / 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
Summary document | 1sxj_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 1sxj_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1sxj_validation.xml.gz | 99.7 KB | Display | |
Data in CIF | 1sxj_validation.cif.gz | 131.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/1sxj ftp://data.pdbj.org/pub/pdb/validation_reports/sx/1sxj | HTTPS FTP |
-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 |