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- PDB-6sqp: Crystal structure of Cat MDM2-S429E RING domain homodimer -

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Basic information

Entry
Database: PDB / ID: 6sqp
TitleCrystal structure of Cat MDM2-S429E RING domain homodimer
Components(E3 ubiquitin-protein ligase ...) x 3
KeywordsLIGASE / MDM2 / MDMX / ubiquitin ligase / E3 / phosphorylation
Function / homology
Function and homology information


regulation of biological quality / ribonucleoprotein complex binding / positive regulation of mitotic cell cycle / ubiquitin binding / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / 5S rRNA binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of DNA-templated transcription ...regulation of biological quality / ribonucleoprotein complex binding / positive regulation of mitotic cell cycle / ubiquitin binding / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / 5S rRNA binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsMagnussen, H.M. / Ahmed, S.F. / Huang, D.T.
Funding support United Kingdom, Belgium, 2items
OrganizationGrant numberCountry
Cancer Research UKA23278 United Kingdom
European Research Council647849 Belgium
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain.
Authors: Magnussen, H.M. / Ahmed, S.F. / Sibbet, G.J. / Hristova, V.A. / Nomura, K. / Hock, A.K. / Archibald, L.J. / Jamieson, A.G. / Fushman, D. / Vousden, K.H. / Weissman, A.M. / Huang, D.T.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: E3 ubiquitin-protein ligase Mdm2
B: E3 ubiquitin-protein ligase Mdm2
C: E3 ubiquitin-protein ligase Mdm2
D: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,62815
Polymers29,9724
Non-polymers65611
Water4,378243
1
A: E3 ubiquitin-protein ligase Mdm2
B: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1707
Polymers14,8732
Non-polymers2975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-30 kcal/mol
Surface area7240 Å2
2
C: E3 ubiquitin-protein ligase Mdm2
D: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4588
Polymers15,0992
Non-polymers3596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-28 kcal/mol
Surface area7580 Å2
Unit cell
Length a, b, c (Å)29.240, 39.760, 104.380
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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E3 ubiquitin-protein ligase ... , 3 types, 4 molecules ABDC

#1: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 7152.696 Da / Num. of mol.: 1 / Mutation: S429E, G443T
Source method: isolated from a genetically manipulated source
Details: Residues 422-491 and contains S429E and G443T mutation. GS at the N-terminus resulted from cloning.
Source: (gene. exp.) Felis catus (domestic cat) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7YRZ8, RING-type E3 ubiquitin transferase
#2: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 7720.328 Da / Num. of mol.: 2 / Mutation: S429E, G443T
Source method: isolated from a genetically manipulated source
Details: Residues 422-491 and contains S429E and G443T. GS at the N-terminus resulted from cloning.
Source: (gene. exp.) Felis catus (domestic cat) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7YRZ8, RING-type E3 ubiquitin transferase
#3: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 7378.926 Da / Num. of mol.: 1 / Mutation: S429E, G443T
Source method: isolated from a genetically manipulated source
Details: Residues 422-491 and contains S429E and G443T. GS at the N-terminus resulted from cloning.
Source: (gene. exp.) Felis catus (domestic cat) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7YRZ8, RING-type E3 ubiquitin transferase

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Non-polymers , 4 types, 254 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.1 M MMT, pH 9.0 and 25% (w/v) PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.21→23.53 Å / Num. obs: 71796 / % possible obs: 98.3 % / Redundancy: 3.2 % / CC1/2: 0.991 / Net I/σ(I): 5.1
Reflection shellResolution: 1.21→1.24 Å / Num. unique obs: 5274 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNJ

5mnj


Resolution: 1.21→23.53 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.212 --
Rwork0.171 --
obs-71796 98.3 %
Refinement stepCycle: LAST / Resolution: 1.21→23.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 14 243 2268

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