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- PDB-6im9: MDM2 bound CueO-PM2 sensor -

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Basic information

Entry
Database: PDB / ID: 6im9
TitleMDM2 bound CueO-PM2 sensor
Components
  • Blue copper oxidase CueO,PM2 peptide,Blue copper oxidase CueO
  • E3 ubiquitin-protein ligase Mdm2
KeywordsOXIDOREDUCTASE / Multicopper oxidase / Laccase / MDM2
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / oxidoreductase activity, acting on metal ions / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission ...oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / oxidoreductase activity, acting on metal ions / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / fibroblast activation / detoxification of copper ion / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / peroxisome proliferator activated receptor binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of vascular associated smooth muscle cell migration / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / negative regulation of protein processing / SUMO transferase activity / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / response to iron ion / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / response to copper ion / positive regulation of muscle cell differentiation / cardiac septum morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / blood vessel development / SUMOylation of ubiquitinylation proteins / ligase activity / cellular response to alkaloid / Constitutive Signaling by AKT1 E17K in Cancer / regulation of protein catabolic process / negative regulation of signal transduction by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / ferroxidase activity / SUMOylation of transcription factors / response to magnesium ion / cellular response to UV-C / protein sumoylation / cellular response to actinomycin D / blood vessel remodeling / cellular response to estrogen stimulus / protein localization to nucleus / ribonucleoprotein complex binding / protein autoubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / NPAS4 regulates expression of target genes / transcription repressor complex / positive regulation of mitotic cell cycle / regulation of heart rate / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / ubiquitin binding / response to cocaine / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / establishment of protein localization / Regulation of RUNX3 expression and activity / cellular response to gamma radiation / Oncogene Induced Senescence / RING-type E3 ubiquitin transferase / protein destabilization / Regulation of TP53 Activity through Methylation / cellular response to growth factor stimulus / response to toxic substance / centriolar satellite / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / p53 binding / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / outer membrane-bounded periplasmic space / 5S rRNA binding / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / periplasmic space / regulation of cell cycle / Ub-specific processing proteases / postsynaptic density / protein ubiquitination / response to xenobiotic stimulus / copper ion binding / protein domain specific binding
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Multicopper oxidase, C-terminal / Multicopper oxidase / Zinc finger, C3HC4 type (RING finger) / Multicopper oxidase, type 1 / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Multicopper oxidase / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Multicopper oxidase CueO / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWongsantichon, J. / Robinson, R. / Ghadessy, F.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Development and structural characterization of an engineered multi-copper oxidase reporter of protein-protein interactions.
Authors: Sana, B. / Chee, S.M.Q. / Wongsantichon, J. / Raghavan, S. / Robinson, R.C. / Ghadessy, F.J.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue copper oxidase CueO,PM2 peptide,Blue copper oxidase CueO
B: E3 ubiquitin-protein ligase Mdm2


Theoretical massNumber of molelcules
Total (without water)69,5962
Polymers69,5962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, 1:1 ratio
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-15 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.636, 83.636, 240.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein Blue copper oxidase CueO,PM2 peptide,Blue copper oxidase CueO / Copper efflux oxidase


Mass: 55846.766 Da / Num. of mol.: 1 / Mutation: M358I
Source method: isolated from a genetically manipulated source
Details: Chimera protein CueO-PM2 multicopper oxidase
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others)
Strain: K12 / Gene: cueO, yacK, b0123, JW0119 / Production host: Escherichia coli (E. coli) / References: UniProt: P36649
#2: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53- ...Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 13749.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase

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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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 15209 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 66.85 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.023 / Rrim(I) all: 0.052 / Χ2: 0.902 / Net I/σ(I): 14.1 / Num. measured all: 77012
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.383.40.2828500.9610.1590.3260.80185.8
3.38-3.463.80.2639750.9670.1460.3030.80296.3
3.46-3.554.50.2369900.9880.1230.2670.84299.7
3.55-3.6650.23110110.9820.1140.2580.876100
3.66-3.785.40.16310020.9920.0780.1810.904100
3.78-3.915.50.12110040.9940.0570.1340.86699.9
3.91-4.075.50.08410030.9970.040.0930.835100
4.07-4.255.60.06510340.9990.0310.0720.88100
4.25-4.485.60.05210050.9970.0250.0580.86599.9
4.48-4.765.40.04310190.9980.020.0470.815100
4.76-5.125.50.04310420.9970.0210.0480.917100
5.12-5.635.40.04910410.9960.0230.0541.207100
5.63-6.445.30.0510410.9970.0240.0561.33100
6.44-8.0950.03210630.9980.0160.0360.94899.7
8.09-304.80.01911290.9990.0090.0210.51798.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KV7 and 5WTS

1kv7

5wts


Resolution: 3.3→28.92 Å / SU ML: 0.4473 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.483 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2493 707 4.99 %
Rwork0.1766 13454 -
obs0.1801 14161 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.27 Å2
Refinement stepCycle: LAST / Resolution: 3.3→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 0 0 4493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01084604
X-RAY DIFFRACTIONf_angle_d1.21516248
X-RAY DIFFRACTIONf_chiral_restr0.0606690
X-RAY DIFFRACTIONf_plane_restr0.009809
X-RAY DIFFRACTIONf_dihedral_angle_d7.80042756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.550.37791010.24951727X-RAY DIFFRACTION60.87
3.55-3.910.28851440.2062837X-RAY DIFFRACTION99.14
3.91-4.470.22551560.15812877X-RAY DIFFRACTION100
4.47-5.630.19431520.15452956X-RAY DIFFRACTION100
5.63-28.920.26671540.17543057X-RAY DIFFRACTION99.47
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)
11.093918576830.4416060782870.4333151018541.84619797511-0.3052404393111.14745516404-0.0283460089867-0.162185608399-0.1438537218650.5016300745090.1163196111950.1887384080820.207626663914-0.49974947726-0.09057059220520.803100673073-0.5692626181580.204927734870.355622486410.004884387551830.44099518477425.4481357921-24.24174386029.71564666953
21.801552933440.182241482591.737046618351.12752286111-0.2722661716811.903909846260.16773333422-0.14975834701-0.1982746187730.420968939024-0.02467435723650.02792229579990.243541584444-0.16417673413-0.1053142095421.21743263837-0.1554584993620.1356134426820.509037468689-0.1344580628680.54436170665538.6144980754-8.7026143653128.0426319
31.021685770460.1091385812550.639971405741.81680465942-0.6134822195291.90065100728-0.139912957703-0.3548384353120.1248898206440.4912505881730.0713565906140.413632684916-0.19815875196-0.4551467759650.05061080903190.873931210523-0.1977648727380.1568876282830.488655509194-0.07894376854730.36983210469526.2805753166-6.5649900513116.9785628177
47.74904561558-4.58367903434-1.01240315235.951460334250.02243695400530.235007850499-0.0183114440587-0.005302248550920.4909651010650.146196733589-0.05997001660130.018089676559-0.150717538310.06829245567210.05560190651830.8936718235030.1376521691440.04037938824430.356096308143-0.07972179962860.37499603669549.939101518-3.4940867031559.0886231526
56.338482414971.289197205122.453819057142.10595354507-1.070995340182.3239302520.00534923783782-0.0559465155283-0.06941208602170.046618844511-0.0939900994312-0.5511658329460.001720124662930.6101454297290.08002080447630.7383634897270.0739619215063-0.07086893964190.482262587947-0.04089952561260.48944923333762.3223693002-3.1987293406456.8046707341
64.55162649245-1.83958006923-1.957268691131.123855073540.4766535384971.102813890750.128301644458-0.310472976170.5745881099440.282134698558-0.0412255888233-0.327444060429-0.7002197691050.475865642718-0.08082144793410.9285822055780.106647663183-0.05925502568220.545980534449-0.1630348917940.54883774728857.00623814053.1418994545756.1176597163
77.84587119266-0.583608794337-2.09212988692.966093382710.3610757828883.55335184172-0.0186828035042-0.1327170384740.198622418993-0.009197190088180.0015678738269-0.207142219085-0.1567442983890.223190789355-0.03653745207260.9670751187570.0731230074371-0.03707766566310.433975809168-0.04472020805260.32137582915356.4482410991-1.6956530225747.3182724537
80.273121196173-0.295686701266-1.012225506110.3245369089341.104365436963.7598657025-0.06983595974580.47440215271-0.35564341134-0.3762706331250.180366252183-0.3998233637580.09411176436130.498019958798-0.1451293882221.002909896750.1373877548590.2185313194360.8044406828160.0009533347661260.88557061552963.7334654326-9.7490388774836.0439525207
93.213175878171.372004553513.801192014790.6030040978741.496338445135.42335118025-0.002486072301380.194175148989-0.345579875281-0.1288182490960.0948684124316-0.642854834310.3191353251370.979533355196-0.1061899431921.087127387150.3667007123270.05882839979080.708255352204-0.1408422272760.7543728621465.3427458817-12.57039757747.6957197394
104.62505140215-1.707258917942.740733411452.73433147017-1.027973483753.06588345394-0.133688953557-0.0898113976896-0.3811216956850.3204203988380.0970612197799-0.1047982303090.4397271511190.1228466474180.02727955971130.980222230290.3308630138830.1966276900070.453261828371-0.2927721143770.79603266014858.5549158892-16.34905379343.7589622711
110.344904695775-0.01732662974340.1494860805510.447939219311-0.095928397492.49811910107-0.04561784898540.117894900433-0.336663420578-0.170535429794-0.03351901233290.1201974715860.2788159092370.07761706269520.07196425069471.039382148820.282478100861-0.06139671922520.280601187602-0.1221276929620.52875388072851.0685401485-12.158121129853.7486831712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 342 )
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 444 )
3X-RAY DIFFRACTION3chain 'A' and (resid 445 through 520 )
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 31 )
5X-RAY DIFFRACTION5chain 'B' and (resid 32 through 39 )
6X-RAY DIFFRACTION6chain 'B' and (resid 40 through 49 )
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 73 )
9X-RAY DIFFRACTION9chain 'B' and (resid 74 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 95 )
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 111 )

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