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- PDB-6v4e: Crystal Structure Analysis of Zebra Fish MDM -

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Basic information

Entry
Database: PDB / ID: 6v4e
TitleCrystal Structure Analysis of Zebra Fish MDM
Components
  • Protein Mdm4
  • Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)
KeywordsAPOPTOSIS / p53 binding
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / Ub-specific processing proteases / ubiquitin-protein transferase activity / protein ubiquitination / regulation of cell cycle / negative regulation of apoptotic process ...Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / Ub-specific processing proteases / ubiquitin-protein transferase activity / protein ubiquitination / regulation of cell cycle / negative regulation of apoptotic process / metal ion binding / nucleus
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 / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. ...MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 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/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2020
Title: Identification of a Structural Determinant for Selective Targeting of HDMX.
Authors: Ben-Nun, Y. / Seo, H.S. / Harvey, E.P. / Hauseman, Z.J. / Wales, T.E. / Newman, C.E. / Cathcart, A.M. / Engen, J.R. / Dhe-Paganon, S. / Walensky, L.D.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Mdm4
B: Protein Mdm4
C: Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)
D: Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)


Theoretical massNumber of molelcules
Total (without water)28,4034
Polymers28,4034
Non-polymers00
Water2,180121
1
A: Protein Mdm4
C: Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)


Theoretical massNumber of molelcules
Total (without water)14,2012
Polymers14,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area5780 Å2
MethodPISA
2
B: Protein Mdm4
D: Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)


Theoretical massNumber of molelcules
Total (without water)14,2012
Polymers14,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 30.720, 69.260
Angle α, β, γ (deg.)90.000, 106.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 17 through 39 or (resid 40...
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
111LEULEULEULEUchain AAA17 - 10615 - 104
211LEULEUALAALA(chain B and (resid 17 through 39 or (resid 40...BB17 - 3915 - 37
221GLNGLNGLUGLU(chain B and (resid 17 through 39 or (resid 40...BB40 - 4238 - 40
231LEULEULEULEU(chain B and (resid 17 through 39 or (resid 40...BB17 - 10615 - 104
241LEULEULEULEU(chain B and (resid 17 through 39 or (resid 40...BB17 - 10615 - 104
251LEULEULEULEU(chain B and (resid 17 through 39 or (resid 40...BB17 - 10615 - 104
261LEULEULEULEU(chain B and (resid 17 through 39 or (resid 40...BB17 - 10615 - 104
112GLNGLNNH2NH2chain CCC16 - 303 - 17
212GLNGLNNH2NH2chain DDD16 - 303 - 17

NCS ensembles :
ID
1
2

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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: 12129.982 Da / Num. of mol.: 2 / Mutation: L46V, V95L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdm4, mdmx / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZUW7
#2: Protein/peptide Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)


Mass: 2071.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium citrate (pH 5.0), 1.8M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.62→54.68 Å / Num. obs: 34317 / % possible obs: 98.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.376 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Net I/σ(I): 12.5 / Num. measured all: 114469
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1 / Num. measured all: 4976 / Num. unique obs: 1599 / Rpim(I) all: 0.825 / Rrim(I) all: 1.502 / % possible all: 93.4

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5T

4n5t


Resolution: 1.62→54.678 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.28
RfactorNum. reflection% reflection
Rfree0.1985 1673 4.88 %
Rwork0.1598 --
obs0.1616 34307 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.19 Å2 / Biso mean: 38.2382 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: final / Resolution: 1.62→54.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 0 121 1783
Biso mean---48.46 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061699
X-RAY DIFFRACTIONf_angle_d0.8462293
X-RAY DIFFRACTIONf_dihedral_angle_d8.5311015
X-RAY DIFFRACTIONf_chiral_restr0.052258
X-RAY DIFFRACTIONf_plane_restr0.005289
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A542X-RAY DIFFRACTION5.169TORSIONAL
12B542X-RAY DIFFRACTION5.169TORSIONAL
21C70X-RAY DIFFRACTION5.169TORSIONAL
22D70X-RAY DIFFRACTION5.169TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.62-1.66770.34011180.2894259295
1.6677-1.72150.3241470.27052725100
1.7215-1.78310.32061360.2515271899
1.7831-1.85450.2921500.2192269999
1.8545-1.93890.22641250.1658274199
1.9389-2.04110.22641450.1493274099
2.0411-2.1690.16471450.1342273499
2.169-2.33640.16081520.1287264197
2.3364-2.57160.17291470.1351274399
2.5716-2.94360.21221450.1642273099
2.9436-3.70860.19781250.1566276198
3.7086-54.6780.18071380.1561281097

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