[English] 日本語
Yorodumi
- PDB-4fyd: Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fyd
TitleCrystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
Components
  • DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
  • DNA polymerase alpha catalytic subunit A
  • DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA replication / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / H3-H4 histone complex chaperone activity / DNA replication initiation / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / H3-H4 histone complex chaperone activity / DNA replication initiation / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / lagging strand elongation / mitotic DNA replication initiation / DNA synthesis involved in DNA repair / leading strand elongation / DNA replication origin binding / DNA replication initiation / replication fork / double-strand break repair / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / chromatin binding / mitochondrion / zinc ion binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / B family DNA polymerase, thumb domain / 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 family B, thumb domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Alpha-Beta Plaits - #2820 / B family DNA polymerase, thumb domain / 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 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 / Topoisomerase I; Chain A, domain 4 / 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-like superfamily/Ribonuclease H / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA polymerase alpha catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPerera, R.L. / Pellegrini, L.
CitationJournal: eLife / Year: 2013
Title: Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha
Authors: Perera, R.L. / Torella, R. / Klinge, S. / Kilkenny, M.L. / Maman, J.D. / Pellegrini, L.
History
DepositionJul 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase alpha catalytic subunit A
B: DNA polymerase alpha catalytic subunit A
C: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
D: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
E: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
F: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,9328
Polymers229,9186
Non-polymers1,0142
Water00
1
A: DNA polymerase alpha catalytic subunit A
C: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
E: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4664
Polymers114,9593
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-26 kcal/mol
Surface area40620 Å2
MethodPISA
2
B: DNA polymerase alpha catalytic subunit A
D: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
F: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4664
Polymers114,9593
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-27 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.689, 145.686, 197.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA polymerase alpha catalytic subunit A


Mass: 103401.703 Da / Num. of mol.: 2 / Fragment: Polymerase domain, UNP residues 349-1258 / Mutation: R508A, N509A, D998N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC17, N2181, POL1, YNL102W / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 / References: UniProt: P13382, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')


Mass: 7627.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis
#3: DNA/RNA hybrid DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')


Mass: 3929.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis
#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.2M MgAc2, 10% PEG8000, microbatch, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→49.39 Å / Num. all: 59154 / Num. obs: 59154 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 97.34 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10.8
Reflection shellResolution: 3.1→3.26 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8380 / Rsym value: 0.974 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1078)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FVM

4fvm


Resolution: 3.1→48.801 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.08 / Stereochemistry target values: ML
Details: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. THE STRUCTURE WAS REFINED WITH RIDING HYDROGENS. THE HYDROGENS OF THE LAST REFINEMENT RUN ARE INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 5699 5.08 %Random
Rwork0.2098 ---
obs0.2116 59154 99.21 %-
all-59154 --
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13530 1152 62 0 14744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315128
X-RAY DIFFRACTIONf_angle_d0.65220714
X-RAY DIFFRACTIONf_dihedral_angle_d15.435910
X-RAY DIFFRACTIONf_chiral_restr0.0392364
X-RAY DIFFRACTIONf_plane_restr0.0032464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13220.40811990.38493358X-RAY DIFFRACTION95
3.1322-3.1690.40151850.35883561X-RAY DIFFRACTION99
3.169-3.20770.3711830.33353576X-RAY DIFFRACTION100
3.2077-3.24830.34722210.3253504X-RAY DIFFRACTION99
3.2483-3.2910.30741960.30473587X-RAY DIFFRACTION100
3.291-3.33610.33051800.29193519X-RAY DIFFRACTION99
3.3361-3.38370.33731870.27363635X-RAY DIFFRACTION99
3.3837-3.43420.32371690.27763491X-RAY DIFFRACTION100
3.4342-3.48790.27961780.26383604X-RAY DIFFRACTION99
3.4879-3.5450.34662340.25083556X-RAY DIFFRACTION99
3.545-3.60610.29151680.24933571X-RAY DIFFRACTION100
3.6061-3.67170.26942160.2283502X-RAY DIFFRACTION99
3.6717-3.74230.25652050.2323565X-RAY DIFFRACTION99
3.7423-3.81870.30092000.23923534X-RAY DIFFRACTION99
3.8187-3.90170.35171610.22333602X-RAY DIFFRACTION99
3.9017-3.99240.26051790.21223553X-RAY DIFFRACTION99
3.9924-4.09220.2551910.20663586X-RAY DIFFRACTION100
4.0922-4.20280.24692040.19753539X-RAY DIFFRACTION99
4.2028-4.32630.2651960.18843514X-RAY DIFFRACTION99
4.3263-4.46590.20552260.18293564X-RAY DIFFRACTION100
4.4659-4.62540.23391840.17443575X-RAY DIFFRACTION100
4.6254-4.81040.19551990.16923565X-RAY DIFFRACTION99
4.8104-5.02920.20691780.17533571X-RAY DIFFRACTION100
5.0292-5.2940.21672010.19323534X-RAY DIFFRACTION100
5.294-5.62520.21011740.18963604X-RAY DIFFRACTION100
5.6252-6.05880.26442080.20683546X-RAY DIFFRACTION100
6.0588-6.66720.25671780.20963563X-RAY DIFFRACTION100
6.6672-7.62880.20011710.20473586X-RAY DIFFRACTION99
7.6288-9.59950.22431790.17353497X-RAY DIFFRACTION98
9.5995-48.80690.1781490.18943496X-RAY DIFFRACTION97

+
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://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