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- PDB-5vk1: Crystal structure of human MDM4 in complex with a 12-mer lysine-c... -

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Basic information

Entry
Database: PDB / ID: 5vk1
TitleCrystal structure of human MDM4 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
Components
  • Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
  • Protein Mdm4
KeywordsSIGNALING PROTEIN/INHIBITOR / MDMX / MDMX-PEPTIDE INHIBITOR COMPLEX / ONCOPROTEIN / METAL-BINDING / NUCLEUS / ZINC-FINGER / stapled peptide / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


atrial septum development / ventricular septum development / atrioventricular valve morphogenesis / heart valve development / endocardial cushion morphogenesis / transcription repressor complex / negative regulation of signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / negative regulation of protein catabolic process / Stabilization of p53 ...atrial septum development / ventricular septum development / atrioventricular valve morphogenesis / heart valve development / endocardial cushion morphogenesis / transcription repressor complex / negative regulation of signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / negative regulation of protein catabolic process / Stabilization of p53 / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / enzyme activator activity / Regulation of TP53 Degradation / protein-containing complex assembly / cellular response to hypoxia / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / nucleoplasm / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
MDM4 / : / 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 ...MDM4 / : / 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
CitationJournal: Chem Sci / Year: 2019
Title: Dithiocarbamate-inspired side chain stapling chemistry for peptide drug design.
Authors: Li, X. / Tolbert, W.D. / Hu, H.G. / Gohain, N. / Zou, Y. / Niu, F. / He, W.X. / Yuan, W. / Su, J.C. / Pazgier, M. / Lu, W.
History
DepositionApr 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 4, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 2.0Jul 10, 2024Group: Derived calculations / Polymer sequence / Category: entity_poly / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Mdm4
B: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
C: Protein Mdm4
D: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
E: Protein Mdm4
F: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
G: Protein Mdm4
H: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
I: Protein Mdm4
J: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
K: Protein Mdm4
L: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
M: Protein Mdm4
N: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
O: Protein Mdm4
P: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)88,95316
Polymers88,95316
Non-polymers00
Water48627
1
A: Protein Mdm4
B: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-12 kcal/mol
Surface area5730 Å2
MethodPISA
2
C: Protein Mdm4
D: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-11 kcal/mol
Surface area5550 Å2
MethodPISA
3
E: Protein Mdm4
F: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-10 kcal/mol
Surface area5780 Å2
MethodPISA
4
G: Protein Mdm4
H: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-12 kcal/mol
Surface area5570 Å2
MethodPISA
5
I: Protein Mdm4
J: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-11 kcal/mol
Surface area5640 Å2
MethodPISA
6
K: Protein Mdm4
L: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-11 kcal/mol
Surface area5730 Å2
MethodPISA
7
M: Protein Mdm4
N: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-11 kcal/mol
Surface area5540 Å2
MethodPISA
8
O: Protein Mdm4
P: Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,1192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-11 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.294, 47.730, 93.394
Angle α, β, γ (deg.)76.72, 89.92, 72.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein Mdm4 / Double minute 4 protein / Mdm2-like p53-binding protein / Protein Mdmx / p53-binding protein Mdm4


Mass: 9575.293 Da / Num. of mol.: 8 / Fragment: residues 24-108 / Mutation: Q68A, Q69A, E70A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#2: Protein/peptide
Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Mass: 1543.828 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% 2-propanol, 30% PEG 3350, and 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 16330 / % possible obs: 86 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.3
Reflection shellResolution: 2.69→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.1 / Num. unique all: 704 / % possible all: 78.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eqy

3eqy


Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.815 / SU B: 60.775 / SU ML: 0.64 / Cross valid method: THROUGHOUT / ESU R Free: 0.605 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33486 835 5.1 %RANDOM
Rwork0.2787 ---
obs0.28145 15495 85.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å22.88 Å20.01 Å2
2--0.78 Å2-1.52 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 0 27 6035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196164
X-RAY DIFFRACTIONr_bond_other_d0.0030.025944
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9968205
X-RAY DIFFRACTIONr_angle_other_deg1.0313.00113762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2324.063256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.641151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5541524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216510
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021202
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0794.0242999
X-RAY DIFFRACTIONr_mcbond_other0.0794.0232998
X-RAY DIFFRACTIONr_mcangle_it0.1185.9763649
X-RAY DIFFRACTIONr_mcangle_other0.1185.9773650
X-RAY DIFFRACTIONr_scbond_it0.0444.0873165
X-RAY DIFFRACTIONr_scbond_other0.0444.0883166
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.0836.124557
X-RAY DIFFRACTIONr_long_range_B_refined0.70575.23623407
X-RAY DIFFRACTIONr_long_range_B_other0.70575.23623408
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.695→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 59 -
Rwork0.36 936 -
obs--71.74 %
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)
13.0310.5058-0.47222.9613-0.51496.0666-0.04720.0996-0.0179-0.0897-0.17260.11050.0397-0.23770.21980.0077-0.01550.00730.1375-0.02270.06499.999814.012-42.2165
22.43720.89150.76171.98470.23914.29320.01560.08170.02170.13010.02220.00880.05270.0264-0.03780.0138-0.02380.00320.155-0.02210.0041-3.0774-6.9686-23.54
35.09491.20981.99773.01362.51836.0036-0.0234-0.08650.04930.18520.0994-0.1178-0.28850.1565-0.0760.0649-0.0006-0.01370.1879-0.05640.024821.76581.6132-2.4298
42.3807-0.1989-1.06121.53821.76895.9326-0.04660.2301-0.0745-0.0815-0.03230.16650.05160.1320.07890.07880.0042-0.03860.2495-0.05950.0861-8.683411.4824-64.8741
52.223-0.15231.06692.87072.53646.40310.00230.29330.1231-0.3492-0.0578-0.1398-0.4120.07530.05550.0904-0.01590.01960.17490.00680.074920.5769-10.5514-46.1627
64.1232-0.1304-1.54481.96570.38626.9002-0.082-0.0135-0.19980.0083-0.16460.15770.2991-0.34820.24660.1-0.01560.04830.1644-0.01950.1293-3.0543-18.77054.2522
72.8458-0.66910.25685.55282.95755.6318-0.23630.0909-0.1024-0.05810.07070.26620.1618-0.02510.16560.0462-0.02250.01130.10030.00430.019220.3769-22.8834-19.978
81.0579-0.7026-0.78922.0113-0.16498.463-0.1132-0.01740.2179-0.16290.11540.0125-0.07560.1329-0.00220.0998-0.0733-0.05370.1261-0.01110.1475-3.1469-18.1239-69.3262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 107
2X-RAY DIFFRACTION2C25 - 106
3X-RAY DIFFRACTION3E25 - 107
4X-RAY DIFFRACTION4G25 - 106
5X-RAY DIFFRACTION5I26 - 107
6X-RAY DIFFRACTION6K26 - 107
7X-RAY DIFFRACTION7M25 - 106
8X-RAY DIFFRACTION8O25 - 106

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