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- PDB-6bkf: Lysyl-adenylate form of human LigIV catalytic domain with bound D... -

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Basic information

Entry
Database: PDB / ID: 6bkf
TitleLysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
  • DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
  • DNA ligase 4
KeywordsLIGASE/DNA / DNA double-strand break repair / ligase / nonhomologous end-joining / LIGASE-DNA complex
Function / homology
Function and homology information


positive regulation of chromosome organization / DN2 thymocyte differentiation / DNA ligase IV complex / DNA ligase activity / T cell receptor V(D)J recombination / DNA ligase (ATP) / pro-B cell differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...positive regulation of chromosome organization / DN2 thymocyte differentiation / DNA ligase IV complex / DNA ligase activity / T cell receptor V(D)J recombination / DNA ligase (ATP) / pro-B cell differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / nucleotide-excision repair, DNA gap filling / single strand break repair / V(D)J recombination / isotype switching / double-strand break repair via classical nonhomologous end joining / positive regulation of neurogenesis / cellular response to lithium ion / DNA biosynthetic process / 2-LTR circle formation / AMP binding / ligase activity / somatic stem cell population maintenance / chromosome organization / response to X-ray / condensed chromosome / neurogenesis / stem cell proliferation / central nervous system development / cellular response to ionizing radiation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / base-excision repair / establishment of integrated proviral latency / double-strand break repair via nonhomologous end joining / positive regulation of fibroblast proliferation / T cell differentiation in thymus / double-strand break repair / neuron apoptotic process / fibroblast proliferation / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / cell population proliferation / cell division / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / DNA ligase/mRNA capping enzyme / 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 AMP-binding site. ...DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / DNA ligase/mRNA capping enzyme / 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DNA / DNA (> 10) / DNA ligase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsMoon, A.F. / Tumbale, P.P. / Schellenberg, M.J. / Williams, R.S. / Williams, J.G. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES 102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01 ES102765 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZES102488-09 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.
Authors: Kaminski, A.M. / Tumbale, P.P. / Schellenberg, M.J. / Williams, R.S. / Williams, J.G. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
History
DepositionNov 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ligase 4
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
T: DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0335
Polymers81,6864
Non-polymers3471
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-29 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.220, 119.220, 137.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA ligase 4 / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4


Mass: 70695.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pOPINS / Details (production host): N-terminal SUMO fusion tag / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) pLysS / References: UniProt: P49917, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules PTD

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


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 5486.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')


Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 76.5mM HEPES pH 7.5, 15.3% PEG 4K, 7.65% isopropanol, 13.5% glycerol, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 22, 2016 / Details: ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 15891 / % possible obs: 98 % / Redundancy: 5.2 % / CC1/2: 0.982 / Rpim(I) all: 0.039 / Rrim(I) all: 0.089 / Rsym value: 0.079 / Χ2: 0.887 / Net I/σ(I): 20
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 769 / CC1/2: 0.982 / Rpim(I) all: 0.178 / Rrim(I) all: 0.429 / Rsym value: 0.389 / Χ2: 0.52 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5O

3w5o


Resolution: 3.25→37.701 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3157 718 5.09 %random
Rwork0.2638 ---
obs0.2664 14106 87.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→37.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 732 22 3 4861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065035
X-RAY DIFFRACTIONf_angle_d0.9886996
X-RAY DIFFRACTIONf_dihedral_angle_d14.2332863
X-RAY DIFFRACTIONf_chiral_restr0.046804
X-RAY DIFFRACTIONf_plane_restr0.005768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2496-3.50030.311060.25171750X-RAY DIFFRACTION59
3.5003-3.85220.46641320.36942502X-RAY DIFFRACTION83
3.8522-4.40890.26991600.2632984X-RAY DIFFRACTION98
4.4089-5.5520.2741560.23553021X-RAY DIFFRACTION98
5.552-37.70320.30771640.2423131X-RAY DIFFRACTION97
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)
10.2372-0.36740.22681.62661.38053.2157-0.2543-0.6057-0.80630.5084-0.68310.07981.114-0.3923-2.95310.37520.27160.0311-0.02280.63410.567120.7895-51.02128.7667
21.2914-1.08680.17162.35030.24790.55580.13070.44161.0691-1.4557-0.4128-0.7649-0.6895-0.23361.02090.70230.3499-0.04730.45750.29230.337821.4025-19.1143-5.8805
30.62540.1065-0.09740.8425-0.41140.33270.3413-0.69070.07830.93550.1102-0.20320.2380.08380.88810.3595-0.3684-0.68960.3686-0.2875-0.187214.78854.426318.6085
40.0412-0.05740.06660.1196-0.14660.1743-0.08410.0250.02650.0188-0.0326-0.1023-0.0002-0.0857-0.03420.4423-0.2276-0.02111.62520.26660.713833.3378-31.188513.7959
50.386-0.2736-0.09810.4721-0.16120.5857-0.4938-0.2402-0.04520.3377-0.17440.3686-0.03960.1435-0.49810.51210.18090.06771.52950.06980.94823.052-29.524415.23
60.397-0.4943-0.24750.70110.26740.15770.0322-0.5905-0.04430.699-0.13350.6910.0302-0.4124-0.8660.4252-0.04980.19221.3970.27880.4794.1675-29.877614.8761
70.6478-0.24580.45180.092-0.16730.421-0.0522-0.4433-0.12970.3590.0341-0.47930.19110.3504-0.23520.27920.0041-0.36551.05830.21780.520733.1188-27.595517.1017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:237 )A9 - 237
2X-RAY DIFFRACTION2( CHAIN A AND RESID 238:458 )A238 - 458
3X-RAY DIFFRACTION3( CHAIN A AND RESID 459:603 )A459 - 603
4X-RAY DIFFRACTION4( CHAIN T AND RESID 1:7 )T1 - 7
5X-RAY DIFFRACTION5( CHAIN T AND RESID 8:18 )T8 - 18
6X-RAY DIFFRACTION6( CHAIN P AND RESID 1:11 )P1 - 11
7X-RAY DIFFRACTION7( CHAIN D AND RESID 2:8 )D2 - 8

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