[English] 日本語
Yorodumi
- PDB-3iay: Ternary complex of DNA polymerase delta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iay
TitleTernary complex of DNA polymerase delta
Components
  • 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
  • 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
  • DNA polymerase delta catalytic subunit
KeywordsTRANSFERASE/DNA / DNA Polymerase / protein-DNA complex / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Metal-binding / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Zinc-finger / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity ...delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / DNA metabolic process / base-excision repair, gap-filling / replication fork / DNA-templated DNA replication / 4 iron, 4 sulfur cluster binding / DNA replication / molecular adaptor activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding / cytosol
Similarity search - Function
Helix Hairpins - #1540 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / B family DNA polymerase, thumb domain / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Topoisomerase I; Chain A, domain 4 / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B ...Helix Hairpins - #1540 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / B family DNA polymerase, thumb domain / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Topoisomerase I; Chain A, domain 4 / 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 / Helix Hairpins / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase delta catalytic subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsSwan, M.K. / Aggarwal, A.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta
Authors: Swan, M.K. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_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_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
P: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
T: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
A: DNA polymerase delta catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,83111
Polymers113,0463
Non-polymers7868
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-74 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.077, 85.948, 86.872
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA chain , 2 types, 2 molecules PT

#1: DNA chain 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'


Mass: 3502.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide synthesis
#2: DNA chain 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'


Mass: 5067.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide synthesis

-
Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase delta catalytic subunit / DNA polymerase III


Mass: 104476.148 Da / Num. of mol.: 1 / Fragment: UNP residues 67 to 985
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Pol3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P15436, DNA-directed DNA polymerase

-
Non-polymers , 4 types, 566 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG 4000, NaAc pH 5.5, 200mM CaAc., VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
1,2,3,41
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONNSLS X29A1
SYNCHROTRONNSLS X12B2
SYNCHROTRONAPS 17-ID3
4
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 13, 2007
ADSC QUANTUM 2102CCDAug 29, 2007
ADSC QUANTUM 3153CCDOct 13, 2007
ADSC QUANTUM 3154CCDNov 8, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3MADMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→41.52 Å / Num. all: 73557 / Num. obs: 69856 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 97.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2→41.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.879 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23589 3692 5 %RANDOM
Rwork0.19281 ---
obs0.19497 69856 98.25 %-
all-73557 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.037 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.5 Å2
2--0.56 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 569 41 558 8154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2272.05910786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95823.86329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.138151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1911549
X-RAY DIFFRACTIONr_chiral_restr0.0810.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215746
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_it0.5541.54438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03327197
X-RAY DIFFRACTIONr_scbond_it1.70833414
X-RAY DIFFRACTIONr_scangle_it2.6634.53583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 239 -
Rwork0.216 4983 -
obs--96.47 %
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)
11.23280.9729-0.39811.3079-0.51610.7275-0.02250.1234-0.0910.0165-0.0223-0.1337-0.01530.14060.0448-0.054-0.0260.00930.0217-0.0251-0.067934.288-5.9429.524
21.4092-0.3874-1.05762.05321.54225.2032-0.0707-0.0247-0.120.1410.1659-0.09050.41920.2776-0.0953-0.04370.04-0.0098-0.0573-0.0442-0.048922.3-29.16912.046
30.66190.2189-0.11461.0905-0.42580.88880.05460.09650.10750.15220.01930.1257-0.2408-0.0131-0.074-0.0057-0.00350.0584-0.0167-0.0125-0.101319.5939.1069.161
41.2836-0.7221-0.81981.39880.72771.3758-0.0362-0.1865-0.00680.07090.0918-0.1484-0.03320.2293-0.0557-0.0037-0.02190.0165-0.0053-0.0137-0.12429.254-6.51538.159
50.8384-0.3001-0.09681.29550.33980.9435-0.0262-0.1830.0510.150.0205-0.0415-0.10370.10690.00560.0293-0.04290.0179-0.0061-0.0214-0.1326-0.114.25747.841
60.4802-0.4222-0.06310.44230.16162.16340.01620.07740.05340.05360.020.0406-0.1557-0.0368-0.03630.0168-0.00440.0442-0.0561-0.0069-0.0733-16.62918.44721.854
70.43030.23550.84871.3377-0.76532.9249-0.0779-0.1256-0.02120.02470.23980.15370.047-0.1653-0.16180.03980.0190.03220.00490.0133-0.048-13.6970.08227.487
80.9731-0.39490.44030.9211-0.44651.4884-0.0831-0.0829-0.189-0.00280.08220.18990.1075-0.09210.001-0.0047-0.04690.0108-0.0462-0.0283-0.0555-10.535-2.69324.887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A96 - 171
2X-RAY DIFFRACTION2A172 - 241
3X-RAY DIFFRACTION3A242 - 577
4X-RAY DIFFRACTION4A578 - 711
5X-RAY DIFFRACTION5A712 - 838
6X-RAY DIFFRACTION6A839 - 985
7X-RAY DIFFRACTION7P2 - 12
8X-RAY DIFFRACTION8T1 - 16

+
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://pdbjlvh1.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