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- PDB-2izo: Structure of an Archaeal PCNA1-PCNA2-FEN1 Complex -

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Basic information

Entry
Database: PDB / ID: 2izo
TitleStructure of an Archaeal PCNA1-PCNA2-FEN1 Complex
Components
  • (DNA POLYMERASE SLIDING CLAMP ...DNA clamp) x 2
  • FLAP STRUCTURE-SPECIFIC ENDONUCLEASE
KeywordsHYDROLASE / DNA REPAIR / DNA-BINDING / ENDONUCLEASE / METAL-BINDING / EXCISION REPAIR / DNA REPLICATION / PCNA / FEN1 / NUCLEASE / MAGNESIUM
Function / homology
Function and homology information


flap endonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA replication ...flap endonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding
Similarity search - Function
Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 1 / DNA polymerase sliding clamp 2 / Flap endonuclease 1
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDore, A.S. / Kilkenny, M.L. / Roe, S.M. / Pearl, L.H.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structure of an Archaeal PCNA1-PCNA2-Fen1 Complex: Elucidating PCNA Subunit and Client Enzyme Specificity.
Authors: Dore, A.S. / Kilkenny, M.L. / Jones, S.A. / Oliver, A.W. / Roe, S.M. / Bell, S.D. / Pearl, L.H.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAP STRUCTURE-SPECIFIC ENDONUCLEASE
B: DNA POLYMERASE SLIDING CLAMP C
C: DNA POLYMERASE SLIDING CLAMP B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,83811
Polymers94,4793
Non-polymers3598
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.986, 99.774, 99.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FLAP STRUCTURE-SPECIFIC ENDONUCLEASE / FEN1


Mass: 39358.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET33B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q980U8, Hydrolases; Acting on ester bonds

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DNA POLYMERASE SLIDING CLAMP ... , 2 types, 2 molecules BC

#2: Protein DNA POLYMERASE SLIDING CLAMP C / PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG C / PCNA C / PCNA2


Mass: 27551.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97Z84
#3: Protein DNA POLYMERASE SLIDING CLAMP B / PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG B / PCNA B / PCNA1


Mass: 27569.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P57766

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Non-polymers , 3 types, 86 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A: ENDONUCLEASE THAT CLEAVES THE 5' OVERHANGING FLAP STRUCTURE THAT IS GENERATED BY ...CHAIN A: ENDONUCLEASE THAT CLEAVES THE 5' OVERHANGING FLAP STRUCTURE THAT IS GENERATED BY DISPLACEMENT SYNTHESIS WHEN DNA POLYMERASE ENCOUNTERS THE 5' END OF A DOWNSTREAM OKAZAKI FRAGMENT. CHAIN B: SLIDING CLAMP SUBUNIT. CHAIN C: SLIDING CLAMP SUBUNIT. RESPONSIBLE FOR TETHERING THE CATALYTIC SUBUNIT OF DNA POLYMERASE TO DNA DURING HIGH-SPEED REPLICATION.
Sequence detailsFIRST FOUR RESIDUES REMOVED FOR CONSTRUCT

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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: 2.45 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop
Details: PRIOR TO CRYSTALLISATION THE PCNA1-PCNA2-PCNA3 COMPLEX WAS MIXED WITH FEN1 AT AN EQUIMOLAR RATIO AND INCUBATED FOR 20 MIN AT 294 K. PCNA1-PCNA2-FEN1 CO-CRYSTALS WERE GROWN BY THE VAPOUR ...Details: PRIOR TO CRYSTALLISATION THE PCNA1-PCNA2-PCNA3 COMPLEX WAS MIXED WITH FEN1 AT AN EQUIMOLAR RATIO AND INCUBATED FOR 20 MIN AT 294 K. PCNA1-PCNA2-FEN1 CO-CRYSTALS WERE GROWN BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS. PCNA3 WAS NOT PRESENT IN THE CRYSTAL LATTICE. DROPS WERE PREPARED BY MIXING 100 MM PROTEIN COMPLEX IN 20 MM TRIS-HCL PH 8.0, 200 MM NACL, 5 MM MGCL2, 2 MM DTT BUFFER SOLUTION WITH EQUAL VOLUMES OF 0.1M ACETATE PH 4.8, 8% PEG 8,000, 220 MM ZNOAC2 AND 30 MM GLYCYL-GLYCYL-GLYCINE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 23534 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 71.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1B43 FOR FEN1 AND 1VYJ FOR PCNA1 AND PCNA2

1b43

1vyj


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.848 / SU B: 40.663 / SU ML: 0.388 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1088 5.1 %RANDOM
Rwork0.25 ---
obs0.253 20108 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2---4.11 Å20 Å2
3---3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 0 8 78 5811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225813
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9777880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93824.502231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2615979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1991530
X-RAY DIFFRACTIONr_chiral_restr0.0680.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024285
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22480
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23975
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3870.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1851.53849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.31926021
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.43632186
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7464.51859
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.398 88
Rwork0.358 1466
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)
10.7649-0.2350.0366.8948-0.25021.573-0.1935-0.21130.41790.95040.2129-1.2028-0.07670.3103-0.01940.00730.0564-0.2056-0.0268-0.1250.1457-15.4857-25.919611.5355
28.32260.62630.75183.39660.3641.09650.0881-0.5293-0.120.4171-0.04850.1844-0.292-0.0847-0.0396-0.1087-0.0346-0.0304-0.23530.0388-0.351810.687716.5624.494
37.5687-2.0781-0.82318.7906-0.16443.57450.03750.0411-0.2311-0.49670.0343-1.5886-0.16860.5661-0.0719-0.0993-0.10790.0238-0.13470.0020.053534.259910.9693-3.8089
40.4053-0.3208-1.55653.48732.072511.7220.02840.2344-0.3491-0.17320.0533-0.15851.00830.428-0.0817-0.00170.0428-0.0746-0.042-0.1547-0.0915-15.9978-10.4636-29.726
54.73111.3318-0.65665.28911.31683.4983-0.04870.078-0.1876-0.0782-0.03650.1030.0198-0.02270.0852-0.28130.0102-0.0427-0.2771-0.0174-0.2473-15.12966.8294-9.2417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 346
2X-RAY DIFFRACTION2B1 - 122
3X-RAY DIFFRACTION3B123 - 245
4X-RAY DIFFRACTION4C1 - 122
5X-RAY DIFFRACTION5C123 - 249

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