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- PDB-4a0k: STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CO... -

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Basic information

Entry
Database: PDB / ID: 4a0k
TitleSTRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX
Components
  • (DNA DAMAGE-BINDING PROTEIN ...) x 2
  • 12 BP DNA
  • 12 BP THF CONTAINING DNA
  • CULLIN-4A
  • E3 UBIQUITIN-PROTEIN LIGASE RBX1
KeywordsLIGASE/DNA-BINDING PROTEIN/DNA / LIGASE-DNA-BINDING PROTEIN-DNA COMPLEX / DNA-BINDING PROTEIN-DNA COMPLEX
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 / Prolactin receptor signaling / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER ...DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Prolactin receptor signaling / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / negative regulation of granulocyte differentiation / Degradation of beta-catenin by the destruction complex / eukaryotic initiation factor 4E binding / Interleukin-1 signaling / negative regulation of response to oxidative stress / KEAP1-NFE2L2 pathway / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / cullin-RING-type E3 NEDD8 transferase / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint / regulation of nucleotide-excision repair / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / VCB complex / positive regulation of protein autoubiquitination / UV-damage excision repair / protein neddylation / NEDD8 ligase activity / biological process involved in interaction with symbiont / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / protein monoubiquitination / site of DNA damage / somatic stem cell population maintenance / cullin family protein binding / hemopoiesis / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / protein K48-linked ubiquitination / response to UV / ubiquitin ligase complex / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / T cell activation / intrinsic apoptotic signaling pathway / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / cellular response to amino acid stimulus / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / protein catabolic process / regulation of circadian rhythm / Dual Incision in GG-NER / G1/S transition of mitotic cell cycle / 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 / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process
Similarity search - Function
DNA damage-binding protein 2 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain ...DNA damage-binding protein 2 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase RBX1 / Cullin-4A / DNA damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
DANIO RERIO (zebrafish)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.93 Å
AuthorsFischer, E.S. / Scrima, A. / 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: Fischer, E.S. / Scrima, A. / Bohm, K. / Matsumoto, S. / Lingaraju, G.M. / Faty, M. / Yasuda, T. / Cavadini, S. / Wakasugi, M. / Hanaoka, F. / Iwai, S. / Gut, H. / Sugasawa, K. / Thoma, N.H.
History
DepositionSep 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CULLIN-4A
B: E3 UBIQUITIN-PROTEIN LIGASE RBX1
C: DNA DAMAGE-BINDING PROTEIN 1
D: DNA DAMAGE-BINDING PROTEIN 2
E: 12 BP THF CONTAINING DNA
F: 12 BP DNA


Theoretical massNumber of molelcules
Total (without water)280,3436
Polymers280,3436
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-71.8 kcal/mol
Surface area124530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.650, 78.020, 276.620
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CULLIN-4A / CULLIN HOMOLOG 4A / CUL-4A


Mass: 86702.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 38-759
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: Q13619
#2: Protein E3 UBIQUITIN-PROTEIN LIGASE RBX1 / RING FINGER PROTEIN 75 / RING-BOX PROTEIN 1 / RBX1


Mass: 13626.354 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: P62878, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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DNA DAMAGE-BINDING PROTEIN ... , 2 types, 2 molecules CD

#3: 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: 129394.898 Da / Num. of mol.: 1
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
#4: Protein DNA DAMAGE-BINDING PROTEIN 2 / DAMAGE-SPECIFIC DNA-BINDING PROTEIN 2


Mass: 43418.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 60-423
Source method: isolated from a genetically manipulated source
Details: VARIANT WITH GLN AT POSITION 180 AND ARG AT POSITION 214 (SIMILAR TO PDB ENTRY 3EI2)
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PFASTBAC DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q2YDS1

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DNA chain , 2 types, 2 molecules EF

#5: DNA chain 12 BP THF CONTAINING DNA


Mass: 3498.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#6: DNA chain 12 BP DNA


Mass: 3702.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 8.3 / Details: 100MM TRIS-HCL PH 8.3, 33% PEG 200

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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: Jul 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5.93→50 Å / Num. obs: 11289 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.1
Reflection shellResolution: 5.93→6.08 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.41 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERMOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HYE AND 3EI2

2hye

3ei2


Resolution: 5.93→19.977 Å / SU ML: 0.91 / σ(F): 2.05 / Phase error: 30.59 / Stereochemistry target values: ML
Details: THE MOLECULAR REPLACEMENT SOLUTION HAS BEEN RIGID BODY REFINED TO OBTAIN THE OVERALL ASSEMBLY OF THE COMPLEX. NO REBUILDING HAS BEEN PERFORMED DUE TO LIMITED RESOLUTION. RBX1 RESIDUES 40-108 ...Details: THE MOLECULAR REPLACEMENT SOLUTION HAS BEEN RIGID BODY REFINED TO OBTAIN THE OVERALL ASSEMBLY OF THE COMPLEX. NO REBUILDING HAS BEEN PERFORMED DUE TO LIMITED RESOLUTION. RBX1 RESIDUES 40-108 HAVE BEEN REMOVED DUE TO UNCERTAINTY OF CONFORMATIONS. STEREOCHEMISTRY IS BASED ON THE SEARCH MODELS 3EI2 AND 2HYE.
RfactorNum. reflection% reflection
Rfree0.2695 552 5 %
Rwork0.2691 --
obs0.2691 11036 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 236.778 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 299 Å2
Refinement stepCycle: LAST / Resolution: 5.93→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17402 483 0 0 17885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918289
X-RAY DIFFRACTIONf_angle_d1.40324837
X-RAY DIFFRACTIONf_dihedral_angle_d18.1936809
X-RAY DIFFRACTIONf_chiral_restr0.092810
X-RAY DIFFRACTIONf_plane_restr0.0073105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.93-6.5080.37781370.34652606X-RAY DIFFRACTION100
6.508-7.40730.28871370.33342599X-RAY DIFFRACTION100
7.4073-9.17930.3021380.28712611X-RAY DIFFRACTION99
9.1793-19.97680.22391400.2252668X-RAY DIFFRACTION99
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)
10.6306-0.5981.02351.0331-1.20874.21490.03710.1693-0.49930.03130.0860.18940.382-0.10620.01333.1879-0.34170.06343.4784-0.21723.83786.3407-27.562588.1813
21.1421.5832-0.52432.2302-1.19082.92250.1206-0.28890.53760.61650.0860.0294-1.59560.523303.63170.03880.14284.533-0.28083.4783-3.402221.23823.1633
33.29390.3049-0.39571.52351.03022.7289-0.5643-1.3764-0.38121.02040.0946-0.16170.02950.5836-0.00063.6971-0.1934-0.09893.7015-0.23043.6823-60.869311.405795.7163
42.4472-2.5183-0.30392.7570.3472.4310.56020.88190.4902-0.58660.04770.1515-0.778-0.9763-03.988-0.0368-0.17143.5877-0.07574.0109-57.068230.706153.1332
51.54331.6867-0.79264.89350.08413.7347-0.2349-0.2978-0.8729-0.57140.173-0.40150.79370.8889-03.64580.06060.20453.5411-0.47413.9367-33.74860.913758.147
61.0437-0.07740.90090.33110.22611.0509-0.0638-1.01740.7716-0.0451-0.6177-0.2682-0.74770.8647-03.5501-0.91680.20443.7396-0.31334.3267-22.440231.881461.8636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR CHAIN B
2X-RAY DIFFRACTION2CHAIN C AND (RESSEQ 394:706)
3X-RAY DIFFRACTION3CHAIN D OR CHAIN E OR CHAIN F
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 14:354)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 1:13 OR RESSEQ 355:393 OR RESSEQ 707:1043)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 1044:1140)

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