PDB-7ah2: Crystal structure of Zebrafish MDM2 RING domain homodimer

ID or keywords:

Entry

Database: PDB / ID: 7ah2

Title

Crystal structure of Zebrafish MDM2 RING domain homodimer

Components

E3 ubiquitin-protein ligase Mdm2

Keywords

LIGASE / Ubiquitin ligase / RING E3

Function / homology

Function and homology information

pronephric glomerulus morphogenesis / AKT phosphorylates targets in the cytosol / SUMOylation of ubiquitinylation proteins / Regulation of RUNX3 expression and activity / Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / negative regulation of epithelial cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.872 Å

Authors

Magnussen, H.M. / Huang, D.T.

Funding support

United Kingdom, 3items

Citation

Journal: 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

Deposition	Sep 24, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2021	Group: 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 1.2	Feb 10, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3	Jan 31, 2024	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ah2.cif.gz	58.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7ah2.ent.gz		Display	PDB format
PDBx/mmJSON format	7ah2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ah2_validation.pdf.gz	435.5 KB	Display	wwPDB validaton report
Full document	7ah2_full_validation.pdf.gz	435.7 KB	Display
Data in XML	7ah2_validation.xml.gz	6.6 KB	Display
Data in CIF	7ah2_validation.cif.gz	8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ah/7ah2 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/7ah2	HTTPS FTP

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Related structure data

Related structure data	7ahyC 7ahzC 7ai0C 7ai1C 2vjfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ahy-d 4fg3-d 4f0o-d 7ahz-1 5m9g-d 4f1f-d 1k5b-d 2y6x-d 4ins-d 6mo9-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (12) #31 - Jul 2002 p53 Tumor Suppressor similarity (11)

Deposited unit

AAA: E3 ubiquitin-protein ligase Mdm2

BBB: E3 ubiquitin-protein ligase Mdm2

hetero molecules

15.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	46.163, 23.859, 54.306
Angle α, β, γ (deg.)	90.000, 101.664, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2 Mass: 7798.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdm2 / Production host: Escherichia coli (E. coli) References: UniProt: O42354, RING-type E3 ubiquitin transferase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.35 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M imidazole, 0.12 M monosaccharides, 37.5 % (w/v) MPD_P1K_P3350 (Morpheus, Molecular Dimensions)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.872→53.185 Å / Num. obs: 2814 / % possible obs: 100 % / Redundancy: 3.2 % / CC_1/2: 0.949 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.872→2.922 Å / Num. unique obs: 129 / CC_1/2: 0.667

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VJF

2vjf

Resolution: 2.872→45.21 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.845 / SU B: 16.441 / SU ML: 0.321 / Cross valid method: FREE R-VALUE / ESU R Free: 0.477
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2811	172	6.114 %
R_work	0.2065	2641	-
all	0.211	-	-
obs	-	2813	99.858 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.532 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.54 Å²	0 Å²	0.157 Å²
2-	-	-1.29 Å²	0 Å²
3-	-	-	-3.055 Å²

Refinement step

Cycle: LAST / Resolution: 2.872→45.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	868	0	4	12	884

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	880
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	845
X-RAY DIFFRACTION	r_angle_refined_deg	1.429	1.658	1188
X-RAY DIFFRACTION	r_angle_other_deg	1.085	1.58	1961
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.462	5	114
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	22.676	18.889	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.754	15	158
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.407	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	122
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	958
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	170
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	141
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	760
X-RAY DIFFRACTION	r_nbtor_refined	0.14	0.2	417
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	427
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	20
X-RAY DIFFRACTION	r_metal_ion_refined	0.046	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.205	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.113	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.268	2.543	462
X-RAY DIFFRACTION	r_mcbond_other	1.269	2.538	461
X-RAY DIFFRACTION	r_mcangle_it	2.149	3.796	574
X-RAY DIFFRACTION	r_mcangle_other	2.147	3.802	575
X-RAY DIFFRACTION	r_scbond_it	1.241	2.682	418
X-RAY DIFFRACTION	r_scbond_other	1.24	2.687	419
X-RAY DIFFRACTION	r_scangle_it	1.992	3.957	614
X-RAY DIFFRACTION	r_scangle_other	1.993	3.957	614
X-RAY DIFFRACTION	r_lrange_it	3.91	28.913	898
X-RAY DIFFRACTION	r_lrange_other	3.87	28.805	896
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.104	0.05	1549

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.872-2.947	0.333	15	0.263	182	0.268	198	0.84	0.863	99.4949	0.224
2.947-3.027	0.436	13	0.245	191	0.254	204	0.789	0.887	100	0.21
3.027-3.115	0.364	10	0.234	172	0.24	183	0.82	0.887	99.4536	0.21
3.115-3.21	0.544	10	0.225	176	0.236	186	0.721	0.923	100	0.207
3.21-3.315	0.382	6	0.211	185	0.215	191	0.915	0.918	100	0.181
3.315-3.431	0.168	6	0.21	175	0.208	181	0.913	0.919	100	0.186
3.431-3.56	0.121	10	0.179	156	0.175	166	0.962	0.944	100	0.162
3.56-3.705	0.217	12	0.191	147	0.193	159	0.921	0.946	100	0.171
3.705-3.868	0.232	10	0.182	151	0.186	161	0.929	0.946	100	0.171
3.868-4.056	0.266	15	0.183	140	0.191	155	0.928	0.942	100	0.165
4.056-4.274	0.291	12	0.186	130	0.194	143	0.918	0.951	99.3007	0.18
4.274-4.532	0.155	7	0.14	134	0.141	141	0.961	0.961	100	0.133
4.532-4.842	0.299	10	0.184	122	0.191	132	0.893	0.954	100	0.185
4.842-5.226	0.644	6	0.208	112	0.221	118	0.802	0.934	100	0.203
5.226-5.72	0.655	6	0.262	107	0.273	113	0.736	0.907	100	0.234
5.72-6.386	0.795	3	0.248	101	0.258	104	0.816	0.886	100	0.208
6.386-7.356	0.182	11	0.233	83	0.227	94	0.934	0.918	100	0.227
7.356-8.966	0.288	4	0.192	76	0.197	80	0.917	0.932	100	0.189
8.966-12.504	0.101	3	0.228	62	0.222	65	0.984	0.947	100	0.25
12.504-53.185	0.285	3	0.258	39	0.26	43	0.905	0.94	97.6744	0.294

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