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- PDB-2zvw: Crystal structure of Proliferating cell nuclear antigen 2 and Sho... -

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Basic information

Entry
Database: PDB / ID: 2zvw
TitleCrystal structure of Proliferating cell nuclear antigen 2 and Short peptide from human P21
Components
  • Cyclin-dependent kinase inhibitor 1
  • Proliferating cell nuclear antigen 2
KeywordsDNA BINDING PROTEIN / protein-peptide complex / DNA replication / DNA-binding / Nucleus
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase activity / cellular response to cell-matrix adhesion / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / PCNA-p21 complex / intestinal epithelial cell maturation / regulation of cell cycle G1/S phase transition / tissue regeneration ...cyclin-dependent protein kinase activating kinase activity / cellular response to cell-matrix adhesion / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / PCNA-p21 complex / intestinal epithelial cell maturation / regulation of cell cycle G1/S phase transition / tissue regeneration / Transcriptional regulation by RUNX2 / PCNA complex / negative regulation of phosphorylation / negative regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to arsenic-containing substance / positive regulation of programmed cell death / oncogene-induced cell senescence / Transcriptional activation of cell cycle inhibitor p21 / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / stress-induced premature senescence / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / response to corticosterone / cellular response to UV-B / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular function inhibitor activity / DNA polymerase processivity factor activity / STAT5 activation downstream of FLT3 ITD mutants / protein kinase inhibitor activity / leading strand elongation / p53-Dependent G1 DNA Damage Response / regulation of DNA replication / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / keratinocyte proliferation / response to X-ray / replicative senescence / positive regulation of protein kinase activity / response to hyperoxia / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / animal organ regeneration / mismatch repair / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / error-prone translesion synthesis / translesion synthesis / Cyclin E associated events during G1/S transition / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of B cell proliferation / keratinocyte differentiation / : / regulation of G2/M transition of mitotic cell cycle / protein sequestering activity / Signaling by FLT3 fusion proteins / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to amino acid starvation / intrinsic apoptotic signaling pathway / cyclin binding / negative regulation of protein phosphorylation / positive regulation of DNA replication / negative regulation of protein binding / molecular function activator activity / cellular response to ionizing radiation / wound healing / DNA Damage/Telomere Stress Induced Senescence / negative regulation of cell growth / response to toxic substance / cellular response to gamma radiation / SCF(Skp2)-mediated degradation of p27/p21 / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / protein import into nucleus / The role of GTSE1 in G2/M progression after G2 checkpoint / Cyclin D associated events in G1 / positive regulation of reactive oxygen species metabolic process / KEAP1-NFE2L2 pathway / cellular senescence / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / Neddylation / heart development / cellular response to heat / fibroblast proliferation / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / in utero embryonic development / Ras protein signal transduction / nuclear body / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression
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
Cyclin-dependent kinase inhibitor 1 / Proliferating cell nuclear antigen 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStrzalka, W. / Oyama, T. / Tori, K. / Morikawa, K.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment
Authors: Strzalka, W. / Oyama, T. / Tori, K. / Morikawa, K.
History
DepositionNov 21, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen 2
B: Proliferating cell nuclear antigen 2
C: Proliferating cell nuclear antigen 2
D: Proliferating cell nuclear antigen 2
E: Proliferating cell nuclear antigen 2
F: Proliferating cell nuclear antigen 2
G: Proliferating cell nuclear antigen 2
H: Proliferating cell nuclear antigen 2
I: Cyclin-dependent kinase inhibitor 1
J: Cyclin-dependent kinase inhibitor 1
K: Cyclin-dependent kinase inhibitor 1
L: Cyclin-dependent kinase inhibitor 1
M: Cyclin-dependent kinase inhibitor 1
N: Cyclin-dependent kinase inhibitor 1
O: Cyclin-dependent kinase inhibitor 1
P: Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,58323
Polymers264,91116
Non-polymers6727
Water2,936163
1
A: Proliferating cell nuclear antigen 2
B: Proliferating cell nuclear antigen 2
C: Proliferating cell nuclear antigen 2
I: Cyclin-dependent kinase inhibitor 1
J: Cyclin-dependent kinase inhibitor 1
K: Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6309
Polymers99,3426
Non-polymers2883
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-89 kcal/mol
Surface area34170 Å2
MethodPISA
2
D: Proliferating cell nuclear antigen 2
E: Proliferating cell nuclear antigen 2
F: Proliferating cell nuclear antigen 2
L: Cyclin-dependent kinase inhibitor 1
M: Cyclin-dependent kinase inhibitor 1
N: Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6309
Polymers99,3426
Non-polymers2883
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-94 kcal/mol
Surface area34110 Å2
MethodPISA
3
G: Proliferating cell nuclear antigen 2
O: Cyclin-dependent kinase inhibitor 1

G: Proliferating cell nuclear antigen 2
O: Cyclin-dependent kinase inhibitor 1

G: Proliferating cell nuclear antigen 2
O: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)99,3426
Polymers99,3426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area7890 Å2
ΔGint-50 kcal/mol
Surface area34690 Å2
MethodPISA
4
H: Proliferating cell nuclear antigen 2
P: Cyclin-dependent kinase inhibitor 1
hetero molecules

H: Proliferating cell nuclear antigen 2
P: Cyclin-dependent kinase inhibitor 1
hetero molecules

H: Proliferating cell nuclear antigen 2
P: Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6309
Polymers99,3426
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area8820 Å2
ΔGint-91 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.693, 223.693, 200.876
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Proliferating cell nuclear antigen 2 / PCNA 2


Mass: 30334.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZW35
#2: Protein/peptide
Cyclin-dependent kinase inhibitor 1 / p21 / CDK-interacting protein 1 / Melanoma differentiation-associated protein 6 / MDA-6


Mass: 2779.233 Da / Num. of mol.: 8 / Fragment: UNP residues 139-160 / Source method: obtained synthetically / Details: A synthetic fragment 139-160 of the human p21/WAF1 / References: UniProt: P38936
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM citric acid, 1.8M ammonium salfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 13, 2008
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 129598 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 45.1 Å2 / Rsym value: 0.047
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.184 / Num. unique all: 129598 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXC

1axc


Resolution: 2.5→36.69 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 211911.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 6499 5 %RANDOM
Rwork0.234 ---
obs0.234 128983 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2552 Å2 / ksol: 0.353001 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å27.01 Å20 Å2
2--3.27 Å20 Å2
3----6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16392 0 35 163 16590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 1090 5.1 %
Rwork0.286 20184 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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