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- PDB-5o6c: Crystal Structure of a threonine-selective RCR E3 ligase -

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Basic information

Entry
Database: PDB / ID: 5o6c
TitleCrystal Structure of a threonine-selective RCR E3 ligase
ComponentsE3 ubiquitin-protein ligase MYCBP2
KeywordsLIGASE / RING Zinc binding threonine E3 ligase
Function / homology
Function and homology information


RCR-type E3 ubiquitin transferase / regulation of axon guidance / regulation of synaptic assembly at neuromuscular junction / branchiomotor neuron axon guidance / central nervous system projection neuron axonogenesis / neuromuscular process / regulation of cytoskeleton organization / protein K48-linked ubiquitination / axon guidance / guanyl-nucleotide exchange factor activity ...RCR-type E3 ubiquitin transferase / regulation of axon guidance / regulation of synaptic assembly at neuromuscular junction / branchiomotor neuron axon guidance / central nervous system projection neuron axonogenesis / neuromuscular process / regulation of cytoskeleton organization / protein K48-linked ubiquitination / axon guidance / guanyl-nucleotide exchange factor activity / positive regulation of protein ubiquitination / circadian regulation of gene expression / negative regulation of protein catabolic process / small GTPase binding / ubiquitin protein ligase activity / regulation of protein localization / microtubule cytoskeleton / protein ubiquitination / axon / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PHR / PHR domain superfamily / PHR domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) ...PHR / PHR domain superfamily / PHR domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Ring finger domain / Ring finger / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MYCBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsPao, K.-C. / Rafie, K.Z. / van Aalten, D. / Virdee, S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_12016/8 United Kingdom
Wellcome Trust110061 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity.
Authors: Pao, K.C. / Wood, N.T. / Knebel, A. / Rafie, K. / Stanley, M. / Mabbitt, P.D. / Sundaramoorthy, R. / Hofmann, K. / van Aalten, D.M.F. / Virdee, S.
History
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase MYCBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1097
Polymers29,7161
Non-polymers3926
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.578, 82.578, 103.303
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein E3 ubiquitin-protein ligase MYCBP2 / Myc-binding protein 2 / Pam/highwire/rpm-1 protein / Protein associated with Myc / RING-type E3 ...Myc-binding protein 2 / Pam/highwire/rpm-1 protein / Protein associated with Myc / RING-type E3 ubiquitin transferase MYCBP2


Mass: 29716.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYCBP2, KIAA0916, PAM / Production host: Escherichia coli (E. coli)
References: UniProt: O75592, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.38 Å3/Da / Density % sol: 63.63 % / Description: Bipyramidal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 23.3 mM Na2HPO4 23.3 mM (NH4)2SO4 23.3 mM NaNO3 18 % PEG500 MME 9 % PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2823 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 40007 / % possible obs: 99.3 % / Observed criterion σ(I): 18.3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.4 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.927 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 823 2.1 %RANDOM
Rwork0.17192 ---
obs0.17245 39140 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 6 257 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192063
X-RAY DIFFRACTIONr_bond_other_d0.0010.021905
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9662775
X-RAY DIFFRACTIONr_angle_other_deg0.9793.0094376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62522.91796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66615339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8891516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
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_it2.5172.571008
X-RAY DIFFRACTIONr_mcbond_other2.5062.5661007
X-RAY DIFFRACTIONr_mcangle_it3.3053.841257
X-RAY DIFFRACTIONr_mcangle_other3.3123.8441258
X-RAY DIFFRACTIONr_scbond_it3.8622.9361055
X-RAY DIFFRACTIONr_scbond_other3.8622.9391056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8984.2491518
X-RAY DIFFRACTIONr_long_range_B_refined7.35521.6672526
X-RAY DIFFRACTIONr_long_range_B_other7.3221.1852417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 49 -
Rwork0.263 2726 -
obs--94.16 %

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