[English] 日本語
Yorodumi
- PDB-3l2p: Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Bet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l2p
TitleHuman DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States
Components
  • 5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3'
  • 5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3'
  • 5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3'
  • DNA ligase 3
KeywordsLIGASE/DNA / DNA ligase / DNA repair / ATP-binding / Cell cycle / Cell division / DNA damage / DNA recombination / DNA replication / Ligase / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Zinc-finger / LIGASE-DNA complex
Function / homology
Function and homology information


DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / double-strand break repair via alternative nonhomologous end joining ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / double-strand break repair via alternative nonhomologous end joining / mitochondrial DNA repair / Resolution of AP sites via the single-nucleotide replacement pathway / DNA biosynthetic process / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / mitochondrion organization / Gap-filling DNA repair synthesis and ligation in GG-NER / double-strand break repair via homologous recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / cell cycle / cell division / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / Dna Ligase; domain 1 - #70 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / DNA ligase/mRNA capping enzyme / 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. / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Zinc finger, PARP-type / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsCotner-Gohara, E.A. / Kim, I.K. / Hammel, M. / Tainer, J.A. / Tomkinson, A. / Ellenberger, T.
CitationJournal: Biochemistry / Year: 2010
Title: Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States.
Authors: Cotner-Gohara, E. / Kim, I.K. / Hammel, M. / Tainer, J.A. / Tomkinson, A.E. / Ellenberger, T.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA ligase 3
B: 5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3'
C: 5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3'
D: 5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8745
Polymers78,5274
Non-polymers3471
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-51 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.149, 130.149, 150.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein DNA ligase 3 / / DNA ligase III / Polydeoxyribonucleotide synthase [ATP] 3


Mass: 65681.766 Da / Num. of mol.: 1 / Fragment: UNP residues 257-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49916, DNA ligase (ATP)
#2: DNA chain 5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3'


Mass: 3390.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#3: DNA chain 5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3'


Mass: 2771.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#4: DNA chain 5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3'


Mass: 6683.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6
Details: 1.8 M ammonium sulfate, 0.1M sodium acetate pH 5.6, VAPOR DIFFUSION, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2006
Details: Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry
RadiationMonochromator: Cryo-Cooled Si(111) double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→49.21 Å / Num. obs: 25407 / Redundancy: 12.9 % / Rsym value: 0.057 / Net I/σ(I): 25
Reflection shellResolution: 3→3.076 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.25 / Rsym value: 0.602 / % possible all: 73.13

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→49.21 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.89 / SU B: 34.042 / SU ML: 0.303 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.806 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27131 1287 5.1 %RANDOM
Rwork0.23325 ---
obs0.23511 24119 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 855 22 0 5022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.842.1827206
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5724.595185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.96615747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9621523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213598
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_it0.5161.52664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01424268
X-RAY DIFFRACTIONr_scbond_it1.67332536
X-RAY DIFFRACTIONr_scangle_it2.6824.52938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 77 -
Rwork0.308 1331 -
obs--73.1 %
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)
14.1114-0.3772-0.14932.41930.01562.2843-0.13770.2796-0.5908-0.3668-0.0013-0.2880.50680.42520.1390.25510.07180.00640.25820.01110.313228.9187.68354.488
23.4009-0.1284-0.46782.1615-0.11983.2157-0.02870.14610.4297-0.25590.02760.2916-0.5717-0.46080.0010.16430.0938-0.11330.18280.04280.30685.30733.63160.501
32.4553-0.10820.96310.2373-0.46163.754-0.070.89950.2828-0.3937-0.02250.0494-0.35530.20240.09261.11470.0283-0.06760.84140.2340.393119.35633.50629.609
41.3831-0.0835-0.08621.7507-0.12691.6315-0.08460.63760.2084-0.6722-0.00580.19060.08020.09560.09050.2686-0.0536-0.08360.38350.05650.361220.46723.80545.675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A159 - 390
2X-RAY DIFFRACTION2A391 - 590
3X-RAY DIFFRACTION3A591 - 745
4X-RAY DIFFRACTION4B1 - 11
5X-RAY DIFFRACTION4C12 - 20
6X-RAY DIFFRACTION4D23 - 42
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2amp.paramp.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top

+
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