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- PDB-2ruh: Chemical Shift Assignments for MIP and MDM2 in bound state -

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Basic information

Entry
Database: PDB / ID: 2ruh
TitleChemical Shift Assignments for MIP and MDM2 in bound state
ComponentsE3 ubiquitin-protein ligase Mdm2
KeywordsPEPTIDE BINDING PROTEIN / Ubiquitin Ligase
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to iron ion / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / ligase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / protein localization to nucleus / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / response to cocaine / proteolysis involved in protein catabolic process / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / establishment of protein localization / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / response to toxic substance / cellular response to gamma radiation / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / cellular response to hypoxia / 5S rRNA binding / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm
Similarity search - Function
MDM2 / SWIB/MDM2 domain / 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 ...MDM2 / SWIB/MDM2 domain / 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, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsNagata, T. / Shirakawa, K. / Kobayashi, N. / Shiheido, H. / Horisawa, K. / Katahira, M. / Doi, N. / Yanagawa, H.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display
Authors: Nagata, T. / Shirakawa, K. / Kobayashi, N. / Shiheido, H. / Tabata, N. / Sakuma-Yonemura, Y. / Horisawa, K. / Katahira, M. / Doi, N. / Yanagawa, H.
History
DepositionJun 3, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Mdm2


Theoretical massNumber of molelcules
Total (without water)15,0311
Polymers15,0311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / p53-binding protein Mdm2


Mass: 15031.417 Da / Num. of mol.: 1 / Fragment: MIP-MDM2 fusion, UNP residues 6-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Protein expresses as HAT-GB1-(Thrombin cleavage site)-MIP-(TEV cleavage site)-MDM2-T7tag fusion.
Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00987, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11413D (H)CCH-COSY

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Sample preparation

DetailsContents: 650 uM [U-100% 13C; U-100% 15N] MIP-MDM2 fusion-1, 20 mM TRIS-2, 300 mM sodium chloride-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
650 uMMIP-MDM2 fusion-1[U-100% 13C; U-100% 15N]1
20 mMTRIS-21
300 mMsodium chloride-31
Sample conditionsIonic strength: 160 / pH: 7.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.0.14Guntert, Mumenthaler and Wuthrichstructure solution
KUJIRA0.984Naohiro Kobayashichemical shift assignment
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
ChimeraUCSFdata analysis
RefinementMethod: distance geometry / Software ordinal: 1
Details: AMBER12 using the AMBER 2003 force field and a generalized Born model
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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