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- PDB-5a3d: Structural insights into the recognition of cisplatin and AAF-dG ... -

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Basic information

Entry
Database: PDB / ID: 5a3d
TitleStructural insights into the recognition of cisplatin and AAF-dG lesions by Rad14 (XPA)
Components
  • 5'-D(*DG 5IUP*GP*A 5IUP*GP*AP*CP*G 5IUP*AP*GP*AP*DGP*AP)-3'
  • 5'-D(*DTP*CP*TP*CP*TP*AP*C 8FGP*TP*CP*AP*TP*CP*DAP*CP)-3'
  • DNA REPAIR PROTEIN RAD14
KeywordsDNA BINDING PROTEIN / XPA / RAD14 / NER / AAF-DG / CISPLATIN
Function / homology
Function and homology information


nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / base-excision repair / damaged DNA binding / DNA damage response / zinc ion binding / nucleus
Similarity search - Function
XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein RAD14
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuper, J. / Koch, S.C. / Gasteiger, K.L. / Wichlein, N. / Schneider, S. / Kisker, C. / Carell, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion by Rad14 (Xpa).
Authors: Koch, S.C. / Kuper, J. / Gasteiger, K.L. / Simon, N. / Strasser, R. / Eisen, D. / Geiger, S. / Schneider, S. / Kisker, C. / Carell, T.
History
DepositionMay 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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 REPAIR PROTEIN RAD14
B: DNA REPAIR PROTEIN RAD14
C: 5'-D(*DTP*CP*TP*CP*TP*AP*C 8FGP*TP*CP*AP*TP*CP*DAP*CP)-3'
D: 5'-D(*DG 5IUP*GP*A 5IUP*GP*AP*CP*G 5IUP*AP*GP*AP*DGP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2136
Polymers37,0824
Non-polymers1312
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-25.8 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.727, 53.727, 130.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.003171, -1, 0.001543), (-1, -0.003171, -3.4E-5), (3.9E-5, -0.001543, -1)
Vector: 26.8, 26.88, 65.41)

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Components

#1: Protein DNA REPAIR PROTEIN RAD14 / RAD14


Mass: 13673.528 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PPSG-IBA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P28519
#2: DNA chain 5'-D(*DTP*CP*TP*CP*TP*AP*C 8FGP*TP*CP*AP*TP*CP*DAP*CP)-3'


Mass: 4701.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*DG 5IUP*GP*A 5IUP*GP*AP*CP*G 5IUP*AP*GP*AP*DGP*AP)-3'


Mass: 5033.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSYNTHESIZED DNA

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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: 2.55 Å3/Da / Density % sol: 51.72 % / Description: NONE
Crystal growDetails: 0.18 M AMMONIUM NITRATE AND 40% 2-METHYL- 1,3,-PROPANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.8→65.3 Å / Num. obs: 34232 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.6 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→53.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.424 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24076 1701 5 %RANDOM
Rwork0.20956 ---
obs0.21109 32435 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.26 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 618 2 43 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0163325
X-RAY DIFFRACTIONr_bond_other_d0.0040.022467
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.6454961
X-RAY DIFFRACTIONr_angle_other_deg1.7343.0135759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51525104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4821510
X-RAY DIFFRACTIONr_chiral_restr0.4630.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
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_it1.6522.688914
X-RAY DIFFRACTIONr_mcbond_other1.6532.686913
X-RAY DIFFRACTIONr_mcangle_it2.6834.0191139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6512.3362411
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 121 -
Rwork0.312 2400 -
obs--99.02 %
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)
11.38512.30460.6453.9370.94880.6633-0.13470.1488-0.3155-0.29080.2959-0.43240.10490.2034-0.16120.31280.0358-0.0530.3419-0.04930.363727.18950.476534.3558
23.30722.6280.69582.81271.35921.07120.0758-0.248-0.59290.17650.0082-0.44140.24570.1715-0.0840.35620.0413-0.05550.36120.00410.359526.73370.065431.5063
33.22221.14092.83012.73894.486111.53680.2915-0.03550.10890.1058-0.22940.1866-0.0458-0.8334-0.06210.0780.02660.02360.1449-0.01540.103624.104721.928164.7377
40.32630.3689-0.57474.82785.01039.6610.16640.07190.00140.33950.3191-0.31060.19390.2304-0.48560.14320.0393-0.04980.0964-0.02770.096232.536716.659559.1544
54.0861.36930.24958.06872.5193.74820.16730.2296-0.29760.3114-0.24490.04140.2943-0.22310.07750.0501-0.0216-0.01880.0594-0.02650.039926.5418.988447.1371
61.28280.6427-0.14864.2933-3.3736.75770.08480.1181-0.01110.0783-0.0952-0.23190.2139-0.14030.01040.03820.0022-0.03690.0506-0.00520.059629.517513.236647.5326
715.1775-12.6132-20.868510.581317.39628.74460.7099-1.6520.7212-1.25760.7768-0.6514-1.75242.2371-1.48671.42580.3383-0.10320.7566-0.03571.279642.5919-6.337443.4016
84.36061.42724.38284.58993.740213.1657-0.15230.11660.2118-0.11490.22610.0539-0.8303-0.0799-0.07380.1252-0.0045-0.02080.04440.01010.07574.97152.75080.6526
94.8395-0.1545.1820.1792-1.105111.32620.33380.246-0.32130.02540.0547-0.00950.2770.1525-0.38840.10350.0334-0.03880.1005-0.06820.116810.1735-5.66476.2459
107.6345-0.37361.83653.1290.06012.1623-0.13540.29030.11170.09990.0636-0.3118-0.15060.25890.07180.1394-0.0297-0.02220.1178-0.03540.113417.86930.369818.2116
114.62590.9091-3.93582.0298-0.3027.4289-0.0497-0.0205-0.19440.08090.0267-0.061-0.06810.27190.0230.09460.0013-0.03150.0955-0.04150.138213.6416-2.682717.9531
126.0364-5.14283.032114.2743-6.42837.6767-0.17880.4859-0.935-0.0668-0.1483-0.5891.08741.00010.32710.27830.13590.10160.4697-0.14710.595932.3207-10.789216.0367
132.46160.89750.91180.33940.32950.35790.20370.0664-0.47140.05310.004-0.23180.13840.091-0.20780.38770.0404-0.03340.3926-0.08570.470526.9211-0.935830.9112
140.19870.06860.39790.09110.13570.80820.15320.0999-0.1169-0.03220.0635-0.23280.29780.2677-0.21670.5441-0.00880.04420.4815-0.06650.657827.71320.217634.3464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 14
2X-RAY DIFFRACTION2D1 - 14
3X-RAY DIFFRACTION3A101 - 123
4X-RAY DIFFRACTION4A124 - 142
5X-RAY DIFFRACTION5A143 - 166
6X-RAY DIFFRACTION6A167 - 191
7X-RAY DIFFRACTION7A206 - 216
8X-RAY DIFFRACTION8B101 - 123
9X-RAY DIFFRACTION9B124 - 142
10X-RAY DIFFRACTION10B143 - 166
11X-RAY DIFFRACTION11B167 - 191
12X-RAY DIFFRACTION12B192 - 214
13X-RAY DIFFRACTION13C1 - 14
14X-RAY DIFFRACTION14D1 - 14

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