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- PDB-5yd8: Crystal structure of human PCNA in complex with APIM of human ZRANB3 -

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Basic information

Entry
Database: PDB / ID: 5yd8
TitleCrystal structure of human PCNA in complex with APIM of human ZRANB3
Components
  • Proliferating cell nuclear antigen
  • ZRANB3
KeywordsDNA BINDING PROTEIN / Complex
Function / homology
Function and homology information


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 / nuclear lamina / replication fork reversal / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis ...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 / nuclear lamina / replication fork reversal / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / ATP-dependent DNA/DNA annealing activity / replisome / K63-linked polyubiquitin modification-dependent protein binding / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / response to cadmium ion / response to UV / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / male germ cell nucleus / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / Translesion synthesis by POLI / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / DNA endonuclease activity / positive regulation of DNA replication / nuclear estrogen receptor binding / helicase activity / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / nuclear body / DNA repair / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
HNH endonuclease / HNH endonuclease / HNH nucleases / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Zinc finger domain / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. ...HNH endonuclease / HNH endonuclease / HNH nucleases / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Zinc finger domain / 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 / HNH nuclease / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / DNA annealing helicase and endonuclease ZRANB3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHashimoto, H. / Tagata, R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2018
Title: Structure of proliferating cell nuclear antigen (PCNA) bound to an APIM peptide reveals the universality of PCNA interaction.
Authors: Hara, K. / Uchida, M. / Tagata, R. / Yokoyama, H. / Ishikawa, Y. / Hishiki, A. / Hashimoto, H.
History
DepositionSep 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: Proliferating cell nuclear antigen
X: Proliferating cell nuclear antigen
Z: Proliferating cell nuclear antigen
W: ZRANB3
U: ZRANB3
V: ZRANB3


Theoretical massNumber of molelcules
Total (without water)90,1876
Polymers90,1876
Non-polymers00
Water81145
1
Y: Proliferating cell nuclear antigen
V: ZRANB3


Theoretical massNumber of molelcules
Total (without water)30,0622
Polymers30,0622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-9 kcal/mol
Surface area12960 Å2
MethodPISA
2
X: Proliferating cell nuclear antigen
U: ZRANB3


Theoretical massNumber of molelcules
Total (without water)30,0622
Polymers30,0622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-10 kcal/mol
Surface area12870 Å2
MethodPISA
3
Z: Proliferating cell nuclear antigen
W: ZRANB3


Theoretical massNumber of molelcules
Total (without water)30,0622
Polymers30,0622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-11 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.678, 83.678, 194.928
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Protein/peptide ZRANB3 / Annealing helicase 2 / AH2 / Zinc finger Ran-binding domain-containing protein 3


Mass: 1266.510 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1069-1079 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q5FWF4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.38 Å / Num. obs: 40892 / % possible obs: 99 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.078 / Net I/av σ(I): 13.4 / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZVM

2zvm


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.777 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1771 5 %RANDOM
Rwork0.21864 ---
obs0.22088 33604 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 0 45 5933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195961
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9838037
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.33225.328244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.563151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0341527
X-RAY DIFFRACTIONr_chiral_restr0.0940.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214292
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3563.2473043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3514.8563781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6843.4592918
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.86544.1228291
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 118 -
Rwork0.303 2481 -
obs--99.88 %
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)
14.2671-2.5468-0.33762.55790.13840.3549-0.0053-0.0158-0.10430.12920.0338-0.02790.09150.0174-0.02850.1177-0.0699-0.03750.09290.02350.169627.9252-32.6701-51.5118
24.75552.05490.64182.54480.62821.2361-0.0015-0.00430.0876-0.0280.02790.0587-0.0583-0.1288-0.02640.01280.01880.01810.03420.02360.080724.514510.7028-48.5881
31.3677-0.2825-0.05846.0333-1.29410.96140.1022-0.02420.1906-0.0778-0.05350.028-0.12890.0336-0.04870.0401-0.0059-0.00340.1098-0.04430.164564.6638-8.0312-50.0439
411.223-1.69784.6925.64742.2963.6414-0.0159-0.2305-0.17520.59930.1567-0.13190.3116-0.0333-0.14080.20720.0142-0.05340.1968-0.01350.14475.3787-15.6338-36.5777
58.6052-0.2686-0.50523.98280.47331.7147-0.0746-0.370.05950.27210.02470.202-0.1803-0.20940.04990.220.02140.04920.2017-0.01710.165123.994223.9462-35.6458
614.11460.22799.20069.7006-7.530312.0797-0.3398-0.27260.0015-0.19680.46970.1458-0.0481-0.5585-0.12990.3802-0.02730.03320.34860.06860.325716.8844-40.5886-38.4725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Y1 - 254
2X-RAY DIFFRACTION2X1 - 255
3X-RAY DIFFRACTION3Z1 - 255
4X-RAY DIFFRACTION4W1070 - 1077
5X-RAY DIFFRACTION5U1069 - 1079
6X-RAY DIFFRACTION6V1071 - 1077

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