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- PDB-4y97: Crystal Structure of human Pol alpha B-subunit in complex with C-... -

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Basic information

Entry
Database: PDB / ID: 4y97
TitleCrystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit
Components
  • DNA polymerase alpha catalytic subunit
  • DNA polymerase alpha subunit B
KeywordsTRANSFERASE / human DNA polymerase alpha
Function / homology
Function and homology information


DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / DNA replication, synthesis of primer / lagging strand elongation / Removal of the Flap Intermediate ...DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / DNA replication, synthesis of primer / lagging strand elongation / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / mitotic DNA replication initiation / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication / leading strand elongation / G1/S-Specific Transcription / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / double-strand break repair via nonhomologous end joining / nuclear matrix / protein import into nucleus / nuclear envelope / single-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / ciliary basal body / DNA repair / nucleotide binding / intracellular membrane-bounded organelle / chromatin binding / protein kinase binding / chromatin / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA Polymerase alpha, zinc finger / Hypothetical protein af0941 / DNA polymerase alpha, subunit B, N-terminal domain superfamily / : / DNA polymerase alpha subunit B, OB domain / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily ...DNA Polymerase alpha, zinc finger / Hypothetical protein af0941 / DNA polymerase alpha, subunit B, N-terminal domain superfamily / : / DNA polymerase alpha subunit B, OB domain / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit / DNA polymerase alpha subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSuwa, Y. / Gu, J. / Baranovskiy, A.G. / Babayeva, N.D. / Tahirov, T.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101167 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Human Pol alpha B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit.
Authors: Suwa, Y. / Gu, J. / Baranovskiy, A.G. / Babayeva, N.D. / Pavlov, Y.I. / Tahirov, T.H.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase alpha subunit B
B: DNA polymerase alpha catalytic subunit
C: DNA polymerase alpha subunit B
D: DNA polymerase alpha catalytic subunit
E: DNA polymerase alpha subunit B
F: DNA polymerase alpha catalytic subunit
G: DNA polymerase alpha subunit B
H: DNA polymerase alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,35116
Polymers348,8278
Non-polymers5238
Water3,639202
1
A: DNA polymerase alpha subunit B
B: DNA polymerase alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3384
Polymers87,2072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-18 kcal/mol
Surface area27500 Å2
MethodPISA
2
C: DNA polymerase alpha subunit B
D: DNA polymerase alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3384
Polymers87,2072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area27150 Å2
MethodPISA
3
E: DNA polymerase alpha subunit B
F: DNA polymerase alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3384
Polymers87,2072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-22 kcal/mol
Surface area27810 Å2
MethodPISA
4
G: DNA polymerase alpha subunit B
H: DNA polymerase alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3384
Polymers87,2072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-21 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.593, 137.135, 132.092
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA polymerase alpha subunit B / DNA polymerase alpha 70 kDa subunit


Mass: 66015.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLA2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q14181
#2: Protein
DNA polymerase alpha catalytic subunit / DNA polymerase alpha catalytic subunit p180


Mass: 21191.299 Da / Num. of mol.: 4 / Fragment: UNP residues 1265-1444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLA1, POLA / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta-2 / References: UniProt: P09884, DNA-directed DNA polymerase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.64 Å3/Da / Density % sol: 53.42 % / Description: elongated plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 116900 / % possible obs: 95 % / Observed criterion σ(I): -1 / Redundancy: 2.8 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.35
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.05 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FLO

3flo


Resolution: 2.51→47.68 Å / Rfactor Rfree error: 0.03 / Data cutoff high absF: 3140059.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 5894 5 %RANDOM
Rwork0.218 ---
obs0.218 116874 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.1168 Å2 / ksol: 0.324432 e/Å3
Displacement parametersBiso mean: 50.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å22.32 Å2
2---1.34 Å20 Å2
3---0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.66 Å
Refinement stepCycle: 1 / Resolution: 2.51→47.68 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 868 5.2 %
Rwork0.416 15819 -
obs--80.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1../TOPPAR/protein_rep.param../TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3../TOPPAR/water_rep.param../TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top
X-RAY DIFFRACTION5../TOPPAR/ion.paramCNS_TOPPAR/ion.top

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