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- PDB-6bkg: Human LigIV catalytic domain with bound DNA-adenylate intermediat... -

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Basic information

Entry
Database: PDB / ID: 6bkg
TitleHuman LigIV catalytic domain with bound DNA-adenylate intermediate in closed 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*(AMP)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 / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / 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 / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / 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 / double-strand break repair via classical nonhomologous end joining / isotype switching / positive regulation of neurogenesis / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / ligase activity / somatic stem cell population maintenance / response to X-ray / chromosome organization / condensed chromosome / neurogenesis / central nervous system development / stem cell proliferation / response to gamma radiation / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / base-excision repair / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / 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 / intracellular membrane-bounded organelle / 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, 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 AMP-binding site. ...DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / 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 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: 2.402 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 2.0Jul 17, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1899
Polymers81,6864
Non-polymers5035
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-70 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.657, 102.747, 110.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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*(AMP)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 , 5 types, 117 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 78.2mM HEPES pH 7.5, 15.64% PEG4000, 7.82% isopropanol, 13.8% glycerol

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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: 2.4→50 Å / Num. obs: 32742 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.798 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Rsym value: 0.065 / Χ2: 0.928 / Net I/σ(I): 31.16
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.45 / Num. unique obs: 1598 / CC1/2: 0.798 / Rpim(I) all: 0.334 / Rrim(I) all: 0.911 / Rsym value: 0.846 / Χ2: 0.898 / % possible all: 100

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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: 2.402→39.2 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1626 4.98 %random
Rwork0.2014 ---
obs0.2036 32630 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 754 7 112 5498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035602
X-RAY DIFFRACTIONf_angle_d0.5857738
X-RAY DIFFRACTIONf_dihedral_angle_d13.7563253
X-RAY DIFFRACTIONf_chiral_restr0.04875
X-RAY DIFFRACTIONf_plane_restr0.004852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4019-2.47260.37241160.26782376X-RAY DIFFRACTION93
2.4726-2.55240.3261420.26592539X-RAY DIFFRACTION100
2.5524-2.64360.30091320.26862571X-RAY DIFFRACTION100
2.6436-2.74940.30211340.26042582X-RAY DIFFRACTION100
2.7494-2.87450.30081310.25732554X-RAY DIFFRACTION100
2.8745-3.0260.30251410.24712578X-RAY DIFFRACTION100
3.026-3.21550.26931310.21912598X-RAY DIFFRACTION100
3.2155-3.46360.22751440.19662559X-RAY DIFFRACTION100
3.4636-3.81190.2281290.18532629X-RAY DIFFRACTION100
3.8119-4.36290.22341410.16232613X-RAY DIFFRACTION100
4.3629-5.49430.18291350.16142645X-RAY DIFFRACTION100
5.4943-39.20510.22161500.18442760X-RAY DIFFRACTION100
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)
12.1503-0.59570.15992.3059-0.52342.1052-0.0145-0.2392-0.3110.03860.01640.50380.1234-0.18420.00510.2293-0.02280.02320.30960.03160.4475-34.3609-7.443319.1284
21.63270.4668-0.35263.32750.18010.9636-0.00740.0944-0.0572-0.02140.0702-0.20890.16790.119700.31060.0549-0.00260.28850.02020.3827-1.1071-19.408914.9608
32.64840.20120.66442.9065-0.31990.7560.07230.29630.5295-0.4383-0.1046-0.2585-0.0470.1372-0.00520.3336-0.01040.07430.33420.08980.347-5.218915.6928.5474
40.57030.4776-0.27451.746-1.85772.13530.4309-0.44460.06920.26490.65080.62371.2681-0.40430.24810.62640.0211-0.0560.46220.05180.2514-14.6503-0.956524.6276
50.30830.07040.15720.5773-0.44530.31530.07380.6709-0.0729-0.25110.2233-0.0126-0.3277-0.00780.00920.45090.0660.00980.5808-0.00190.2456-18.5597-1.6816-3.1554
61.1178-0.1906-0.0920.01230.04510.02030.18770.6339-0.7163-0.25320.09060.0477-0.47550.5710.00220.528-0.0161-0.05560.4954-0.03730.2535-18.1717-1.7941-1.3025
70.36920.01420.05220.40290.12910.61440.2576-0.61640.19530.61880.3204-0.20630.25470.18780.05280.4384-0.03720.02790.34150.02340.2155-10.98881.988923.9755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:237)
2X-RAY DIFFRACTION2(chain A and resid 238:458)
3X-RAY DIFFRACTION3(chain A and resid 459:616)
4X-RAY DIFFRACTION4(chain T and resid 1:7)
5X-RAY DIFFRACTION5(chain T and resid 8:18)
6X-RAY DIFFRACTION6(chain P and resid 1:11)
7X-RAY DIFFRACTION7(chain D and resid 2:8)

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