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- PDB-5trb: Crystal structure of the RNF20 RING domain -

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Basic information

Entry
Database: PDB / ID: 5trb
TitleCrystal structure of the RNF20 RING domain
ComponentsE3 ubiquitin-protein ligase BRE1A
KeywordsLIGASE
Function / homology
Function and homology information


histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / ubiquitin ligase complex / negative regulation of cell migration / mRNA 3'-UTR binding / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / ubiquitin ligase complex / negative regulation of cell migration / mRNA 3'-UTR binding / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / p53 binding / E3 ubiquitin ligases ubiquitinate target proteins / histone binding / ubiquitin-dependent protein catabolic process / transcription coactivator activity / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
E3 ubiquitin ligase Bre1 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin ligase Bre1 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase BRE1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsFoglizzo, M. / Middleton, A.J. / Day, C.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure and Function of the RING Domains of RNF20 and RNF40, Dimeric E3 Ligases that Monoubiquitylate Histone H2B.
Authors: Foglizzo, M. / Middleton, A.J. / Day, C.L.
History
DepositionOct 25, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionNov 2, 2016ID: 5DNG
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase BRE1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8463
Polymers8,7151
Non-polymers1312
Water54030
1
A: E3 ubiquitin-protein ligase BRE1A
hetero molecules

A: E3 ubiquitin-protein ligase BRE1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6926
Polymers17,4312
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556-x+1/2,y,-z+11
Buried area1850 Å2
ΔGint-17 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.830, 61.290, 78.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein E3 ubiquitin-protein ligase BRE1A / hBRE1 / RING finger protein 20


Mass: 8715.255 Da / Num. of mol.: 1 / Fragment: residues 906-975
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF20, BRE1A / Production host: Escherichia coli (E. coli)
References: UniProt: Q5VTR2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% (w/v) PEG 4000 (polyethylene glycol 4000), 16% (v/v) glycerol, 0.02 M of each carboxylic acid (sodium formate, ammonium acetate, trisodium citrate and sodium potassium L-tartrate) and 0.1 ...Details: 8% (w/v) PEG 4000 (polyethylene glycol 4000), 16% (v/v) glycerol, 0.02 M of each carboxylic acid (sodium formate, ammonium acetate, trisodium citrate and sodium potassium L-tartrate) and 0.1 M MES/Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.2816, 1.2856, 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28161
21.28561
30.95371
ReflectionResolution: 1.8→39.34 Å / Num. obs: 8140 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 26.28 Å2 / Rsym value: 0.097 / Net I/av σ(I): 5.497 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.99.41.0740.61100
1.9-2.019.30.6411100
2.01-2.159.30.33821100
2.15-2.329.30.22431100
2.32-2.559.30.1424.91100
2.55-2.859.10.0917.71100
2.85-3.298.90.079.11100
3.29-4.038.60.0619.81100
4.03-5.698.10.05411.21100
1.8-5.697.70.03914.5199.1

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
PHENIXphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.335 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.99
RfactorNum. reflection% reflection
Rfree0.2355 384 4.72 %
Rwork0.2156 --
obs0.2166 8140 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.65 Å2 / Biso mean: 30.83 Å2 / Biso min: 19.28 Å2
Refinement stepCycle: final / Resolution: 1.8→39.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 2 30 599
Biso mean--25.26 35.2 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008578
X-RAY DIFFRACTIONf_angle_d0.844772
X-RAY DIFFRACTIONf_chiral_restr0.05681
X-RAY DIFFRACTIONf_plane_restr0.00599
X-RAY DIFFRACTIONf_dihedral_angle_d9.607358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-2.5960.21561380.19792667X-RAY DIFFRACTION100
1.8001-2.06050.311150.25962552X-RAY DIFFRACTION100
2.0605-2.5960.25361310.24142537X-RAY DIFFRACTION100

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