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- PDB-3wup: Crystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Doma... -

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Basic information

Entry
Database: PDB / ID: 3wup
TitleCrystal Structure of the Ubiquitin-Binding Zinc Finger (UBZ) Domain of the Human DNA Polymerase Eta
ComponentsDNA polymerase eta
KeywordsTRANSFERASE / Ubiquitin-binding zinc finger / Zinc finger / Ubiquitin and ubiquitin-binding domain
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / error-prone translesion synthesis / replication fork / regulation of DNA repair / translesion synthesis / Termination of translesion DNA synthesis / response to radiation / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / error-prone translesion synthesis / replication fork / regulation of DNA repair / translesion synthesis / Termination of translesion DNA synthesis / response to radiation / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSuzuki, N. / Wakatsuki, S. / Kawasaki, S.
CitationJournal: Febs J. / Year: 2016
Title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.
Authors: Suzuki, N. / Rohaim, A. / Kato, R. / Dikic, I. / Wakatsuki, S. / Kawasaki, M.
History
DepositionMay 1, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6155
Polymers4,3991
Non-polymers2164
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA polymerase eta
hetero molecules

A: DNA polymerase eta
hetero molecules

A: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,84515
Polymers13,1973
Non-polymers64812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area3150 Å2
ΔGint-62 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.188, 49.188, 49.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-702-

CL

21A-703-

NA

31A-814-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 4398.964 Da / Num. of mol.: 1
Fragment: UBIQUITIN-BINDING ZINC FINGER, UNP RESIDUES 630-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: PGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4.3M sodium chloride, 0.1M HEPES , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 5450 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / Num. unique all: 267 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→34.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.388 / SU ML: 0.049 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22554 245 4.5 %RANDOM
Rwork0.16865 ---
obs0.17116 5189 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.698 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms253 0 9 17 279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021266
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.969360
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.67426.42914
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9131542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022205
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_it1.4811.5156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7062253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3113110
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7414.5107
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: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 12 -
Rwork0.232 392 -
obs--99.75 %

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