[English] 日本語
Yorodumi
- PDB-5l1j: Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l1j
TitleCrystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite O6-Methyl-2'-deoxyguanosine
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(*CP*AP*TP*(6OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTransferase/DNA / Catalytic Domain / DNA Damage / DNA Polymerase / Lesion bypass / O6-Methyl-2'-deoxyguanosine / Y-family polymerase / translesion DNA synthesis (TLS) / DNA Binding protein. / Transferase-DNA complex
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / DNA repair / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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 ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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-1FZ / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPatra, A. / Egli, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES010375 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES010546 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA160032 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta.
Authors: Patra, A. / Zhang, Q. / Guengerich, F.P. / Egli, M.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.conn_type_id / _struct_conn.id / _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_conn_type.id
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase eta
T: DNA (5'-D(*CP*AP*TP*(6OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3437
Polymers54,7213
Non-polymers6224
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-39 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.004, 99.004, 81.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 48617.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*CP*AP*TP*(6OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3676.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Non-polymers , 4 types, 414 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1FZ / 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine


Mass: 481.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N3O13P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES pH 5.5, 5mM Magnesium chloride, 16% PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 33771 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 27.375
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.548 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3N

4o3n


Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.723 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20166 1715 5.1 %RANDOM
Rwork0.15857 ---
obs0.1608 32023 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å2-0 Å2
2---0.16 Å20 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 390 37 410 4203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0184002
X-RAY DIFFRACTIONr_bond_other_d0.0020.023693
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.8865511
X-RAY DIFFRACTIONr_angle_other_deg1.13238532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43523.924158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96315662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4041530
X-RAY DIFFRACTIONr_chiral_restr0.1150.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024241
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02899
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_it3.0123.0351753
X-RAY DIFFRACTIONr_mcbond_other3.0133.0341752
X-RAY DIFFRACTIONr_mcangle_it4.2284.5232197
X-RAY DIFFRACTIONr_mcangle_other4.2274.5242198
X-RAY DIFFRACTIONr_scbond_it3.7693.5322249
X-RAY DIFFRACTIONr_scbond_other3.7683.5352243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5415.1653300
X-RAY DIFFRACTIONr_long_range_B_refined8.15258.1117209
X-RAY DIFFRACTIONr_long_range_B_other8.01757.73516832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 143 -
Rwork0.211 2347 -
obs--100 %

+
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