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- PDB-3p87: Structure of human PCNA bound to RNASEH2B PIP box peptide -

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Basic information

Entry
Database: PDB / ID: 3p87
TitleStructure of human PCNA bound to RNASEH2B PIP box peptide
Components
  • Proliferating cell nuclear antigen
  • Ribonuclease H2 subunit B
KeywordsHYDROLASE/DNA BINDING PROTEIN / DNA binding / DNA replication / DNA repair / sliding clamp / PCNA Peptide Interacting Peptide (PIP) motif / PIP-box motif / DNA clamp / processivity factor / RNase H2 / FEN-1 / Ligase / polymerases / helicases / nucleases / nucleus / HYDROLASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


ribonucleotide metabolic process / ribonuclease H2 complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina ...ribonucleotide metabolic process / ribonuclease H2 complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / 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 / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / regulation of DNA damage checkpoint / 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 / replisome / RNA catabolic process / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / regulation of G2/M transition of mitotic cell cycle / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / gene expression / heart development / fibroblast proliferation / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / nuclear body / negative regulation of gene expression / centrosome / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain / 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 / Ribonuclease H2 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsBubeck, D. / Reijns, M.A. / Graham, S.C. / Astell, K.R. / Jones, E.Y. / Jackson, A.P.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: PCNA directs type 2 RNase H activity on DNA replication and repair substrates.
Authors: Bubeck, D. / Reijns, M.A. / Graham, S.C. / Astell, K.R. / Jones, E.Y. / Jackson, A.P.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Structure summary
Revision 1.3Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
G: Ribonuclease H2 subunit B
B: Proliferating cell nuclear antigen
H: Ribonuclease H2 subunit B
C: Proliferating cell nuclear antigen
I: Ribonuclease H2 subunit B
D: Proliferating cell nuclear antigen
J: Ribonuclease H2 subunit B
E: Proliferating cell nuclear antigen
K: Ribonuclease H2 subunit B
F: Proliferating cell nuclear antigen
L: Ribonuclease H2 subunit B


Theoretical massNumber of molelcules
Total (without water)188,15312
Polymers188,15312
Non-polymers00
Water0
1
A: Proliferating cell nuclear antigen
G: Ribonuclease H2 subunit B
C: Proliferating cell nuclear antigen
I: Ribonuclease H2 subunit B
E: Proliferating cell nuclear antigen
K: Ribonuclease H2 subunit B


Theoretical massNumber of molelcules
Total (without water)94,0776
Polymers94,0776
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-51 kcal/mol
Surface area31670 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
H: Ribonuclease H2 subunit B
D: Proliferating cell nuclear antigen
J: Ribonuclease H2 subunit B
F: Proliferating cell nuclear antigen
L: Ribonuclease H2 subunit B


Theoretical massNumber of molelcules
Total (without water)94,0776
Polymers94,0776
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-52 kcal/mol
Surface area31650 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-113 kcal/mol
Surface area57610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.108, 81.788, 116.558
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28795.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12004
#2: Protein/peptide
Ribonuclease H2 subunit B / RNase H2 subunit B / Aicardi-Goutieres syndrome 2 protein / AGS2 / Deleted in lymphocytic leukemia ...RNase H2 subunit B / Aicardi-Goutieres syndrome 2 protein / AGS2 / Deleted in lymphocytic leukemia 8 / Ribonuclease HI subunit B


Mass: 2563.088 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 290-306 / Mutation: RNASEH2B:290-312 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. It correspond to residues 290-312 of RNASEH2B
Source: (synth.) Homo sapiens (human) / References: UniProt: Q5TBB1

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 3M NaCl, 0.1M citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.982 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 2.99→47.5 Å / Num. all: 31807 / Num. obs: 31807 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 68.32 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 8
Reflection shellResolution: 2.99→3.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2930 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXC

1axc


Resolution: 2.99→47.45 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9265 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1609 5.06 %RANDOM
Rwork0.2227 ---
obs0.2241 31807 --
Displacement parametersBiso mean: 72.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.8425 Å20 Å2-1.9268 Å2
2---1.4534 Å20 Å2
3----2.3891 Å2
Refine analyzeLuzzati coordinate error obs: 0.511 Å
Refinement stepCycle: LAST / Resolution: 2.99→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11486 0 0 0 11486
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.009116362
X-RAY DIFFRACTIONt_angle_deg1.09157262
X-RAY DIFFRACTIONt_dihedral_angle_d40122
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2502
X-RAY DIFFRACTIONt_gen_planes16835
X-RAY DIFFRACTIONt_it1163620
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion20.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion16175
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact129284
LS refinement shellResolution: 2.99→3.09 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2835 156 5.32 %
Rwork0.2576 2774 -
all0.2591 2930 -
obs-2930 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8149-0.08930.74222.79120.03412.72250.18190.2750.5478-0.1513-0.2259-0.1584-0.4618-0.14790.044-0.17270.12450.0652-0.01030.15520.0204-7.2478.6372-42.1719
22.2288-1.29960.513.63590.02861.33210.07880.3113-0.5414-0.2039-0.03110.5392-0.0194-0.2291-0.0476-0.2995-0.0049-0.0935-0.0230.04970.2364-47.8257-25.0907-38.5954
33.2344-1.36670.58342.92841.01480.81290.29970.5494-0.536-0.5465-0.26040.0794-0.0744-0.1936-0.0393-0.03030.08980.00210.0059-0.1497-0.1761-17.1595-32.0278-55.4218
41.17880.08830.95612.1204-0.60474.83980.1708-0.2090.50850.4130.01160.3296-0.5352-0.3995-0.1824-0.08990.03610.1489-0.1501-0.15110.0361-31.70779.1119-16.0513
53.28771.15630.4123.8002-0.07910.64170.1144-0.2896-0.54450.4893-0.2248-0.5301-0.0660.07170.1104-0.09740.0094-0.0808-0.10670.0672-0.00897.6776-26.1819-19.6502
62.76881.0370.74023.0819-0.78191.36220.2011-0.5447-0.53790.538-0.13540.2499-0.19380.0123-0.0656-0.0574-0.00040.1514-0.12870.152-0.0255-23.4007-32.2394-2.7956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 256
2X-RAY DIFFRACTION2{ B|* }B1 - 256
3X-RAY DIFFRACTION3{ C|* }C1 - 256
4X-RAY DIFFRACTION4{ D|* }D1 - 256
5X-RAY DIFFRACTION5{ E|* }E1 - 256
6X-RAY DIFFRACTION6{ F|* }F1 - 256

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