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- PDB-5a39: Structure of Rad14 in complex with cisplatin containing DNA -

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Basic information

Entry
Database: PDB / ID: 5a39
TitleStructure of Rad14 in complex with cisplatin containing DNA
Components
  • 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
  • 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
  • DNA REPAIR PROTEIN RAD14
  • DNA
KeywordsREPLICATION / DNA REPAIR / DNA DAMAGE RECOGNITION / CISPLATIN
Function / homology
Function and homology information


nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / Dual incision in TC-NER / base-excision repair / damaged DNA binding / 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
Cisplatin / DNA / DNA (> 10) / DNA repair protein RAD14
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKoch, S.C. / Kuper, J. / Gasteiger, K.L. / Wichlein, N. / Strasser, R. / Eisen, D. / Geiger, S. / 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 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references

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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: DNA
D: DNA
E: 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
F: 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
G: 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
H: 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,83114
Polymers52,5008
Non-polymers1,3316
Water0
1
A: DNA REPAIR PROTEIN RAD14
hetero molecules

B: DNA REPAIR PROTEIN RAD14
C: DNA
D: DNA
E: 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
F: 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
G: 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
H: 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,83114
Polymers52,5008
Non-polymers1,3316
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z+1/21
identity operation1_555x,y,z1
MethodPISA
2
A: DNA REPAIR PROTEIN RAD14
hetero molecules

B: DNA REPAIR PROTEIN RAD14
C: DNA
D: DNA
E: 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
F: 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'
G: 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
H: 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,83114
Polymers52,5008
Non-polymers1,3316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,-y,z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)54.421, 54.421, 130.773
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: (-0.000733, 1, -0.000468), (1, 0.000732, -0.002188), (-0.002188, -0.000469, -1)
Vector: 27.22, -27.2, 0.1081)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA REPAIR PROTEIN RAD14 / / RAD14


Mass: 13673.528 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, UNP RESIDUES 188-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P28519

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DNA chain , 3 types, 6 molecules CDEFGH

#2: DNA chain DNA /


Mass: 4519.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#3: DNA chain 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'


Mass: 4015.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#4: DNA chain 5'-D(*DGP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP*GP)-3'


Mass: 4040.647 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)

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Non-polymers , 2 types, 6 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM

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Details

Sequence detailsCHAINS E,G AND CHAINS F,H DISPLAY MICROHETEROGENEITY

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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: 2.15 Å3/Da / Density % sol: 42.74 % / Description: NONE
Crystal growDetails: 0.2M MAGNESIUM ACETATE 0.1M MES PH 6.5 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 2.8→54.4 Å / Num. obs: 9402 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.8→54.42 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.903 / SU B: 52.619 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED BIOMOLECULE IS COMPLETED BY CRYSTAL SYMMETRY
RfactorNum. reflection% reflectionSelection details
Rfree0.25554 455 4.8 %RANDOM
Rwork0.21255 ---
obs0.21462 8935 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.729 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2--2 Å20 Å2
3----3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.8→54.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 1682 14 0 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0154401
X-RAY DIFFRACTIONr_bond_other_d0.0120.023002
X-RAY DIFFRACTIONr_angle_refined_deg1.571.5846409
X-RAY DIFFRACTIONr_angle_other_deg1.80737023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09224.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3411510
X-RAY DIFFRACTIONr_chiral_restr0.1060.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023561
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02977
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_it0.8421.148914
X-RAY DIFFRACTIONr_mcbond_other0.8411.147913
X-RAY DIFFRACTIONr_mcangle_it1.4771.7141139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8810.8413487
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 36 -
Rwork0.388 686 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.51690.51731.375510.92020.02414.21460.3378-0.29040.34880.1434-0.3245-0.6761-0.30260.376-0.01330.4484-0.01240.05610.52840.05310.427329.1138-22.67496.6962
23.4569-1.0177-5.71680.34091.62199.5827-0.1248-0.1816-0.1101-0.0415-0.0441-0.03420.38630.47670.16890.43190.02320.03460.52550.00060.481428.8127-21.9593-4.2994
31.1306-0.114-0.15314.621-5.088511.9423-0.0416-0.084-0.12590.18610.2110.201-0.0411-0.4809-0.16940.34810.01550.06430.4320.00030.44720.7134-14.3665-8.853
43.1798-1.991-1.38916.4031-0.75092.79350.22390.20080.2447-0.0787-0.20540.2431-0.1471-0.231-0.01840.4514-0.02730.00750.4303-0.03770.430525.1511-4.6246-19.4071
57.30971.16386.3934.01593.49757.33240.09190.2251-0.0331-0.37680.1169-0.7009-0.090.333-0.20880.47350.01740.1240.48320.06620.700931.4873-14.4788-16.5378
62.3274-0.59160.01253.6350.93064.5143-0.1113-0.33150.29050.589-0.12670.5612-0.2603-0.07750.2380.3696-0.05430.03560.32490.0040.476522.681-7.4813-15.6499
715.2805-5.2787-2.08356.76350.03010.3878-0.110.0902-0.2575-0.10450.17220.4746-0.0181-0.0262-0.06220.61850.00180.03940.5747-0.0330.635812.11877.3506-21.5084
86.84082.27041.57821.33342.01674.2362-0.06320.42560.2586-0.0770.08790.0144-0.19720.0021-0.02460.5899-0.0115-0.0150.4977-0.01550.47844.64031.7829-6.5754
92.85833.43123.2158.71789.14459.7022-0.12630.48530.33450.06680.11290.060.0916-0.06310.01340.51270.02880.00140.4495-0.01120.4215.30990.66114.3167
106.424-0.24611.94783.6863-1.54482.0290.13450.0587-0.4817-0.056-0.1315-0.24510.37120.5621-0.00310.35740.01590.04490.4158-0.05830.397818.0503-4.25514.3892
115.71334.904-5.06435.721-7.03449.2965-0.0688-0.07220.1359-0.09790.00310.04070.0318-0.05950.06570.42360.02440.02930.3808-0.06550.50549.6038-0.164721.2642
122.347-0.6951-1.00992.74020.51012.91040.12560.4332-0.1578-0.2691-0.1845-0.3472-0.06990.2410.05890.3645-0.0472-0.02680.453-0.0220.42819.9811-1.638913.3038
132.7695-0.1932-1.58344.9185-2.98815.9695-0.3850.2478-0.211-0.0335-0.2295-0.36340.4630.30420.61440.55660.00870.07730.5235-0.00980.606732.6501-11.033914.131
142.83613.1332-0.6436.8221-0.57940.21980.2778-0.0025-0.23860.5979-0.16050.3958-0.09350.0994-0.11730.756-0.01820.0610.7403-0.08430.838335.7207-18.41824.1126
150.43030.8207-0.52733.85131.20893.1532-0.1857-0.0403-0.2279-0.36080.1184-0.28680.15940.21510.06730.31080.0414-0.12630.45650.02610.634326.90720.223234.0665
164.8972-3.2863.30642.27-2.17393.33920.1541-0.2628-0.0193-0.09870.0198-0.1407-0.1864-0.2121-0.17390.386-0.0143-0.01750.52660.0530.73928.02661.219932.4043
170.0290.36450.05738.67321.87584.1877-0.0793-0.0013-0.0655-0.97430.24860.1326-0.06270.0995-0.16930.29980.0014-0.0460.36240.05590.75828.31060.800133.821
183.8011-0.20152.25880.61380.21474.03510.3213-0.7794-0.4656-0.1174-0.2249-0.6413-0.5-0.3869-0.09640.3278-0.0454-0.08540.62560.20811.074528.0611.070732.3123
192.753-1.05752.96882.07650.5376.41440.1192-0.5804-0.1281-0.10380.1585-1.00650.1608-0.3273-0.27770.25-0.01090.07110.37490.23881.242826.97920.277931.336
200.91430.2764-1.78273.97981.40364.4685-0.20880.1783-0.2382-0.77080.126-0.77210.0127-0.27120.08280.3863-0.0571-0.09410.34510.00350.575926.0895-0.826233.0989
214.6120.44591.17570.73080.93344.22310.3264-0.819-0.18290.0549-0.3709-0.5203-0.1459-0.16370.04450.1231-0.0797-0.09240.5640.11430.746226.7312-1.320431.7628
220.94611.0608-1.47119.12443.50286.0415-0.30610.2356-0.3643-1.05230.2477-0.6745-0.021-0.34150.05830.376-0.0478-0.07460.3513-0.00170.770126.0427-0.781133.0106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A100 - 110
2X-RAY DIFFRACTION2A111 - 128
3X-RAY DIFFRACTION3A129 - 144
4X-RAY DIFFRACTION4A145 - 157
5X-RAY DIFFRACTION5A158 - 166
6X-RAY DIFFRACTION6A167 - 204
7X-RAY DIFFRACTION7A205 - 213
8X-RAY DIFFRACTION8B100 - 110
9X-RAY DIFFRACTION9B111 - 130
10X-RAY DIFFRACTION10B131 - 157
11X-RAY DIFFRACTION11B158 - 174
12X-RAY DIFFRACTION12B175 - 196
13X-RAY DIFFRACTION13B197 - 207
14X-RAY DIFFRACTION14B208 - 214
15X-RAY DIFFRACTION15C1 - 14
16X-RAY DIFFRACTION16G0 - 12
17X-RAY DIFFRACTION17C1 - 15
18X-RAY DIFFRACTION18E2 - 14
19X-RAY DIFFRACTION19D1 - 15
20X-RAY DIFFRACTION20H0 - 12
21X-RAY DIFFRACTION21D1 - 14
22X-RAY DIFFRACTION22F2 - 14

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