[English] 日本語
Yorodumi
- PDB-4y97: Crystal Structure of human Pol alpha B-subunit in complex with C-... -

+
Open data


ID or keywords:

Loading...

-
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 / alpha DNA polymerase:primase complex / regulation of type I interferon production / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation ...DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / regulation of type I interferon production / Polymerase switching / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / leading strand elongation / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / nuclear matrix / double-strand break repair via nonhomologous end joining / protein import into nucleus / nuclear envelope / single-stranded DNA binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / chromatin binding / chromatin / nucleolus / protein kinase binding / 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 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 ...DNA Polymerase alpha, zinc finger / Hypothetical protein af0941 / DNA polymerase alpha, subunit B, N-terminal domain superfamily / 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, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more