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- PDB-5iio: Crystal structure of the DNA polymerase lambda binary complex -

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Basic information

Entry
Database: PDB / ID: 5iio
TitleCrystal structure of the DNA polymerase lambda binary complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å
AuthorsBurak, M.J. / Guja, K.E. / Garcia-Diaz, M.
CitationJournal: Embo J. / Year: 2016
Title: A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG.
Authors: Burak, M.J. / Guja, K.E. / Hambardjieva, E. / Derkunt, B. / Garcia-Diaz, M.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
C: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
F: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
G: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
H: DNA (5'-D(P*GP*CP*CP*G)-3')
J: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
K: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
L: DNA (5'-D(P*GP*CP*CP*G)-3')
N: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
O: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
P: DNA (5'-D(P*GP*CP*CP*G)-3')
A: DNA polymerase lambda
E: DNA polymerase lambda
I: DNA polymerase lambda
M: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,09722
Polymers174,95916
Non-polymers1386
Water21,8521213
1
B: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
C: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7866
Polymers43,7404
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
G: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
H: DNA (5'-D(P*GP*CP*CP*G)-3')
E: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7635
Polymers43,7404
Non-polymers231
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
K: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
L: DNA (5'-D(P*GP*CP*CP*G)-3')
I: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7635
Polymers43,7404
Non-polymers231
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
N: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
O: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
P: DNA (5'-D(P*GP*CP*CP*G)-3')
M: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7866
Polymers43,7404
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.423, 98.980, 105.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 3 types, 12 molecules BFJNCGKODHLP

#1: DNA chain
DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')


Mass: 3406.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')


Mass: 1793.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 4 molecules AEIM

#4: Protein
DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 37348.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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Non-polymers , 2 types, 1219 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1213 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.08→45.09 Å / Num. obs: 118537 / % possible obs: 98.2 % / Redundancy: 6.9 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.08→45.086 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2351 2598 2.19 %
Rwork0.1913 --
obs0.1923 118516 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→45.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10139 1712 6 1213 13070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812276
X-RAY DIFFRACTIONf_angle_d1.02816941
X-RAY DIFFRACTIONf_dihedral_angle_d17.8854626
X-RAY DIFFRACTIONf_chiral_restr0.0431861
X-RAY DIFFRACTIONf_plane_restr0.0051913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0769-2.11470.29481160.25775132X-RAY DIFFRACTION83
2.1147-2.15530.29761240.25535532X-RAY DIFFRACTION89
2.1553-2.19930.31421360.255748X-RAY DIFFRACTION94
2.1993-2.24720.26581360.24256039X-RAY DIFFRACTION98
2.2472-2.29940.28331480.23176137X-RAY DIFFRACTION100
2.2994-2.35690.29261350.22276146X-RAY DIFFRACTION100
2.3569-2.42060.26951340.21936174X-RAY DIFFRACTION100
2.4206-2.49190.2591360.21446187X-RAY DIFFRACTION100
2.4919-2.57230.26871320.2136145X-RAY DIFFRACTION100
2.5723-2.66420.30731410.21886202X-RAY DIFFRACTION100
2.6642-2.77090.26211460.21586188X-RAY DIFFRACTION100
2.7709-2.8970.24961390.21036167X-RAY DIFFRACTION100
2.897-3.04970.26351350.20946198X-RAY DIFFRACTION100
3.0497-3.24070.28131420.21176243X-RAY DIFFRACTION100
3.2407-3.49080.24421350.18456216X-RAY DIFFRACTION100
3.4908-3.84190.20891430.17566265X-RAY DIFFRACTION100
3.8419-4.39750.18361400.15386285X-RAY DIFFRACTION100
4.3975-5.53880.1821370.15836348X-RAY DIFFRACTION100
5.5388-45.09690.19841430.16676566X-RAY DIFFRACTION100

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