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- PDB-5mlo: Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide -

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Basic information

Entry
Database: PDB / ID: 5mlo
TitleCrystal structure of human PCNA in complex with ZRANB3 PIP box peptide
Components
  • Proliferating cell nuclear antigen
  • ZRANB3 PIP box peptide
KeywordsHYDROLASE / endonuclease / metalloprotein / PCNA / DNA-binding
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 / MutLalpha complex binding ...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 / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / 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 / 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 / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / K63-linked polyubiquitin modification-dependent protein binding / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / mismatch repair / response to UV / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / positive regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / nuclear estrogen receptor binding / DNA endonuclease activity / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / helicase activity / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / nuclear body / DNA repair / DNA damage response / centrosome / chromatin binding / chromatin / protein-containing complex binding / 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 / Zn-finger in Ran binding protein and others / HNH nuclease / 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: 1.96 Å
AuthorsAriza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK16304 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the function of ZRANB3 in replication stress response.
Authors: Sebesta, M. / Cooper, C.D.O. / Ariza, A. / Carnie, C.J. / Ahel, D.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: ZRANB3 PIP box peptide
C: Proliferating cell nuclear antigen
D: ZRANB3 PIP box peptide
E: Proliferating cell nuclear antigen
F: ZRANB3 PIP box peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,15610
Polymers92,0646
Non-polymers924
Water6,936385
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4797
Polymers86,3873
Non-polymers924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-44 kcal/mol
Surface area34730 Å2
MethodPISA
2
B: ZRANB3 PIP box peptide


  • defined by software
  • 1.89 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,8921
Polymers1,8921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1470 Å2
MethodPISA
3
D: ZRANB3 PIP box peptide


Theoretical massNumber of molelcules
Total (without water)1,8921
Polymers1,8921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1560 Å2
MethodPISA
4
F: ZRANB3 PIP box peptide


  • defined by software
  • 1.89 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,8921
Polymers1,8921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.136, 86.802, 156.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 255 / Label seq-ID: 1 - 255

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12AA
22EE
13CC
23EE

NCS ensembles :
ID
1
2
3

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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 PIP box peptide


Mass: 1892.117 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5FWF4*PLUS
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM NaCl + 8% (v/v) DMSO + 31% pentaerythitol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.1402 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1402 Å / Relative weight: 1
ReflectionResolution: 1.96→78.34 Å / Num. obs: 67566 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.2
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 13 % / Rmerge(I) obs: 1.763 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.566 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYM

1vym


Resolution: 1.96→78.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.139 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25933 3325 4.9 %RANDOM
Rwork0.21129 ---
obs0.21363 64155 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.945 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2---2.22 Å20 Å2
3---2.49 Å2
Refinement stepCycle: 1 / Resolution: 1.96→78.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 4 385 6564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196419
X-RAY DIFFRACTIONr_bond_other_d0.0050.026206
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9778697
X-RAY DIFFRACTIONr_angle_other_deg1.091314366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.64725.433289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.252151207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8181533
X-RAY DIFFRACTIONr_chiral_restr0.0970.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027273
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021356
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_it2.4522.8393235
X-RAY DIFFRACTIONr_mcbond_other2.452.8373234
X-RAY DIFFRACTIONr_mcangle_it3.9044.2344049
X-RAY DIFFRACTIONr_mcangle_other3.9044.2364050
X-RAY DIFFRACTIONr_scbond_it2.8553.2963184
X-RAY DIFFRACTIONr_scbond_other2.8553.2973185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6174.7994629
X-RAY DIFFRACTIONr_long_range_B_refined8.49822.9216945
X-RAY DIFFRACTIONr_long_range_B_other8.40422.5816828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A29898
12C29898
21A30064
22E30064
31C30278
32E30278
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 234 -
Rwork0.314 4706 -
obs--99.82 %
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)
10.3059-0.5097-0.22590.95890.70981.3350.0362-0.0658-0.0808-0.10310.1050.0856-0.21010.2672-0.14120.1257-0.07620.04060.3595-0.05340.061975.3732.33129.009
20.6926-0.33560.33410.2023-0.0710.47050.02920.05370.03140.0047-0.0316-0.0070.05090.06330.00240.1277-0.0154-0.01290.23530.03390.026557.968-9.795-9.965
30.46470.16050.61530.4184-0.00020.9495-0.0791-0.10080.05040.10280.04420.0932-0.1501-0.16570.03490.16630.07050.05770.2529-0.00570.037841.04524.68611.793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION1B518 - 527
3X-RAY DIFFRACTION2C1 - 255
4X-RAY DIFFRACTION2D517 - 527
5X-RAY DIFFRACTION3E1 - 256
6X-RAY DIFFRACTION3F518 - 528

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