[English] 日本語
Yorodumi
- PDB-7kr3: Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kr3
TitleHuman DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate
Components
  • DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3')
  • DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3')
  • DNA ligase 1
KeywordsLIGASE/DNA / DNA ligase / DNA replication / DNA repair / Replication / fidelity / LIGASE / LIGASE-DNA complex
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation ...Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / lagging strand elongation / DNA biosynthetic process / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mismatch repair / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA recombination / cell division / intracellular membrane-bounded organelle / DNA repair / mitochondrion / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. ...DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.778 Å
AuthorsTumbale, P.P. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nat Commun / Year: 2021
Title: High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication.
Authors: Williams, J.S. / Tumbale, P.P. / Arana, M.E. / Rana, J.A. / Williams, R.S. / Kunkel, T.A.
History
DepositionNov 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 ligase 1
B: DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3')
C: DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5996
Polymers83,1934
Non-polymers4062
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-54 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.681, 101.665, 115.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA ligase 1 / / DNA ligase I / Polydeoxyribonucleotide synthase [ATP] 1


Mass: 71916.227 Da / Num. of mol.: 1 / Mutation: E346A, E592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18858, DNA ligase (ATP)

-
DNA chain , 3 types, 3 molecules BCD

#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*TP*CP*TP*GP*CP*CP*CP*C)-3')


Mass: 3598.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*CP*TP*GP*C)-3')


Mass: 2088.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: DNA chain DNA (5'-D(*GP*CP*AP*GP*AP*AP*TP*GP*GP*GP*CP*AP*GP*AP*CP*AP*TP*T)-3')


Mass: 5589.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

-
Non-polymers , 3 types, 19 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 150 mM lithium acetate, 10% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.778→50 Å / Num. obs: 21959 / % possible obs: 97.5 % / Redundancy: 6 % / Rsym value: 0.066 / Net I/σ(I): 21.53
Reflection shellResolution: 2.778→2.85 Å / Num. unique obs: 1097 / CC1/2: 0.924 / Rsym value: 0.422

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P09

6p09


Resolution: 2.778→36.84 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1998 9.14 %
Rwork0.1932 19868 -
obs0.1974 21866 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.2 Å2 / Biso mean: 87.7862 Å2 / Biso min: 43.84 Å2
Refinement stepCycle: final / Resolution: 2.778→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 750 42 17 5738
Biso mean--72.93 73.09 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025901
X-RAY DIFFRACTIONf_angle_d0.5088149
X-RAY DIFFRACTIONf_chiral_restr0.035916
X-RAY DIFFRACTIONf_plane_restr0.003928
X-RAY DIFFRACTIONf_dihedral_angle_d16.5943463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7782-2.84760.35991400.3101140196
2.8476-2.92460.34991410.2951138898
2.9246-3.01060.38721410.2867141299
3.0106-3.10770.30781450.2682143599
3.1077-3.21880.33361430.2361140898
3.2188-3.34760.28021410.2154139497
3.3476-3.49980.27281440.2047143999
3.4998-3.68410.28031440.205142899
3.6841-3.91470.2371430.1956142498
3.9147-4.21660.21761410.1811140797
4.2166-4.64020.20041420.1565141395
4.6402-5.30990.21111430.1626142496
5.3099-6.68340.2451470.1931147098
6.6834-36.840.18351430.1672142590
Refinement TLS params.Method: refined / Origin x: 19.7658 Å / Origin y: -4.302 Å / Origin z: -10.6125 Å
111213212223313233
T0.5948 Å20.0428 Å20.0061 Å2-0.7289 Å20.02 Å2--0.3051 Å2
L1.3036 °20.2297 °2-0.187 °2-1.3255 °20.0903 °2--1.3974 °2
S0.1038 Å °-0.1219 Å °0.0779 Å °0.0507 Å °-0.0907 Å °0.0574 Å °-0.0653 Å °0.1547 Å °-0.0188 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA262 - 901
2X-RAY DIFFRACTION1allB3 - 14
3X-RAY DIFFRACTION1allC1 - 7
4X-RAY DIFFRACTION1allD9 - 26
5X-RAY DIFFRACTION1allD101
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allS2 - 49

+
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