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- PDB-4a0l: Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site co... -

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Basic information

Entry
Database: PDB / ID: 4a0l
TitleStructure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex
Components
  • (DNA DAMAGE-BINDING PROTEIN ...) x 2
  • 12 BP DNA DUPLEX
  • 12 BP THF CONTAINING DNA DUPLEX
  • CULLIN-4B
  • E3 UBIQUITIN-PROTEIN LIGASE RBX1
KeywordsLIGASE/DNA-BINDING PROTEIN/DNA / LIGASE-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 / Ub-specific processing proteases / 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 ...DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Prolactin receptor signaling / Ub-specific processing proteases / 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 / Degradation of beta-catenin by the destruction complex / eukaryotic initiation factor 4E binding / Interleukin-1 signaling / anaphase-promoting complex / KEAP1-NFE2L2 pathway / 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 / 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 / astrocyte differentiation / UV-damage excision repair / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / biological process involved in interaction with symbiont / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / protein monoubiquitination / site of DNA damage / cullin family protein binding / viral release from host cell / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / ectopic germ cell programmed cell death / positive regulation of viral genome replication / ubiquitin ligase complex / response to UV / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / T cell activation / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / cellular response to amino acid stimulus / DNA Damage Recognition in GG-NER / protein catabolic process / G1/S transition of mitotic cell cycle / RING-type E3 ubiquitin transferase / 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 / protein polyubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / neuron projection development / cellular response to UV / rhythmic process / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome biogenesis / site of double-strand break
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. / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase RBX1 / Cullin-4B / DNA damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DANIO RERIO (zebrafish)
MUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.4 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 1.1Nov 7, 2012Group: Database references
Revision 1.2Mar 27, 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_seq_map_depositor_info / struct_biol / struct_conn
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Apr 3, 2019Group: Data collection / Category: pdbx_seq_map_depositor_info / Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 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: DNA DAMAGE-BINDING PROTEIN 1
B: DNA DAMAGE-BINDING PROTEIN 2
C: DNA DAMAGE-BINDING PROTEIN 1
D: DNA DAMAGE-BINDING PROTEIN 2
E: CULLIN-4B
F: E3 UBIQUITIN-PROTEIN LIGASE RBX1
H: CULLIN-4B
I: E3 UBIQUITIN-PROTEIN LIGASE RBX1
R: 12 BP THF CONTAINING DNA DUPLEX
S: 12 BP DNA DUPLEX
T: 12 BP THF CONTAINING DNA DUPLEX
U: 12 BP DNA DUPLEX


Theoretical massNumber of molelcules
Total (without water)548,73612
Polymers548,73612
Non-polymers00
Water0
1
A: DNA DAMAGE-BINDING PROTEIN 1
B: DNA DAMAGE-BINDING PROTEIN 2
E: CULLIN-4B
F: E3 UBIQUITIN-PROTEIN LIGASE RBX1
R: 12 BP THF CONTAINING DNA DUPLEX
S: 12 BP DNA DUPLEX


Theoretical massNumber of molelcules
Total (without water)274,3686
Polymers274,3686
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-79.9 kcal/mol
Surface area123470 Å2
MethodPISA
2
C: DNA DAMAGE-BINDING PROTEIN 1
D: DNA DAMAGE-BINDING PROTEIN 2
H: CULLIN-4B
I: E3 UBIQUITIN-PROTEIN LIGASE RBX1
T: 12 BP THF CONTAINING DNA DUPLEX
U: 12 BP DNA DUPLEX


Theoretical massNumber of molelcules
Total (without water)274,3686
Polymers274,3686
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-74.5 kcal/mol
Surface area121070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.800, 155.840, 255.390
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA DAMAGE-BINDING PROTEIN ... , 2 types, 4 molecules ACBD

#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: 127425.812 Da / Num. of mol.: 2
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
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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Protein , 2 types, 4 molecules EHFI

#3: Protein CULLIN-4B / CULLIN HOMOLOG 4B / CUL-4B


Mass: 84992.195 Da / Num. of mol.: 2 / Fragment: RESIDUES 193-913
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: Q13620
#4: Protein E3 UBIQUITIN-PROTEIN LIGASE RBX1 / RING FINGER PROTEIN 75 / RING-BOX PROTEIN 1 / RBX1


Mass: 11330.942 Da / Num. of mol.: 2 / 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

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DNA chain , 2 types, 4 molecules RTSU

#5: DNA chain 12 BP THF CONTAINING DNA DUPLEX


Mass: 3498.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#6: DNA chain 12 BP DNA DUPLEX


Mass: 3702.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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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: 4.6 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 6.2 / Details: 100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0015
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 7.4→30 Å / Num. obs: 13547 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 7.4→7.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3EI2, 4A0C

3ei2

4a0c


Resolution: 7.4→29.862 Å / SU ML: 2.21 / σ(F): 2 / Phase error: 34.97 / 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 AND CUL4B RESIDUES 208-209 HAVE BEEN REMOVED DUE TO UNCERTAINTY OF CONFORMATIONS. STEREOCHEMISTRY IS BASED ON THE SEARCH MODELS 3EI2 AND 4A0C.
RfactorNum. reflection% reflection
Rfree0.3199 1352 10 %
Rwork0.3178 --
obs0.318 13523 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 143.782 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 344 Å2
Refinement stepCycle: LAST / Resolution: 7.4→29.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34587 966 0 0 35553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836315
X-RAY DIFFRACTIONf_angle_d1.23349309
X-RAY DIFFRACTIONf_dihedral_angle_d18.54513521
X-RAY DIFFRACTIONf_chiral_restr0.0835617
X-RAY DIFFRACTIONf_plane_restr0.0066162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.4001-7.66030.39251340.38471202X-RAY DIFFRACTION99
7.6603-7.96150.37981340.39381206X-RAY DIFFRACTION99
7.9615-8.31640.42031320.36611198X-RAY DIFFRACTION99
8.3164-8.74440.33541370.36151241X-RAY DIFFRACTION99
8.7444-9.27680.33671340.34821205X-RAY DIFFRACTION99
9.2768-9.96830.27981340.31061206X-RAY DIFFRACTION99
9.9683-10.92650.30091360.27061219X-RAY DIFFRACTION99
10.9265-12.40730.23791340.25571205X-RAY DIFFRACTION99
12.4073-15.27540.30221370.26621234X-RAY DIFFRACTION99
15.2754-29.86230.35971400.37051255X-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)
12.16092.75872.21584.06970.87253.06240.40510.1255-0.340.69880.14120.0398-0.1921-0.4892-0.41971.64320.09560.67292.3331-0.06111.64669.0148-1.741427.691
23.89641.0343-0.47680.62480.00954.6669-0.8249-1.3288-0.7139-0.1346-0.61490.972-0.39220.06081.10214.5984-0.8239-0.76513.73710.49633.193829.28362.088178.0278
32.16671.0471.73693.6670.97351.82660.10940.4382-0.57330.10550.07220.5298-0.1616-0.3858-0.07351.711-0.06950.82122.53060.09161.3205-40.783758.30922.5275
42.0569-1.31091.47495.76832.74933.55641.1303-1.1532-0.69230.70350.31160.53681.951-1.1286-1.29542.332-0.5710.08552.28010.46471.9873-12.355562.868469.1982
50.09150.8887-0.14221.4119-0.2719-0.0962-0.892-1.56180.23882.21090.5971-0.4475-1.3757-0.7753-0.25623.72930.43480.25043.7199-0.47772.1247-6.1137-53.088175.563
61.81390.4156-0.33791.0881-0.81660.11160.1779-0.99410.27291.1918-0.1075-0.0393-0.4284-0.2648-0.14884.4176-0.4538-0.41723.2456-0.10552.948-71.975931.482677.202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B OR CHAIN R OR CHAIN S
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D OR CHAIN T OR CHAIN U
5X-RAY DIFFRACTION5CHAIN E OR CHAIN F
6X-RAY DIFFRACTION6CHAIN H OR CHAIN I

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