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- PDB-6hfa: Crystal structure of hDM2 in complex with a C-terminal triurea ca... -

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Basic information

Entry
Database: PDB / ID: 6hfa
TitleCrystal structure of hDM2 in complex with a C-terminal triurea capped peptide chimera foldamer.
Components
  • E3 ubiquitin-protein ligase Mdm2
  • LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea
KeywordsONCOPROTEIN / PROTEIN FOLDAMER COMPLEX / PROTEIN PROTEIN INTERACTION INHIBITOR / UREA BASED CHIMERA FOLDAMER
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / fibroblast activation / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Trafficking of AMPA receptors ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / fibroblast activation / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / peroxisome proliferator activated receptor binding / positive regulation of vascular associated smooth muscle cell migration / negative regulation of signal transduction by p53 class mediator / negative regulation of protein processing / SUMO transferase activity / response to steroid hormone / NEDD8 ligase activity / response to iron ion / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / cellular response to alkaloid / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / regulation of postsynaptic neurotransmitter receptor internalization / cardiac septum morphogenesis / blood vessel development / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / regulation of protein catabolic process / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / blood vessel remodeling / cellular response to UV-C / cellular response to actinomycin D / 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 / Stabilization of p53 / ubiquitin binding / positive regulation of protein export from nucleus / Regulation of RUNX3 expression and activity / Oncogene Induced Senescence / response to cocaine / DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / establishment of protein localization / cellular response to gamma radiation / protein destabilization / RING-type E3 ubiquitin transferase / cellular response to growth factor stimulus / response to toxic substance / centriolar satellite / endocytic vesicle membrane / cellular response to hydrogen peroxide / Signaling by ALK fusions and activated point mutants / protein polyubiquitination / Regulation of TP53 Degradation / ubiquitin-protein transferase activity / disordered domain specific binding / ubiquitin protein ligase activity / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / 5S rRNA binding / protein-containing complex assembly / Oxidative Stress Induced Senescence / ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / cellular response to hypoxia / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / protein ubiquitination / regulation of cell cycle / postsynaptic density / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / glutamatergic synapse / enzyme binding
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / 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 ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsBuratto, J. / Mauran, L. / Goudreau, S. / Fribourg, S. / Guichard, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE07-0010-01 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Structural Basis for alpha-Helix Mimicry and Inhibition of Protein-Protein Interactions with Oligourea Foldamers.
Authors: Cussol, L. / Mauran-Ambrosino, L. / Buratto, J. / Belorusova, A.Y. / Neuville, M. / Osz, J. / Fribourg, S. / Fremaux, J. / Dolain, C. / Goudreau, S.R. / Rochel, N. / Guichard, G.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0May 24, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 3.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea
D: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Theoretical massNumber of molelcules
Total (without water)25,2534
Polymers25,2534
Non-polymers00
Water1,17165
1
A: E3 ubiquitin-protein ligase Mdm2
D: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Theoretical massNumber of molelcules
Total (without water)12,6272
Polymers12,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area5660 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase Mdm2
C: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Theoretical massNumber of molelcules
Total (without water)12,6272
Polymers12,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area5320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.350, 49.410, 82.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 26:35 or (resid 36 and (name...
21(chain B and (resseq 26:30 or (resid 31 and (name...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRLEULEU(chain A and (resseq 26:35 or (resid 36 and (name...AA26 - 3513 - 22
121LYSLYSLYSLYS(chain A and (resseq 26:35 or (resid 36 and (name...AA3623
131GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
141GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
151GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
161GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
171GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
211THRTHRPROPRO(chain B and (resseq 26:30 or (resid 31 and (name...BB26 - 3013 - 17
221LYSLYSLYSLYS(chain B and (resseq 26:30 or (resid 31 and (name...BB3118
231GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
241GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
251GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
261GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
271GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
281GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
291GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
2101GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
112THRTHRURVURVchain CCC17 - 261 - 10
212THRTHRURVURVchain DDD17 - 261 - 10

NCS ensembles :
ID
1
2

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Components

#1: 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: 11397.342 Da / Num. of mol.: 2 / Fragment: residues 17-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein/peptide LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Mass: 1229.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM HEPES, 1.26 M Na Citrate, 10% glycerol. Cryo: +30% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9811 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9811 Å / Relative weight: 1
ReflectionResolution: 1.79→44.35 Å / Num. obs: 17433 / % possible obs: 98.6 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.044 / Rrim(I) all: 0.155 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.8310.41.811470.4720.5511.88889.7
8-44.359.90.0512490.9990.0170.05499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→42.339 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.09
RfactorNum. reflection% reflection
Rfree0.2384 863 5 %
Rwork0.1908 --
obs0.1931 17262 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.35 Å2 / Biso mean: 37.7329 Å2 / Biso min: 18.31 Å2
Refinement stepCycle: final / Resolution: 1.79→42.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 20 65 1647
Biso mean--57.01 47.09 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061616
X-RAY DIFFRACTIONf_angle_d1.0142181
X-RAY DIFFRACTIONf_chiral_restr0.056250
X-RAY DIFFRACTIONf_plane_restr0.008271
X-RAY DIFFRACTIONf_dihedral_angle_d14.516965
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A698X-RAY DIFFRACTION8.111TORSIONAL
12B698X-RAY DIFFRACTION8.111TORSIONAL
21C58X-RAY DIFFRACTION8.111TORSIONAL
22D58X-RAY DIFFRACTION8.111TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7901-1.90220.36971320.31092510264292
1.9022-2.04910.29051420.24262698284098
2.0491-2.25530.27721420.20792715285799
2.2553-2.58160.2521460.21592761290799
2.5816-3.25240.24691460.19152778292499
3.2524-42.35050.2031550.162929373092100
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)
10.0528-0.10170.15370.439-0.69610.77050.02380.14570.0253-0.0478-0.0986-0.0703-0.0320.0734-0.00010.23670.0088-0.00260.2675-0.01210.258-3.6371.8563-9.8267
20.0106-0.02370.02870.073-0.11850.1919-0.152-0.081-0.1524-0.03610.38770.2582-0.1819-0.23860.00010.24520.01740.01130.28880.02640.285-20.548910.2043-7.664
30.0162-0.0090.00960.04830.03520.0158-0.0204-0.1634-0.42310.22920.18690.06940.41160.53470.00070.33420.08310.00390.2793-0.00560.3586-12.77442.63-0.528
40.21680.14810.08020.2540.38170.5335-0.2276-0.1490.17480.27940.1908-0.0942-0.0597-0.04850.00030.28210.0181-0.0180.3336-0.02280.2497-5.20479.6338-0.2485
50.248-0.04130.20570.80620.42230.44590.3467-0.3101-0.2178-0.2479-0.2338-0.1193-0.31940.086400.3409-0.03520.0410.25780.00290.368-17.517225.7633-28.9787
60.0808-0.04920.06440.1349-0.1920.2169-0.14540.0253-0.0028-0.05360.01320.0359-0.0737-0.25510.00030.29010.0338-0.01680.2786-0.00230.3369-22.820318.1261-24.3653
70.40140.21120.3710.34750.01470.2127-0.0429-0.0016-0.0024-0.16120.12870.12130.1615-0.126-00.2890.0016-0.01230.3112-0.00560.2203-12.69828.1834-22.4658
80.04230.04950.03910.04120.02490.04370.3793-0.2901-0.3077-0.21980.21490.2180.0719-0.1491-0.00020.43-0.0372-0.07390.4038-0.01160.4219-14.70050.8346-29.9967
90.0246-0.0246-0.01430.0340.01540.00950.4566-0.31870.2801-0.6031-0.13180.3299-0.1088-0.35050.00120.4377-0.0371-0.07680.381-0.06480.375-18.9658.1091-33.4223
100.0499-0.01720.03290.0033-0.00930.01080.32070.3905-0.0849-0.6529-0.2316-0.2663-0.17960.007-0.00010.49140.1008-0.00310.377300.3115-7.92065.4001-32.732
110.1647-0.0009-0.26290.1850.1060.35480.12110.25120.0579-0.0625-0.241-0.1724-0.0614-0.0228-00.3395-0.04520.02510.3488-0.00290.3445-12.07218.8047-33.8409
120.02880.0369-0.02170.0697-0.02810.00420.2272-0.2728-0.00220.1925-0.1888-0.40560.18910.3228-0.00050.25330.04560.0110.32470.04450.2911-4.86517.4937-20.9232
130.02120.05160.00730.08640.0104-0.00220.34020.05960.3403-0.26-0.03360.09790.07170.1841-0.00020.20980.0198-0.0090.21230.0010.2334-12.945316.7503-12.948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 63 )A25 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 80 )A64 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 86 )A81 - 86
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 111 )A87 - 111
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 31 )B25 - 31
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 49 )B32 - 49
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 73 )B50 - 73
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 80 )B74 - 80
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 86 )B81 - 86
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 95 )B87 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 111 )B96 - 111
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 23 )C17 - 23
13X-RAY DIFFRACTION13chain 'D' and (resid 17 through 23 )D17 - 23

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