PDB-7ahy: Crystal structure of Western clawed frog MDM2 RING domain homodimer

ID or keywords:

Entry

Database: PDB / ID: 7ahy

Title

Crystal structure of Western clawed frog MDM2 RING domain homodimer

Components

E3 ubiquitin-protein ligase Mdm2

Keywords

LIGASE / Ubiquitin ligase / RING E3

Function / homology

Function and homology information

Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Stabilization of p53 / SUMOylation of ubiquitinylation proteins / regulation of biological quality / positive regulation of mitotic cell cycle / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / negative regulation of apoptotic process ...
Similarity search - Function

Biological species

Xenopus tropicalis (tropical clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.532 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 25, 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	7ahy.cif.gz	56.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7ahy.ent.gz		Display	PDB format
PDBx/mmJSON format	7ahy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ah/7ahy ftp://data.pdbj.org/pub/pdb/validation_reports/ah/7ahy	HTTPS FTP

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Related structure data

Related structure data	7ah2SC 7ahzC 7ai0C 7ai1C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ah2-d 2bp3-2 1our-d 7ahz-1 4ewz-d 4fg3-d 4eyn-d 4f4v-d 3e7z-d 4f4t-d 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 (13) #31 - Jul 2002 p53 Tumor Suppressor similarity (12)

Deposited unit

AAA: E3 ubiquitin-protein ligase Mdm2

BBB: E3 ubiquitin-protein ligase Mdm2

hetero molecules

16.1 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)	42.559, 23.760, 55.744
Angle α, β, γ (deg.)	90.000, 101.224, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain: (Details: Chains A B)

#1: Protein	E3 ubiquitin-protein ligase Mdm2 Mass: 7908.426 Da / Num. of mol.: 2 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: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.16 Å³/Da / Density % sol: 42.94 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP, 25 % w/v PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97997 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 24, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97997 Å / Relative weight: 1
Reflection	Resolution: 2.53→41.75 Å / Num. obs: 3830 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC_1/2: 0.983 / Net I/σ(I): 3.7
Reflection shell	Resolution: 2.53→2.6 Å / Num. unique obs: 274 / CC_1/2: 0.652

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
xia2		data reduction
Aimless	0.5.32	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7AH2

7ah2

Resolution: 2.532→41.745 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.87 / SU B: 15.064 / SU ML: 0.319 / Cross valid method: FREE R-VALUE / ESU R: 0.888 / ESU R Free: 0.343
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2788	198	5.17 %
R_work	0.2167	3632	-
all	0.22	-	-
obs	-	3830	99.532 %

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: 42.802 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.339 Å²	0 Å²	0.296 Å²
2-	-	1.592 Å²	-0 Å²
3-	-	-	-1.899 Å²

Refinement step

Cycle: LAST / Resolution: 2.532→41.745 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	822	0	4	4	830

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	836
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	775
X-RAY DIFFRACTION	r_angle_refined_deg	1.377	1.664	1137
X-RAY DIFFRACTION	r_angle_other_deg	1.226	1.574	1807
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.02	5	111
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.057	22.5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.365	15	132
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.219	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	122
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	909
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	145
X-RAY DIFFRACTION	r_nbd_refined	0.183	0.2	147
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	673
X-RAY DIFFRACTION	r_nbtor_refined	0.151	0.2	391
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	358
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.103	0.2	15
X-RAY DIFFRACTION	r_metal_ion_refined	0.018	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.268	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.227	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.135	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.598	4.703	450
X-RAY DIFFRACTION	r_mcbond_other	2.598	4.698	449
X-RAY DIFFRACTION	r_mcangle_it	4.195	7.045	559
X-RAY DIFFRACTION	r_mcangle_other	4.192	7.05	560
X-RAY DIFFRACTION	r_scbond_it	2.609	4.998	386
X-RAY DIFFRACTION	r_scbond_other	2.606	5.002	387
X-RAY DIFFRACTION	r_scangle_it	4.22	7.342	578
X-RAY DIFFRACTION	r_scangle_other	4.22	7.342	578
X-RAY DIFFRACTION	r_lrange_it	6.951	56.566	839
X-RAY DIFFRACTION	r_lrange_other	6.948	56.602	840
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	1414

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
2.532-2.598	0.335	11	0.307	258	0.308	279	0.777	0.785	96.4158	0.303
2.598-2.669	0.36	16	0.303	257	0.306	275	0.711	0.755	99.2727	0.309
2.669-2.746	0.337	8	0.306	245	0.307	253	0.528	0.758	100	0.304
2.746-2.83	0.273	12	0.277	243	0.277	255	0.857	0.782	100	0.282
2.83-2.922	0.288	12	0.281	241	0.282	253	0.881	0.809	100	0.282
2.922-3.024	0.311	16	0.26	226	0.263	242	0.832	0.834	100	0.256
3.024-3.138	0.401	14	0.232	206	0.24	220	0.7	0.866	100	0.231
3.138-3.265	0.267	8	0.213	227	0.215	237	0.87	0.88	99.1561	0.21
3.265-3.41	0.28	13	0.227	200	0.231	213	0.925	0.878	100	0.224
3.41-3.575	0.308	11	0.214	196	0.22	207	0.842	0.895	100	0.209
3.575-3.767	0.265	17	0.176	186	0.185	205	0.934	0.927	99.0244	0.177
3.767-3.993	0.259	7	0.199	185	0.202	192	0.949	0.921	100	0.199
3.993-4.266	0.214	16	0.193	156	0.195	172	0.919	0.941	100	0.192
4.266-4.604	0.285	9	0.161	158	0.167	167	0.916	0.956	100	0.167
4.604-5.037	0.209	7	0.157	143	0.159	150	0.95	0.958	100	0.169
5.037-5.621	0.162	5	0.188	140	0.187	146	0.933	0.948	99.3151	0.195
5.621-6.471	0.612	3	0.229	120	0.236	123	0.764	0.92	100	0.236
6.471-7.879	0.244	4	0.191	110	0.192	114	0.837	0.941	100	0.205
7.879-10.949	0.273	4	0.255	84	0.255	88	0.946	0.942	100	0.295
10.949-41.745	0.349	5	0.224	50	0.23	55	0.912	0.963	100	0.265

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