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- PDB-4ci1: Structure of the DDB1-CRBN E3 ubiquitin ligase bound to thalidomide -

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Basic information

Entry
Database: PDB / ID: 4ci1
TitleStructure of the DDB1-CRBN E3 ubiquitin ligase bound to thalidomide
Components
  • DNA DAMAGE-BINDING PROTEIN 1
  • PROTEIN CEREBLON
KeywordsDNA BINDING PROTEIN/PROTEIN / DNA BINDING PROTEIN-PROTEIN COMPLEX / DNA BINDING PROTEIN-PROTEIN BINDING COMPLEX / UBIQUITIN / CONT
Function / homology
Function and homology information


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 / Cul4A-RING E3 ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4B-RING E3 ubiquitin ligase complex ...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 / Cul4A-RING E3 ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / 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 / chromosome, telomeric region / damaged DNA binding / 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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Peptide methionine sulfoxide reductase. / DNA polymerase; domain 1 - #910 / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / CULT domain / CULT domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Peptide methionine sulfoxide reductase. / DNA polymerase; domain 1 - #910 / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / 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 / PUA-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Beta Complex / DNA polymerase; domain 1 / Roll / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-Thalidomide / Protein cereblon / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
GALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsFischer, E.S. / Boehm, K. / Thoma, N.H.
CitationJournal: Nature / Year: 2014
Title: Structure of the Ddb1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide.
Authors: Fischer, E.S. / Bohm, K. / Lydeard, J.R. / Yang, H. / Stadler, M.B. / Cavadini, S. / Nagel, J. / Serluca, F. / Acker, V. / Lingaraju, G.M. / Tichkule, R.B. / Schebesta, M. / Forrester, W.C. ...Authors: Fischer, E.S. / Bohm, K. / Lydeard, J.R. / Yang, H. / Stadler, M.B. / Cavadini, S. / Nagel, J. / Serluca, F. / Acker, V. / Lingaraju, G.M. / Tichkule, R.B. / Schebesta, M. / Forrester, W.C. / Schirle, M. / Hassiepen, U. / Ottl, J. / Hild, M. / Beckwith, R.E.J. / Harper, J.W. / Jenkins, J.L. / Thoma, N.H.
History
DepositionDec 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Structure summary
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Aug 13, 2014Group: Database references
Revision 1.4Apr 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 / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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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: PROTEIN CEREBLON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,0254
Polymers183,7012
Non-polymers3242
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-17.8 kcal/mol
Surface area60260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.180, 172.180, 140.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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: 129493.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC DUAL / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q16531
#2: Protein PROTEIN CEREBLON


Mass: 54207.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PFASTBAC DUAL / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P0CF65
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EF2 / S-Thalidomide / Thalidomide


Mass: 258.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.18 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE; 80 MM NAH2PO4; 120 MM K2HPO4; 800 MM TRI-NA CITRATE., pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.98→30 Å / Num. obs: 49202 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 97.97 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.77
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.22 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DDB1

Resolution: 2.98→29.82 Å / Cor.coef. Fo:Fc: 0.9359 / Cor.coef. Fo:Fc free: 0.9044 / SU R Cruickshank DPI: 1.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.89 / SU Rfree Blow DPI: 0.324 / SU Rfree Cruickshank DPI: 0.334
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2460 5 %RANDOM
Rwork0.1969 ---
obs0.1987 49199 99.97 %-
Displacement parametersBiso mean: 87.64 Å2
Baniso -1Baniso -2Baniso -3
1-5.9433 Å20 Å20 Å2
2--5.9433 Å20 Å2
3----11.8865 Å2
Refine analyzeLuzzati coordinate error obs: 0.483 Å
Refinement stepCycle: LAST / Resolution: 2.98→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11405 0 20 35 11460
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811655HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1115829HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4013SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes289HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1678HARMONIC5
X-RAY DIFFRACTIONt_it11655HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion16.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1555SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12604SEMIHARMONIC4
LS refinement shellResolution: 2.98→3.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3069 179 5 %
Rwork0.2769 3402 -
all0.2784 3581 -
obs--99.97 %
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)
12.0864-0.4234-0.03830.37920.14620.7967-0.1327-0.10180.02540.20990.15470.1163-0.205-0.0604-0.02190.00720.0158-0.1341-0.2312-0.0633-0.2698-61.959448.776218.7705
21.8304-1.3382-0.35292.1196-0.03390.1610.05120.16230.195-0.2055-0.24460.0352-0.2074-0.08730.1934-0.04460.0652-0.07490.0045-0.0708-0.1636-16.71618.818213.4487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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