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- PDB-4rjf: Crystal structure of the human sliding clamp at 2.0 angstrom reso... -

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Basic information

Entry
Database: PDB / ID: 4rjf
TitleCrystal structure of the human sliding clamp at 2.0 angstrom resolution
Components
  • Cyclin-dependent kinase inhibitor 1Cyclin-dependent kinase inhibitor protein
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / sliding clamp / processivity factor / p21 / DNA polymerase / Nucleus
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity ...cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / intestinal epithelial cell maturation / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / : / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / tissue regeneration / regulation of cell cycle G1/S phase transition / Transcriptional regulation by RUNX2 / negative regulation of phosphorylation / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of DNA biosynthetic process / response to arsenic-containing substance / replisome / oncogene-induced cell senescence / positive regulation of programmed cell death / Transcriptional activation of cell cycle inhibitor p21 / RUNX3 regulates CDKN1A transcription / AKT phosphorylates targets in the cytosol / response to L-glutamate / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone acetyltransferase binding / leading strand elongation / stress-induced premature senescence / DNA polymerase processivity factor activity / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / response to corticosterone / replication fork processing / cellular response to UV-B / G1/S-Specific Transcription / molecular function inhibitor activity / response to dexamethasone / protein kinase inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / nuclear replication fork / p53-Dependent G1 DNA Damage Response / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / SUMOylation of DNA replication proteins / estrous cycle / keratinocyte proliferation / PCNA-Dependent Long Patch Base Excision Repair / response to X-ray / replicative senescence / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / response to hyperoxia / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / translesion synthesis / positive regulation of protein kinase activity / positive regulation of DNA replication / animal organ regeneration / response to cadmium ion / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / DNA polymerase binding / Cyclin E associated events during G1/S transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of B cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / base-excision repair, gap-filling / keratinocyte differentiation / response to organonitrogen compound / positive regulation of DNA repair / epithelial cell differentiation / cellular response to amino acid starvation / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / cyclin binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / protein sequestering activity / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest
Similarity search - Function
Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. ...Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Cyclin-dependent kinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0072 Å
AuthorsKroker, A.J. / Bruning, J.B.
CitationJournal: Biochemistry / Year: 2015
Title: p21 Exploits Residue Tyr151 as a Tether for High-Affinity PCNA Binding.
Authors: Kroker, A.J. / Bruning, J.B.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Cyclin-dependent kinase inhibitor 1
C: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1
E: Proliferating cell nuclear antigen
F: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)94,6776
Polymers94,6776
Non-polymers00
Water34,7151927
1
A: Proliferating cell nuclear antigen
B: Cyclin-dependent kinase inhibitor 1

A: Proliferating cell nuclear antigen
B: Cyclin-dependent kinase inhibitor 1

A: Proliferating cell nuclear antigen
B: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)94,6776
Polymers94,6776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
2
C: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1

C: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1

C: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)94,6776
Polymers94,6776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
3
E: Proliferating cell nuclear antigen
F: Cyclin-dependent kinase inhibitor 1

E: Proliferating cell nuclear antigen
F: Cyclin-dependent kinase inhibitor 1

E: Proliferating cell nuclear antigen
F: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)94,6776
Polymers94,6776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)142.970, 142.970, 41.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Proliferating cell nuclear antigen / / PCNA / Cyclin


Mass: 28795.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12004
#2: Protein/peptide Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor protein / CDK-interacting protein 1 / Melanoma differentiation-associated protein 6 / MDA-6 / p21


Mass: 2763.233 Da / Num. of mol.: 3 / Fragment: 22 C TERMINAL RESIDUES (139 - 160) / Mutation: Y151F / Source method: obtained synthetically / Details: p21 peptide chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P38936
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1927 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.08M strontium chloride hexahydrate, 0.02M magnesium chloride hexahydrate, 0.04M sodium cacodylate trihydrate (pH7.0), 20% v/v (+/-)-2-methyl-2,4-pentanediol and 0.012M spermine ...Details: 0.08M strontium chloride hexahydrate, 0.02M magnesium chloride hexahydrate, 0.04M sodium cacodylate trihydrate (pH7.0), 20% v/v (+/-)-2-methyl-2,4-pentanediol and 0.012M spermine tetrahydrochloride, final [PCNA] = 11.6mg/mL = 0.40mM, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 22, 2014 / Details: mirrors
RadiationMonochromator: Rigaku VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.49
ReflectionResolution: 2.0072→41.41 Å / Num. all: 63388 / Num. obs: 63388 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 25 / Scaling rejects: 1365
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.0072-2.066.40.4493.828350444499.9
9.19-41.417.40.02483.8487965898.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å39.27 Å
Translation2.01 Å39.27 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXC

1axc


Resolution: 2.0072→39.272 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.98 / σ(I): 0 / Phase error: 20.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 1976 3.12 %random
Rwork0.1478 ---
all0.1546 63385 --
obs0.1546 63385 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.97 Å2 / Biso mean: 26.152 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: LAST / Resolution: 2.0072→39.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 0 1927 8177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026358
X-RAY DIFFRACTIONf_angle_d0.6318566
X-RAY DIFFRACTIONf_chiral_restr0.0251007
X-RAY DIFFRACTIONf_plane_restr0.0031093
X-RAY DIFFRACTIONf_dihedral_angle_d12.8482375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 97 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0072-2.05740.30631460.214943904536
2.0574-2.11290.25361400.200343674507
2.1129-2.1750.25321410.195144244565
2.175-2.24510.21761400.185643034443
2.2451-2.32530.27251460.180144104556
2.3253-2.41820.20381380.178243854523
2.4182-2.52810.26121390.169343484487
2.5281-2.66110.17361400.164743884528
2.6611-2.82730.181390.161243844523
2.8273-3.04490.21641400.150843864526
3.0449-3.35010.16271430.143843424485
3.3501-3.83180.18621390.137143984537
3.8318-4.81630.17141360.120643714507
4.8163-19.88860.14961490.138843834532

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