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- PDB-5mlw: Crystal structure of human PCNA in complex with ZRANB3 APIM motif... -

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Basic information

Entry
Database: PDB / ID: 5mlw
TitleCrystal structure of human PCNA in complex with ZRANB3 APIM motif peptide
Components
  • APIM motif peptide
  • Proliferating cell nuclear antigen
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: 2.45 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: APIM motif peptide
C: Proliferating cell nuclear antigen
D: APIM motif peptide
E: Proliferating cell nuclear antigen
F: APIM motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,85913
Polymers90,1876
Non-polymers6727
Water1,72996
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)87,06010
Polymers86,3873
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APIM motif peptide


Theoretical massNumber of molelcules
Total (without water)1,2671
Polymers1,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: APIM motif peptide


Theoretical massNumber of molelcules
Total (without water)1,2671
Polymers1,2671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: APIM motif peptide


Theoretical massNumber of molelcules
Total (without water)1,2671
Polymers1,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.631, 84.631, 201.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14C
24E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA1 - 2551 - 255
21METMETILEILECC1 - 2551 - 255
12METMETILEILEAA1 - 2551 - 255
22METMETILEILEEE1 - 2551 - 255
13GLYGLYLYSLYSBB1069 - 10791 - 11
23GLYGLYLYSLYSDD1069 - 10791 - 11
14METMETILEILECC1 - 2551 - 255
24METMETILEILEEE1 - 2551 - 255

NCS ensembles :
ID
1
2
3
4

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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 APIM motif peptide


Mass: 1266.510 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5FWF4*PLUS
#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.: 96 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM lithium sulfate + 30% (w/v) polyvinylpyrrolidone + 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2822 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.45→73.29 Å / Num. obs: 31686 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.1
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.297 / Mean I/σ(I) obs: 2 / CC1/2: 0.565 / % 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: 2.45→73.29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 25.41 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.645 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1605 5.1 %RANDOM
Rwork0.22093 ---
obs0.22308 30026 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.671 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å21.22 Å2-0 Å2
2--2.44 Å20 Å2
3----7.92 Å2
Refinement stepCycle: 1 / Resolution: 2.45→73.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 35 96 6186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196346
X-RAY DIFFRACTIONr_bond_other_d0.0050.026159
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9878605
X-RAY DIFFRACTIONr_angle_other_deg0.995314257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3625830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.31925.58276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.096151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1671531
X-RAY DIFFRACTIONr_chiral_restr0.0880.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027129
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021312
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_it3.4912.5613198
X-RAY DIFFRACTIONr_mcbond_other3.4892.5593197
X-RAY DIFFRACTIONr_mcangle_it5.7113.8053996
X-RAY DIFFRACTIONr_mcangle_other5.7123.8073997
X-RAY DIFFRACTIONr_scbond_it3.9523.0493148
X-RAY DIFFRACTIONr_scbond_other3.6272.9943121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9444.3054543
X-RAY DIFFRACTIONr_long_range_B_refined10.59919.2946509
X-RAY DIFFRACTIONr_long_range_B_other10.52919.1876492
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A297420.07
12C297420.07
21A298100.09
22E298100.09
31B9740.17
32D9740.17
41C294860.09
42E294860.09
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 135 -
Rwork0.305 2178 -
obs--99.96 %
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)
11.76650.6758-0.3111.0243-0.22990.1834-0.01170.0426-0.24120.0313-0.0644-0.1170.0190.08880.0760.28970.05510.05130.14520.06480.8985-21.244-18.82419.632
20.84170.0177-0.08612.41470.04790.0239-0.01120.01110.02950.03980.09870.24840.02650.0131-0.08750.22180.04450.06210.24570.04370.8632-58.4335.75115.368
32.3587-0.6080.70091.3842-0.64720.40220.3931-0.2362-0.0279-0.0929-0.3199-0.08370.10620.0407-0.07320.1007-0.10840.09720.44390.01110.8696-18.67725.57516.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION1B1069 - 1079
3X-RAY DIFFRACTION2C1 - 255
4X-RAY DIFFRACTION2D1069 - 1079
5X-RAY DIFFRACTION3E1 - 256
6X-RAY DIFFRACTION3F1069 - 1078

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