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- PDB-6sqr: Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub -

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Basic information

Entry
Database: PDB / ID: 6sqr
TitleCrystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub
Components
  • (E3 ubiquitin-protein ligase ...) x 3
  • Polyubiquitin-C
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / MDM2 / MDMX / p53 / E3 / E2 / ubiquitin / ubiquitin ligase / phosphorylation
Function / homology
Function and homology information


regulation of biological quality / (E3-independent) E2 ubiquitin-conjugating enzyme / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / Ribosomal scanning and start codon recognition / Translation initiation complex formation / ubiquitin conjugating enzyme activity / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis ...regulation of biological quality / (E3-independent) E2 ubiquitin-conjugating enzyme / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / Ribosomal scanning and start codon recognition / Translation initiation complex formation / ubiquitin conjugating enzyme activity / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / protein K48-linked ubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein autoubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / positive regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex
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, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. ...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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Ubiquitin-ribosomal protein eS31 fusion protein / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-ribosomal protein eS31 fusion protein / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesFelis catus (domestic cat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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: 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Mdm2
B: Ubiquitin-conjugating enzyme E2 D2
C: Ubiquitin-40S ribosomal protein S27a
D: E3 ubiquitin-protein ligase Mdm2
E: Ubiquitin-conjugating enzyme E2 D2
F: Ubiquitin-40S ribosomal protein S27a
G: E3 ubiquitin-protein ligase Mdm2
H: Ubiquitin-conjugating enzyme E2 D2
I: Polyubiquitin-C
J: E3 ubiquitin-protein ligase Mdm2
K: Ubiquitin-conjugating enzyme E2 D2
L: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,40535
Polymers130,95112
Non-polymers1,45423
Water7,566420
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: surface plasmon resonance, Activity assays validated the assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25230 Å2
ΔGint-54 kcal/mol
Surface area49150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.510, 163.880, 70.600
Angle α, β, γ (deg.)90.00, 96.03, 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 ADJG

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


Mass: 7849.443 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
#4: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 7249.811 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
#5: 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. 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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Protein , 3 types, 8 molecules BEHKCFLI

#2: Protein
Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16720.186 Da / Num. of mol.: 4 / Mutation: S22R, C85K
Source method: isolated from a genetically manipulated source
Details: Contains S22R and C85K mutations. K85 in Chains B, H, K form a covalent bond with G76 in Chains C, I and L, respectively.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 8663.908 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Contains a GSGGS at the N-terminus resulted from cloning. G76 in Chains C, F, L form a covalent bond with K85 sidechain in Chains B, E, K, respectively.
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli (E. coli) / References: UniProt: J3QTR3, UniProt: P62979*PLUS
#6: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains a GSGGS at the N-terminus resulted from cloning. G76 in Chain I form a covalent bond with K85 sidechain in Chain H.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

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Non-polymers , 4 types, 443 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.1 M Tris-HCl, pH 8.5, 20% (v/v) PEG Smear High

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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: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.18→70 Å / Num. obs: 65509 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.994 / Net I/σ(I): 9.4
Reflection shellResolution: 2.18→2.22 Å / Num. unique obs: 3248 / CC1/2: 0.56

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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: 2.18→70 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.227 --
Rwork0.166 --
obs-65509 98.8 %
Refinement stepCycle: LAST / Resolution: 2.18→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9061 0 68 420 9549

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