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- PDB-2ybf: Complex of Rad18 (Rad6 binding domain) with Rad6b -

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Basic information

Entry
Database: PDB / ID: 2ybf
TitleComplex of Rad18 (Rad6 binding domain) with Rad6b
Components
  • E3 UBIQUITIN-PROTEIN LIGASE RAD18
  • UBIQUITIN-CONJUGATING ENZYME E2 B
KeywordsLIGASE / E2 UBIQUITIN CONJUGATING ENZYME / E3 UBIQUITIN LIGASE / TRANSLESION SYNTHESIS / PCNA UBIQUITINATION
Function / homology
Function and homology information


synaptonemal complex organization / negative regulation of post-translational protein modification / positive regulation of reciprocal meiotic recombination / chiasma assembly / Rad6-Rad18 complex / positive regulation of chromosome segregation / HULC complex / sperm axoneme assembly / meiotic telomere clustering / Y-form DNA binding ...synaptonemal complex organization / negative regulation of post-translational protein modification / positive regulation of reciprocal meiotic recombination / chiasma assembly / Rad6-Rad18 complex / positive regulation of chromosome segregation / HULC complex / sperm axoneme assembly / meiotic telomere clustering / Y-form DNA binding / nuclear inclusion body / protein K11-linked ubiquitination / XY body / negative regulation of cAMP-mediated signaling / postreplication repair / E2 ubiquitin-conjugating enzyme / negative regulation of reproductive process / negative regulation of developmental process / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / polyubiquitin modification-dependent protein binding / ectopic germ cell programmed cell death / protein autoubiquitination / protein K48-linked ubiquitination / response to UV / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / replication fork / Recognition of DNA damage by PCNA-containing replication complex / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / site of double-strand break / single-stranded DNA binding / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / in utero embryonic development / damaged DNA binding / nuclear body / protein stabilization / protein ubiquitination / response to xenobiotic stimulus / DNA repair / centrosome / apoptotic process / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / chromatin / negative regulation of apoptotic process / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase Rad18 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...E3 ubiquitin-protein ligase Rad18 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Ubiquitin-conjugating enzyme E2 B / E3 ubiquitin-protein ligase RAD18
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHibbert, R.G. / Sixma, T.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: E3 Ligase Rad18 Promotes Monoubiquitination Rather Than Ubiquitin Chain Formation by E2 Enzyme Rad6.
Authors: Hibbert, R.G. / Huang, A. / Boelens, R. / Sixma, T.K.
History
DepositionMar 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2 B
B: E3 UBIQUITIN-PROTEIN LIGASE RAD18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8396
Polymers20,5462
Non-polymers2934
Water1,53185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-47.4 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.210, 58.210, 167.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 B / RAD6 HOMOLOG B / HR6B / HHR6B / UBIQUITIN CARRIER PROTEIN B / UBIQUITIN-CONJUGATING ENZYME E2-17 ...RAD6 HOMOLOG B / HR6B / HHR6B / UBIQUITIN CARRIER PROTEIN B / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA / UBIQUITIN-PROTEIN LIGASE B / RAD6B


Mass: 17328.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63146, ubiquitin-protein ligase
#2: Protein/peptide E3 UBIQUITIN-PROTEIN LIGASE RAD18 / POSTREPLICATION REPAIR PROTEIN RAD18 / HHR18 / HRAD18 / RING FINGER PROTEIN 73


Mass: 3217.808 Da / Num. of mol.: 1 / Fragment: RAD6-BINDING DOMAIN, RESIDUES 340-366 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: Q9NS91, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 4 types, 89 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.99 Å3/Da / Density % sol: 38.1 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2→24.92 Å / Num. obs: 12029 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16
Reflection shellResolution: 2→2.11 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYZ

1ayz


Resolution: 2→24.92 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.518 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24204 599 5 %RANDOM
Rwork0.1989 ---
obs0.20099 11364 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.216 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å20 Å2
2---0.95 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 15 85 1490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221486
X-RAY DIFFRACTIONr_bond_other_d0.0010.021056
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9622022
X-RAY DIFFRACTIONr_angle_other_deg0.7793.0012571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5985183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86424.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70515259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1131512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
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_it0.3591.5881
X-RAY DIFFRACTIONr_mcbond_other0.0781.5340
X-RAY DIFFRACTIONr_mcangle_it0.68121440
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0953605
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7854.5575
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
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 39 -
Rwork0.23 741 -
obs--91.02 %
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)
18.27566.5613-1.99819.58111.71024.1273-0.24230.3319-0.1754-0.26170.25250.2959-0.04940.0331-0.01020.01430.00610.00660.1123-0.01940.025234.901221.7186-7.3071
24.0694-0.1843-0.96351.60061.45353.0827-0.0710.09630.0998-0.07730.00390.1001-0.1456-0.08010.06710.0512-0.0144-0.01040.06440.0140.011423.153832.16582.5521
326.6128-4.26499.03215.8483-3.06110.2139-0.795-1.27712.2020.84160.14110.3587-1.2852-0.49830.65390.3321-0.03390.03060.1782-0.19240.351722.587546.232613.8887
410.1623-0.086-1.90346.2544-1.629910.81430.002-0.6075-0.13170.68480.0999-0.1633-0.24830.1125-0.10190.09460.0348-0.02240.1746-0.07440.060337.154730.939610.6826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 20
2X-RAY DIFFRACTION2A21 - 131
3X-RAY DIFFRACTION2A1153
4X-RAY DIFFRACTION3A132 - 152
5X-RAY DIFFRACTION4B341 - 361

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