[English] 日本語
Yorodumi
- PDB-5kt3: Teranry complex of human DNA polymerase iota(26-445) inserting dC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kt3
TitleTeranry complex of human DNA polymerase iota(26-445) inserting dCMPNPP opposite template G in the presence of Mn2+
Components
  • DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase iota
KeywordsTRANSFERASE / DNA polymerase / POLI / manganese
Function / homology
Function and homology information


translesion synthesis / error-prone translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck ...translesion synthesis / error-prone translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / 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 Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0KX / : / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å
AuthorsChoi, J.Y. / Patra, A. / Yeom, M. / Lee, Y.S. / Zhang, Q. / Egli, M. / Guengerich, F.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES010375 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES010546 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota.
Authors: Choi, J.Y. / Patra, A. / Yeom, M. / Lee, Y.S. / Zhang, Q. / Egli, M. / Guengerich, F.P.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
T: DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')
P: DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8187
Polymers52,1873
Non-polymers6314
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-42 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.829, 97.829, 202.887
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

-
DNA chain , 2 types, 2 molecules TP

#1: DNA chain DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')


Mass: 3051.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 2107.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase iota / Eta2 / RAD30 homolog B


Mass: 47027.344 Da / Num. of mol.: 1 / Fragment: UNP residues 26-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

-
Non-polymers , 3 types, 69 molecules

#4: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.64→44.06 Å / Num. obs: 17727 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 46.65 Å2 / Rmerge(I) obs: 0.124 / Net I/av σ(I): 31.8 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.64-2.6921.80.8290.9461100
2.69-2.7321.80.7840.9581100
2.73-2.7921.90.7040.9651100
2.79-2.8421.90.6240.9771100
2.84-2.9121.70.5160.9771100
2.91-2.9721.90.4260.9831100
2.97-3.0521.70.360.9881100
3.05-3.1321.80.2750.9931100
3.13-3.2221.70.2230.9961100
3.22-3.3321.60.1710.9971100
3.33-3.4421.60.1410.9981100
3.44-3.5821.50.1310.9981100
3.58-3.7521.50.110.9991100
3.75-3.9421.40.0990.9991100
3.94-4.1921.30.0910.9991100
4.19-4.5120.90.0920.9981100
4.51-4.9720.70.090.9991100
4.97-5.6920.50.0910.9991100
5.69-7.1620.20.0640.9991100
7.16-5017.90.0351199.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→44.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.248 904 5.12 %
Rwork0.2042 --
obs0.2065 17652 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.85 Å2 / Biso mean: 51.5588 Å2 / Biso min: 14.7 Å2
Refinement stepCycle: final / Resolution: 2.64→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 345 31 65 3375
Biso mean--34.74 41.12 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093390
X-RAY DIFFRACTIONf_angle_d1.0244661
X-RAY DIFFRACTIONf_chiral_restr0.056549
X-RAY DIFFRACTIONf_plane_restr0.007539
X-RAY DIFFRACTIONf_dihedral_angle_d17.5582023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6368-2.8020.29961400.225427072847
2.802-3.01830.30431360.244127372873
3.0183-3.32190.27041690.217227322901
3.3219-3.80240.25511350.201527782913
3.8024-4.78960.23161460.185528142960
4.7896-44.06610.22321780.200129803158

+
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