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- PDB-6pai: Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound... -

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Basic information

Entry
Database: PDB / ID: 6pai
TitleStructure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820
Components
  • DDB1- and CUL4-associated factor 15
  • DET1- and DDB1-associated protein 1
  • DNA damage-binding protein 1
  • RNA-binding protein 39
KeywordsLIGASE / sulfonamide / RBM39 / DCAF15
Function / homology
Function and homology information


RS domain binding / regulation of natural killer cell activation / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / U1 snRNP binding / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / regulation of mRNA splicing, via spliceosome / biological process involved in interaction with symbiont ...RS domain binding / regulation of natural killer cell activation / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / U1 snRNP binding / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / regulation of mRNA splicing, via spliceosome / 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 / small molecule binding / immune system process / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / centriolar satellite / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / RNA processing / positive regulation of gluconeogenesis / mRNA Splicing - Major Pathway / RNA splicing / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / 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 / mRNA processing / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / microtubule cytoskeleton / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / nuclear speck / DNA repair / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / apoptotic process / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DDB1- and CUL4-associated factor 15, WD40 repeat-containing domain / DDB1- and CUL4-associated factor 15 / : / DDB1-and CUL4-substrate receptor 15, WD repeat / Splicing factor, RBM39-like / DET1- and DDB1-associated protein 1, N-terminal / Splicing factor RBM39, linker / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / linker between RRM2 and RRM3 domains in RBM39 protein ...DDB1- and CUL4-associated factor 15, WD40 repeat-containing domain / DDB1- and CUL4-associated factor 15 / : / DDB1-and CUL4-substrate receptor 15, WD repeat / Splicing factor, RBM39-like / DET1- and DDB1-associated protein 1, N-terminal / Splicing factor RBM39, linker / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / linker between RRM2 and RRM3 domains in RBM39 protein / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-O6M / RNA-binding protein 39 / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 15 / Uncharacterized protein DKFZp781I1140 / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVolkov, O.A. / Du, X.
Citation
Journal: Structure / Year: 2019
Title: Structural Basis and Kinetic Pathway of RBM39 Recruitment to DCAF15 by a Sulfonamide Molecular Glue E7820.
Authors: Du, X. / Volkov, O.A. / Czerwinski, R.M. / Tan, H. / Huerta, C. / Morton, E.R. / Rizzi, J.P. / Wehn, P.M. / Xu, R. / Nijhawan, D. / Wallace, E.M.
#1: Journal: Biorxiv / Year: 2019
Title: Structural basis of recruitment of RBM39 to DCAF15 by a sulfonamide molecular glue E7820
Authors: Du, X. / Volkov, O.A. / Czerwinski, R. / Tan, H.L. / Huerta, C. / Morton, E. / Rizzi, J. / Wehn, P. / Xu, R. / Nijhawan, D. / Wallace, E.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: DDB1- and CUL4-associated factor 15
D: RNA-binding protein 39
E: DET1- and DDB1-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,3458
Polymers207,4664
Non-polymers8784
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-44 kcal/mol
Surface area68930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.507, 94.767, 145.706
Angle α, β, γ (deg.)90.000, 98.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ACDE

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein DDB1- and CUL4-associated factor 15


Mass: 56414.852 Da / Num. of mol.: 1 / Mutation: UNP residues 2-275,384-600
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF15, C19orf72 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q66K64
#3: Protein RNA-binding protein 39


Mass: 12098.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp781I1140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3L0, UniProt: Q14498*PLUS
#4: Protein DET1- and DDB1-associated protein 1 / Placenta cross-immune reaction antigen 1 / PCIA-1


Mass: 11855.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDA1, C19orf58, PCIA1 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BW61

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Non-polymers , 4 types, 5 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-O6M / 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide


Mass: 336.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N4O2S
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M sodium HEPES, pH 7.0, 15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 47114 / % possible obs: 96.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.102 / Χ2: 0.753 / Net I/av σ(I): 12.3 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.30.4871.422040.8180.2980.5750.45892.3
2.95-33.30.41922580.8640.2560.4930.48194.2
3-3.063.30.34623070.9020.2130.4090.46194.7
3.06-3.123.40.31923360.9110.1950.3760.50696.2
3.12-3.193.30.26623040.9350.1650.3150.51995.7
3.19-3.273.20.23822150.930.150.2830.55790.6
3.27-3.353.60.20323200.9480.1230.2380.57798
3.35-3.443.70.16924160.9730.1010.1980.63798.8
3.44-3.543.70.16324200.9690.0980.1910.65499.2
3.54-3.653.70.14723720.9730.0890.1730.69699
3.65-3.783.60.13424130.9730.0820.1580.76299.1
3.78-3.943.60.13723920.3080.0860.1620.76698.5
3.94-4.113.60.09922900.9850.060.1170.85294
4.11-4.333.90.08224100.9890.0480.0960.85299.2
4.33-4.63.80.06724110.9930.0390.0780.89899.3
4.6-4.963.80.05824250.9950.0340.0680.93499.1
4.96-5.463.60.05823420.9950.0340.0670.995.6
5.46-6.243.90.06124500.9950.0350.070.88199.6
6.24-7.863.60.05223930.9960.0310.0610.92297.6
7.86-503.70.04324360.9960.0250.051.41196.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3E0C & 2JRS

3e0c

2jrs


Resolution: 2.9→49.45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 48.769 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.408 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 2310 4.9 %RANDOM
Rwork0.2083 ---
obs0.2104 44775 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.12 Å2 / Biso mean: 86.922 Å2 / Biso min: 46.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å22.33 Å2
2---0.71 Å20 Å2
3---2.59 Å2
Refinement stepCycle: final / Resolution: 2.9→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13087 0 55 1 13143
Biso mean--74.02 57.99 -
Num. residues----1649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01213460
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.63418227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89451637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15122.518695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99152342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2141580
X-RAY DIFFRACTIONr_chiral_restr0.0960.21749
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210138
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 163 -
Rwork0.342 2877 -
all-3040 -
obs--85.27 %
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)
12.80440.1622-0.16482.01910.81471.5227-0.05560.00880.36180.0675-0.10290.3898-0.0745-0.2980.15840.04110.0455-0.09770.34130.04060.579211.516414.526333.0629
24.7120.8996-0.26844.8045-1.25723.78030.16-0.136-0.8078-0.2557-0.1566-0.00530.695-0.2685-0.00340.2985-0.1444-0.15040.5390.01810.516213.039410.7641-15.2188
32.4605-0.86340.61513.36570.18431.3699-0.09620.30270.352-0.08320.1056-0.122-0.19710.2287-0.00940.0322-0.0521-0.02190.37370.06540.27442.740111.446424.5512
47.19460.61656.64981.63681.257910.264-0.0369-0.8980.72390.6547-0.13280.1528-0.116-0.51530.16960.4420.1150.08930.3805-0.05310.592343.272310.827647.1537
53.61760.62161.11417.17012.92696.6837-0.223-0.51350.7089-0.13530.3618-0.7786-0.8450.8461-0.13880.2691-0.10790.04860.6839-0.09220.675356.922831.185759.4923
63.6804-1.2192-1.6762.1740.80933.0330.23020.13660.4834-0.2932-0.0667-0.2941-0.59560.2036-0.16360.5158-0.094-0.06450.2063-0.03060.634535.968844.451860.7005
77.27471.6629-2.091416.8135.106211.9943-0.5203-0.5920.35360.4301-0.12760.6288-0.5958-1.01210.64790.31430.09090.03850.501-0.07230.536946.207717.063856.6559
85.53270.4075-0.6275.98180.93157.9831-0.0302-0.2274-0.37680.55890.071-0.26760.84080.353-0.04080.52240.07950.00710.26230.01380.562433.788823.166176.5512
95.8589-0.8555-1.96695.2210.47695.4579-0.23490.45050.3858-0.49470.26140.22650.2072-0.2072-0.02650.1362-0.0755-0.17790.5410.04160.54213.29385.369116.0003
100.37560.4729-0.13921.87532.96489.54650.18750.10590.4802-0.0237-0.22220.4396-1.0186-1.29520.03470.52030.156-0.00780.58750.03050.933712.454538.865643.1659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 396
2X-RAY DIFFRACTION2A397 - 710
3X-RAY DIFFRACTION3A711 - 1140
4X-RAY DIFFRACTION4C33 - 75
5X-RAY DIFFRACTION5C76 - 138
6X-RAY DIFFRACTION6C139 - 576
7X-RAY DIFFRACTION7C577 - 600
8X-RAY DIFFRACTION8D248 - 327
9X-RAY DIFFRACTION9E2 - 31
10X-RAY DIFFRACTION10E32 - 70

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