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- PDB-4a0b: Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidin... -

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Basic information

Entry
Database: PDB / ID: 4a0b
TitleStructure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.8 A resolution (CPD 4)
Components
  • 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'
  • 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3'
  • DNA DAMAGE-BINDING PROTEIN 1
  • DNA DAMAGE-BINDING PROTEIN 2
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / DNA DAMAGE REPAIR
Function / homology
Function and homology information


DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Ub-specific processing proteases / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair ...DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Ub-specific processing proteases / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #3280 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Helix Hairpins - #3280 / DNA damage-binding protein 2 / DNA polymerase; domain 1 - #910 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / Helix Hairpins / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DANIO RERIO (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsScrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation
Authors: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H.
History
DepositionSep 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval ..._entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA DAMAGE-BINDING PROTEIN 1
B: DNA DAMAGE-BINDING PROTEIN 2
C: DNA DAMAGE-BINDING PROTEIN 1
D: DNA DAMAGE-BINDING PROTEIN 2
G: 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3'
H: 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'
I: 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3'
J: 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)365,0398
Polymers365,0398
Non-polymers00
Water0
1
A: DNA DAMAGE-BINDING PROTEIN 1
B: DNA DAMAGE-BINDING PROTEIN 2
G: 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3'
H: 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)182,5194
Polymers182,5194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-39.8 kcal/mol
Surface area61990 Å2
MethodPISA
2
C: DNA DAMAGE-BINDING PROTEIN 1
D: DNA DAMAGE-BINDING PROTEIN 2
I: 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3'
J: 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)182,5194
Polymers182,5194
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-41.3 kcal/mol
Surface area61780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.100, 145.900, 224.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13B
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLYGLY2AA4 - 39323 - 412
211ASNASNGLYGLY2CC4 - 39323 - 412
121LYSLYSHISHIS2AA709 - 1140728 - 1159
221LYSLYSHISHIS2CC709 - 1140728 - 1159
112ILEILEGLNGLN2AA394 - 708413 - 727
212ILEILEGLNGLN2CC394 - 708413 - 727
113GLNGLNGLUGLU4BB102 - 45527 - 380
213GLNGLNGLUGLU4DD102 - 45527 - 380

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA DAMAGE-BINDING PROTEIN 1


Mass: 129352.867 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q16531
#2: Protein DNA DAMAGE-BINDING PROTEIN 2 / DAMAGE-SPECIFIC DNA-BINDING PROTEIN 2


Mass: 43418.102 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q2YDS1
#3: DNA chain 5'-D(*DGP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3'


Mass: 5018.265 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DAMAGED STRAND. CONTAINS CYCLOBUTANE PYRIMIDINE DIMER (CPD)
Source: (synth.) synthetic construct (others)
#4: DNA chain 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'


Mass: 4730.069 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: UNDAMAGED STRAND / Source: (synth.) synthetic construct (others)
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 224 TO SER ENGINEERED RESIDUE IN CHAIN C, GLU 224 TO SER

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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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 5.3 / Details: 100 MM MES, 15 MM NAOH, 18% PEG 350MME., pH 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 37310 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.9
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EI1

3ei1


Resolution: 3.8→47.72 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.829 / SU B: 147.543 / SU ML: 0.945 / Cross valid method: THROUGHOUT / ESU R Free: 1.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.31889 1864 5 %RANDOM
Rwork0.2434 ---
obs0.24719 35416 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.484 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2--3.23 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 3.8→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22807 1131 0 0 23938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02224532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1232.0233494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99352878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99524.4521058
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.705154065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.14915130
X-RAY DIFFRACTIONr_chiral_restr0.0730.23826
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117987
X-RAY DIFFRACTIONr_gen_planes_other
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_it01.514375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0223297
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.038310157
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0754.510193
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3104tight positional0.310.05
12C3104tight positional0.310.05
21A1224tight positional0.010.05
22C1224tight positional0.010.05
11A3008medium positional0.690.5
12C3008medium positional0.690.5
21A1149medium positional0.020.5
22C1149medium positional0.020.5
31B2839medium positional0.250.5
32D2839medium positional0.250.5
11A3104tight thermal00.5
12C3104tight thermal00.5
21A1224tight thermal00.5
22C1224tight thermal00.5
11A3008medium thermal02
12C3008medium thermal02
21A1149medium thermal02
22C1149medium thermal02
31B2839medium thermal02
32D2839medium thermal02
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 135 -
Rwork0.289 2570 -
obs--100 %
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)
12.42010.1161-0.34032.2505-2.17483.8975-0.0303-0.1790.14780.1931-0.1698-0.2868-0.13020.20280.20010.12070.0052-0.08210.070.05990.15937.785-36.3279-36.3783
22.7327-0.5962-1.25691.95131.73473.67830.1171-0.03640.3428-0.20980.1705-0.0171-0.17090.2047-0.28760.1312-0.0598-0.00110.0442-0.03650.176948.3035-29.149632.535
33.5221-0.8318-0.53922.4715-0.6064.1196-0.056-0.16740.52470.17320.124-0.07760.01340.3229-0.0680.19690.05220.02570.23630.16880.261941.4057-52.0195-27.1947
46.73750.9309-1.59541.95180.68934.2108-0.16120.88540.0191-0.12520.06880.0721-0.1838-0.83140.09230.2556-0.02990.07090.2641-0.09490.17615.7186-45.112723.5991
513.80590.6881-9.27127.4574-0.74616.2949-1.2578-1.4265-1.6815-0.2450.2089-1.17081.02291.10531.0490.69120.5583-0.19091.480.39080.896961.6217-68.5698-21.8803
68.14634.462-9.30112.7875-5.334210.81420.8558-2.5461-0.50010.9903-1.5893-0.7599-1.47093.00660.73351.1063-0.1402-0.41581.51850.41941.06763.3565-68.6525-24.3851
716.3174-2.2456-11.10538.365-1.42679.0137-0.79033.4743-1.5686-0.32370.93481.64140.8763-2.8928-0.14460.4235-0.7357-0.19852.3984-0.65261.5602-5.6525-60.666119.172
813.61177.75122.38566.46292.68311.3039-0.41822.2863-1.6896-1.7096-0.01150.3436-1.0503-0.58220.42971.60750.2568-0.5052.9761-1.09111.5525-5.3552-61.195219.3029
93.361-0.0397-2.25690.56850.79113.6380.3826-0.4410.28850.1659-0.07750.4809-1.2623-0.2828-0.30512.42050.3310.28580.868-0.00171.7501-11.74115.7393-24.2393
102.9932-0.89670.14532.62920.14793.8147-0.19150.77740.2208-0.337-0.347-0.8144-0.42190.58180.53851.5145-0.44340.31570.98810.22021.881468.298113.12321.5544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 393
2X-RAY DIFFRACTION1A709 - 1140
3X-RAY DIFFRACTION2C1 - 393
4X-RAY DIFFRACTION2C709 - 1140
5X-RAY DIFFRACTION3B102 - 455
6X-RAY DIFFRACTION4D101 - 455
7X-RAY DIFFRACTION5G2 - 16
8X-RAY DIFFRACTION6H2 - 15
9X-RAY DIFFRACTION7I2 - 15
10X-RAY DIFFRACTION8J2 - 14
11X-RAY DIFFRACTION9A394 - 708
12X-RAY DIFFRACTION10C394 - 708

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