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- PDB-5g35: Structure of Rad14 in complex with acetylaminopyren-C8-guanine co... -

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Basic information

Entry
Database: PDB / ID: 5g35
TitleStructure of Rad14 in complex with acetylaminopyren-C8-guanine containing DNA
Components
  • 5'-D(*GP*CP*TP*CP*TP*AP*8PYP*TP*CP*AP*TP*CP*AP*CP)-3'
  • 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
  • RAD14
KeywordsCELL CYCLE / DNA REPAIR / NUCLEOTIDE EXCISION REPAIR
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
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: 2 Å
AuthorsSimon, N. / Ebert, C. / Schneider, S.
CitationJournal: Chemistry / Year: 2016
Title: Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14.
Authors: Schneider, S. / Simon, N. / Ebert, C.
History
DepositionApr 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 2.0May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.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: RAD14
B: RAD14
C: 5'-D(*GP*CP*TP*CP*TP*AP*8PYP*TP*CP*AP*TP*CP*AP*CP)-3'
D: 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
E: 5'-D(*GP*CP*TP*CP*TP*AP*8PYP*TP*CP*AP*TP*CP*AP*CP)-3'
F: 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6508
Polymers49,5206
Non-polymers1312
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.170, 53.170, 131.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A188 - 303
2114B188 - 303

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.000689, -0.999996, 0.002749), (-0.999999, 0.000687, -0.001031), (0.001029, -0.00275, -0.999996)79.82015, 79.70065, -66.87814

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Components

#1: Protein RAD14


Mass: 15612.728 Da / Num. of mol.: 2 / Fragment: RESIDUES 188-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: RAD14, YMR201C, YM8325.02C / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P28519
#2: DNA chain 5'-D(*GP*CP*TP*CP*TP*AP*8PYP*TP*CP*AP*TP*CP*AP*CP)-3'


Mass: 4762.222 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'


Mass: 4384.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) 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 / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGUANOSINE AT POS.8 IS MODIFIED AT C8 BY ACETYLAMINOPYRENE

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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: 1.92 Å3/Da / Density % sol: 0.43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→37.6 Å / Num. obs: 24353 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A3D
Resolution: 2→53.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.344 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25421 1255 5.2 %RANDOM
Rwork0.21729 ---
obs0.21911 23113 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 1169 2 53 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0163230
X-RAY DIFFRACTIONr_bond_other_d0.0020.022402
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.6684606
X-RAY DIFFRACTIONr_angle_other_deg1.34335598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3424.423104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11315340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7741512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02726
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_it1.5642.592914
X-RAY DIFFRACTIONr_mcbond_other1.5622.592913
X-RAY DIFFRACTIONr_mcangle_it2.4263.8761139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.412.4672316
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1794 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.330.5
medium thermal1.712
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 92 -
Rwork0.36 1738 -
obs--99.29 %
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)
10.67570.044-1.3651.0564-1.65276.74060.02040.1021-0.0675-0.05650.05230.00250.14490.1351-0.07270.14320.01340.01030.1449-0.0190.103748.550850.3487-65.7211
27.5735-0.6072-3.69343.55590.76334.71430.19890.02910.1485-0.0606-0.0606-0.0718-0.1352-0.0755-0.13820.09850.00790.02980.10490.0350.038144.797358.2082-64.4418
310.93030.8131-0.50161.19931.57762.39670.08310.21210.2987-0.045-0.04620.0509-0.1432-0.1729-0.03690.14130.02720.03460.1020.05220.089334.409658.9719-48.8089
48.0683-0.9344-5.09111.2964-0.81524.8756-0.0235-0.0182-0.2853-0.07990.02640.18210.1068-0.0301-0.00290.1475-0.01340.00440.1221-0.00960.105134.738948.2146-47.6403
57.44290.19622.0885.01432.818511.95110.18830.09480.3214-0.1195-0.1449-0.4341-0.0285-0.2316-0.04330.0880.01020.01390.03530.02910.062247.032956.9728-41.3401
612.31171.03565.29210.2955-0.63029.26370.01350.24910.2412-0.11540.06030.06470.0892-0.3156-0.07380.26280.0571-0.01830.05920.01250.073134.665854.5605-55.5411
77.0136-2.853-0.51233.20355.351913.078-0.29150.68910.1491-0.1306-0.6840.4103-0.6694-1.06440.97550.15820.00070.05350.54340.0720.547122.445959.625-54.4071
83.70690.28241.273713.04032.06033.0303-0.0076-0.25680.5147-0.416-0.644-0.0118-0.6467-0.44630.65160.50870.09340.03920.4833-0.02830.552819.097167.3389-44.2898
92.2988-0.0799-1.39340.7667-2.02847.69310.0611-0.0758-0.00920.0413-0.0077-0.06760.16180.167-0.05340.13630.0071-0.02290.11710.0080.112729.396131.2158-1.1939
104.4406-1.4874-1.13248.4109-3.00285.4145-0.1341-0.1526-0.15070.1960.2830.2162-0.1415-0.3336-0.14890.09680.00630.0220.09980.02920.0321.455534.9388-2.4723
112.1486-0.16051.82228.45140.6111.6209-0.1878-0.0520.08420.07540.11640.3053-0.1686-0.05610.07130.08930.00730.03860.13110.04220.105220.799945.3675-18.1361
127.904-2.2767-0.528210.1436-3.4634.16680.23640.09130.137-0.1298-0.1644-0.1840.06620.039-0.0720.1196-0.0260.00730.12630.02450.086131.272446.7916-21.5722
1311.08225.27467.90948.11729.761412.0623-0.13540.0577-0.0872-0.40320.4042-0.2673-0.44960.4313-0.26880.15770.0180.05310.17630.0250.106329.767838.0441-17.2413
147.821-2.27424.88469.07551.17228.291-0.1260.0436-0.0842-0.29850.0120.54510.07750.05680.1140.0451-0.0225-0.00540.109-0.00460.048821.64832.976-27.6021
151.13970.1383-0.51528.8071.52127.44560.1074-0.1450.30050.4437-0.07660.2508-0.51310.1247-0.03090.12710.00540.04270.09250.00140.108325.287548.0858-11.8171
167.0534-0.23446.99324.4176-1.16269.7246-0.36550.03130.61540.31120.21970.4416-0.8742-0.76950.14570.46680.06490.04820.3698-0.00890.417814.564459.6676-17.7754
179.8596-3.00821.35355.1267-4.51999.82780.1195-0.16090.8703-0.63630.14680.52180.0568-0.1407-0.26640.1835-0.001-0.10620.00870.01190.27439.489861.5108-40.8363
1812.19742.41015.17990.4851.03672.25260.0782-1.1184-0.0569-0.0103-0.16610.00330.0976-0.34410.08790.41850.01990.20670.54270.18970.310525.441156.7584-29.5565
197.4488-4.35934.59723.0012-4.12668.34940.90850.884-0.3253-0.3276-0.47020.42550.2961-0.2931-0.43830.4137-0.1940.21190.6474-0.34430.513215.685244.3306-35.2128
2011.9463-8.35844.72316.7497-0.187912.843-0.1650.08740.78150.03840.1924-0.5731-0.20981.0798-0.02740.1156-0.0178-0.07390.1465-0.11990.307620.059942.736-29.7879
210.6565-0.36042.44124.7877-0.11749.409-0.0195-0.00580.0458-0.767-0.0931-0.2211-0.2797-0.08540.11260.13880.00560.06460.2410.01130.205823.903559.4392-38.2457
2211.0739-5.5784-3.79043.1850.68127.6308-1.2454-0.41131.01230.94730.4381-0.5549-0.36340.10450.80720.52850.20340.05110.52370.12380.631637.331863.631-30.775
233.3303-1.591-4.1894.9044-1.423912.11720.0622-0.63780.463-0.20230.29980.8312-0.09440.3382-0.3620.04280.0133-0.06870.1782-0.21470.630718.292140.2836-26.0429
241.55351.67111.69654.36544.78095.2607-0.3942-0.32350.2807-0.6808-0.11730.4484-0.6901-0.06940.51150.43690.05950.12270.36680.1870.390722.953254.2507-37.176
2510.5472-9.3131-0.487711.59792.27984.577-0.99630.1691.3430.79180.5211-0.0935-0.2830.29910.47520.1444-0.0805-0.12340.29770.15260.572935.471764.0559-31.7779
2610.6047-1.1209-4.19889.62774.464712.9381-0.062-0.0250.7155-0.30460.09821.17280.4457-0.3622-0.03620.06620.0132-0.04810.08630.04510.227636.962259.6485-37.1426
276.6673-0.7648-1.33910.08770.168913.4875-0.2134-1.1082-0.09910.02370.12610.00990.0803-0.3460.08730.25730.01390.04950.21150.02850.280920.246455.9138-28.8015
2810.612-9.2388-1.06768.4675-1.014411.62630.69581.4835-0.5061-0.5458-1.26940.5530.5375-0.57160.57360.4839-0.07330.17350.2796-0.11780.652616.132242.4451-36.1798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A188 - 210
2X-RAY DIFFRACTION2A211 - 225
3X-RAY DIFFRACTION3A226 - 238
4X-RAY DIFFRACTION4A239 - 251
5X-RAY DIFFRACTION5A252 - 266
6X-RAY DIFFRACTION6A267 - 278
7X-RAY DIFFRACTION7A279 - 292
8X-RAY DIFFRACTION8A293 - 302
9X-RAY DIFFRACTION9B188 - 210
10X-RAY DIFFRACTION10B211 - 225
11X-RAY DIFFRACTION11B226 - 238
12X-RAY DIFFRACTION12B239 - 247
13X-RAY DIFFRACTION13B248 - 254
14X-RAY DIFFRACTION14B255 - 266
15X-RAY DIFFRACTION15B267 - 283
16X-RAY DIFFRACTION16B284 - 303
17X-RAY DIFFRACTION17C1 - 4
18X-RAY DIFFRACTION18C5 - 9
19X-RAY DIFFRACTION19C10 - 14
20X-RAY DIFFRACTION20D1 - 6
21X-RAY DIFFRACTION21D7 - 10
22X-RAY DIFFRACTION22D11 - 14
23X-RAY DIFFRACTION23E1 - 4
24X-RAY DIFFRACTION24E5 - 9
25X-RAY DIFFRACTION25E10 - 14
26X-RAY DIFFRACTION26F1 - 6
27X-RAY DIFFRACTION27F7 - 10
28X-RAY DIFFRACTION28F11 - 14

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