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- PDB-7ahz: Crystal structure of Western clawed frog MDM2 RING domain homodim... -

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Basic information

Entry
Database: PDB / ID: 7ahz
TitleCrystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub
Components
  • E3 ubiquitin-protein ligase Mdm2
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
KeywordsLIGASE / Ubiquitin ligase / RING E3
Function / homology
Function and homology information


Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / Peroxisomal protein import / Inactivation of CSF3 (G-CSF) signaling / Antigen processing: Ubiquitination & Proteasome degradation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Stabilization of p53 ...Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / Peroxisomal protein import / Inactivation of CSF3 (G-CSF) signaling / Antigen processing: Ubiquitination & Proteasome degradation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Stabilization of p53 / : / (E3-independent) E2 ubiquitin-conjugating enzyme / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / 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 / positive regulation of mitotic cell cycle / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / 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 / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / regulation of neuron apoptotic process / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / Pexophagy / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of CDH1 / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Degradation of CRY and PER proteins / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / 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 / Regulation of NF-kappa B signaling / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway
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. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMagnussen, H.M. / Huang, D.T.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKA17196 United Kingdom
Cancer Research UKA29256 United Kingdom
European Research Council (ERC)647849 United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Identification of a Catalytic Active but Non-Aggregating MDM2 RING Domain Variant.
Authors: Magnussen, H.M. / Huang, D.T.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: E3 ubiquitin-protein ligase Mdm2
BBB: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
CCC: Polyubiquitin-B
DDD: E3 ubiquitin-protein ligase Mdm2
EEE: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
FFF: Polyubiquitin-B
GGG: E3 ubiquitin-protein ligase Mdm2
HHH: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
III: Polyubiquitin-B
JJJ: E3 ubiquitin-protein ligase Mdm2
KKK: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
LLL: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,28721
Polymers134,72812
Non-polymers5599
Water6,413356
1
AAA: E3 ubiquitin-protein ligase Mdm2
DDD: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0786
Polymers15,8172
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: E3 ubiquitin-protein ligase Mdm2
BBB: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
CCC: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8135
Polymers33,6823
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
DDD: E3 ubiquitin-protein ligase Mdm2
EEE: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
FFF: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8135
Polymers33,6823
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
GGG: E3 ubiquitin-protein ligase Mdm2
JJJ: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0786
Polymers15,8172
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
GGG: E3 ubiquitin-protein ligase Mdm2
HHH: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
III: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8486
Polymers33,6823
Non-polymers1663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
JJJ: E3 ubiquitin-protein ligase Mdm2
KKK: Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
LLL: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8135
Polymers33,6823
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.030, 153.150, 82.080
Angle α, β, γ (deg.)90.000, 107.010, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A D
22Chains A G
33Chains A J
44Chains B E
55Chains B H
66Chains B K
77Chains C F
88Chains C I
99Chains C L
1010Chains D G
1111Chains D J
1212Chains E H
1313Chains E K
1414Chains F I
1515Chains F L
1616Chains G J
1717Chains H K
1818Chains I L

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

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Protein , 3 types, 12 molecules AAADDDGGGJJJBBBEEEHHHKKKCCCFFFIIILLL

#1: Protein
E3 ubiquitin-protein ligase Mdm2


Mass: 7908.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: G412, S413: Expression tag.
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: mdm2, irak1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P3Q9, RING-type E3 ubiquitin transferase
#2: Protein
Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast) / Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog)


Mass: 16851.381 Da / Num. of mol.: 4 / Mutation: S22R, C85K
Source method: isolated from a genetically manipulated source
Details: C85K is covalently linked to G76 (Molecule 3).
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: ube2d3, ube2d2, TGas005e16.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28EY6
#3: Protein
Polyubiquitin-B


Mass: 8922.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: G-4,S-3,G-2,G-1,S0: Expression tag G76 is covalently linked to C85K (Molecule 2).
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 3 types, 365 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.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.82→52.623 Å / Num. obs: 113701 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 13.8
Reflection shellResolution: 1.82→1.85 Å / Num. unique obs: 5647 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNJ

5mnj


Resolution: 1.82→52.623 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.044 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2305 5516 4.853 %
Rwork0.1949 108144 -
all0.197 --
obs-113660 98.025 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.827 Å2-0 Å2-0.094 Å2
2---3.237 Å2-0 Å2
3---3.472 Å2
Refinement stepCycle: LAST / Resolution: 1.82→52.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8781 0 9 356 9146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139017
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178498
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.6612241
X-RAY DIFFRACTIONr_angle_other_deg1.3561.57919786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25351118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.46121.576425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.674151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5831561
X-RAY DIFFRACTIONr_chiral_restr0.0720.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021783
X-RAY DIFFRACTIONr_nbd_refined0.1970.21568
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.27814
X-RAY DIFFRACTIONr_nbtor_refined0.1610.24384
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2345
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.223
X-RAY DIFFRACTIONr_nbd_other0.2270.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.213
X-RAY DIFFRACTIONr_mcbond_it4.24.9514484
X-RAY DIFFRACTIONr_mcbond_other4.2014.9514482
X-RAY DIFFRACTIONr_mcangle_it5.5817.4125586
X-RAY DIFFRACTIONr_mcangle_other5.587.4125586
X-RAY DIFFRACTIONr_scbond_it5.215.5534533
X-RAY DIFFRACTIONr_scbond_other5.215.5534534
X-RAY DIFFRACTIONr_scangle_it7.7548.0916651
X-RAY DIFFRACTIONr_scangle_other7.7538.0916652
X-RAY DIFFRACTIONr_lrange_it9.50758.1639687
X-RAY DIFFRACTIONr_lrange_other9.49158.0159617
X-RAY DIFFRACTIONr_ncsr_local_group_10.1140.051571
X-RAY DIFFRACTIONr_ncsr_local_group_20.1050.051547
X-RAY DIFFRACTIONr_ncsr_local_group_30.0880.051568
X-RAY DIFFRACTIONr_ncsr_local_group_40.1060.054635
X-RAY DIFFRACTIONr_ncsr_local_group_50.1030.054698
X-RAY DIFFRACTIONr_ncsr_local_group_60.0840.054608
X-RAY DIFFRACTIONr_ncsr_local_group_70.0660.052251
X-RAY DIFFRACTIONr_ncsr_local_group_80.0630.052293
X-RAY DIFFRACTIONr_ncsr_local_group_90.0910.052019
X-RAY DIFFRACTIONr_ncsr_local_group_100.1030.051544
X-RAY DIFFRACTIONr_ncsr_local_group_110.110.051547
X-RAY DIFFRACTIONr_ncsr_local_group_120.0950.054634
X-RAY DIFFRACTIONr_ncsr_local_group_130.1160.054439
X-RAY DIFFRACTIONr_ncsr_local_group_140.0730.052259
X-RAY DIFFRACTIONr_ncsr_local_group_150.0930.051998
X-RAY DIFFRACTIONr_ncsr_local_group_160.1050.051555
X-RAY DIFFRACTIONr_ncsr_local_group_170.1110.054522
X-RAY DIFFRACTIONr_ncsr_local_group_180.090.052013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.82-1.8670.3534160.34679290.34685760.5090.51797.30640.344
1.867-1.9180.3283860.31277310.31383350.6390.64497.38450.306
1.918-1.9740.3043560.29675340.29780990.7130.70897.41940.285
1.974-2.0350.2674030.25773030.25778780.8310.82697.81670.238
2.035-2.1010.2553720.23971050.23976390.8570.86197.87930.218
2.101-2.1750.2483440.21668500.21873400.8830.89998.01090.196
2.175-2.2570.2443460.20766400.20971150.90.91798.18690.187
2.257-2.3490.2433280.264090.20268930.9120.92797.73680.181
2.349-2.4530.2283260.19561100.19765410.9220.93298.39470.179
2.453-2.5720.2452830.20359240.20463020.9190.9398.49250.188
2.572-2.7110.2222760.256440.20160110.9320.93898.48610.189
2.711-2.8750.2612800.253070.20356580.9150.93398.74510.196
2.875-3.0730.212150.18650540.18753380.9390.94498.70740.189
3.073-3.3180.2152200.19246800.19349530.9350.94398.92990.202
3.318-3.6330.2532050.19843120.245800.9260.9498.62450.212
3.633-4.060.2222100.18638180.18841250.9450.94997.64850.21
4.06-4.6830.2062020.15734070.1636720.9510.96398.28430.188
4.683-5.7250.2181650.17128620.17330820.9580.96398.21540.21
5.725-8.0480.2341100.19822490.19924270.9380.95397.19820.241
8.048-52.6230.182730.16612760.16713820.9660.96997.61220.204

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