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- PDB-4ebc: Conformationally Restrained North-methanocarba-2'-deoxyadenosine ... -

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Basic information

Entry
Database: PDB / ID: 4ebc
TitleConformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota
Components
  • 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'
  • 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'
  • DNA polymerase iota
KeywordsTRANSFERASE/DNA / polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck ...error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
North-methanocarba-2'-deoxyadenosine triphosphate / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsEoff, R.L. / Ketkar, A. / Banerjee, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota.
Authors: Ketkar, A. / Zafar, M.K. / Banerjee, S. / Marquez, V.E. / Egli, M. / Eoff, R.L.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Sep 13, 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_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase iota
P: 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'
T: 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5558
Polymers51,8423
Non-polymers7145
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-52 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.797, 97.797, 203.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase iota / Eta2 / RAD30 homolog B


Mass: 47027.344 Da / Num. of mol.: 1 / Fragment: UNP residues 26-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Plasmid: pBG101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

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


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 7-mer primer DNA
#3: DNA chain 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'


Mass: 2722.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 9-mer template DNA

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Non-polymers , 4 types, 83 molecules

#4: Chemical ChemComp-0OH / North-methanocarba-2'-deoxyadenosine triphosphate


Mass: 501.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N5O11P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 20 mM Tris-HCl, pH 7.9, 5% glycerol, 10 mM 2-mercaptoethanol, 150 mM calcium chloride, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2011
RadiationMonochromator: Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.901→84.695 Å / Num. obs: 12777 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.6
Reflection shellResolution: 2.901→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.9 / % possible all: 86

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAUTOMRmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GV5

3gv5


Resolution: 2.901→48.899 Å / SU ML: 0.75 / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1278 10 %
Rwork0.2063 --
obs0.211 12775 95.06 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.737 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.061 Å20 Å20 Å2
2--5.061 Å2-0 Å2
3----10.1219 Å2
Refine analyzeLuzzati sigma a obs: 0.412 Å
Refinement stepCycle: LAST / Resolution: 2.901→48.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 325 40 78 3365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173365
X-RAY DIFFRACTIONf_angle_d1.4924616
X-RAY DIFFRACTIONf_dihedral_angle_d19.1571292
X-RAY DIFFRACTIONf_chiral_restr0.085542
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-3.01730.41051240.29651117X-RAY DIFFRACTION86
3.0173-3.15460.30081330.25211194X-RAY DIFFRACTION91
3.1546-3.32090.26931340.20951209X-RAY DIFFRACTION92
3.3209-3.52890.28931400.21451251X-RAY DIFFRACTION95
3.5289-3.80130.25071410.21641273X-RAY DIFFRACTION97
3.8013-4.18370.28351430.19671292X-RAY DIFFRACTION97
4.1837-4.78860.1941490.1681334X-RAY DIFFRACTION99
4.7886-6.03140.27211500.21381354X-RAY DIFFRACTION98
6.0314-48.90540.21961640.19831473X-RAY DIFFRACTION99
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)
10.16290.1107-0.14170.8843-0.51861.03030.0410.02810.02430.2542-0.2176-0.5666-0.53070.2606-0.04090.529-0.1986-0.09280.46770.07810.564699.1574-16.8799224.8018
21.03170.6843-0.08340.92120.760.86310.0163-0.04560.0736-0.1706-0.18450.0452-0.0445-0.196800.38290.03590.04680.3571-0.03140.320781.7366-16.6678208.6886
30.4363-0.1363-0.14270.3147-0.16230.1104-0.0926-0.1111-0.7587-0.0495-0.1275-0.75780.37810.1115-0.00050.6674-0.07040.16280.5093-0.06210.75898.3102-37.6061201.2618
40.02490.431-0.00111.1617-0.08040.65910.4937-0.4998-0.52890.165-0.2652-0.25460.4736-0.4116-0.20840.7177-0.3382-0.11630.64470.21450.655390.3928-40.9611235.2371
50.1255-0.06760.32250.2464-0.06450.54580.1442-0.7368-0.5727-0.4085-0.4861-0.1387-0.2413-0.4547-0.09170.6639-0.15750.08270.48220.18131.050194.128-41.0484219.1591
60.0525-0.0884-0.00960.1209-0.13910.15760.157-0.2722-1.2664-0.4884-0.1937-0.89860.31950.28410.00560.5814-0.29380.04010.57280.10240.610392.3517-36.3562222.863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 26:99)
2X-RAY DIFFRACTION2chain 'A' and (resseq 100:232)
3X-RAY DIFFRACTION3chain 'A' and (resseq 233:286)
4X-RAY DIFFRACTION4chain 'A' and (resseq 287:414)
5X-RAY DIFFRACTION5chain 'P' and (resseq 1:7)
6X-RAY DIFFRACTION6chain 'T' and (resseq 3:11)

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