[English] 日本語
Yorodumi
- PDB-7ai1: Crystal structure of human MDM2-G443T RING domain homodimer bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ai1
TitleCrystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2)
Components
  • E3 ubiquitin-protein ligase Mdm2
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin ligase / RING E3
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 / (E3-independent) E2 ubiquitin-conjugating enzyme ...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 / (E3-independent) E2 ubiquitin-conjugating enzyme / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / cellular response to alkaloid / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / virus tail / 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 / ubiquitin conjugating enzyme activity / 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 K48-linked ubiquitination / protein autoubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / NPAS4 regulates expression of target genes / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / transcription repressor complex / positive regulation of mitotic cell cycle / regulation of heart rate / Negative regulators of DDX58/IFIH1 signaling / proteolysis involved in protein catabolic process / Peroxisomal protein import / Stabilization of p53 / Regulation of TNFR1 signaling / ubiquitin binding / positive regulation of protein export from nucleus / Regulation of RUNX3 expression and activity / Oncogene Induced Senescence / Inactivation of CSF3 (G-CSF) signaling / response to cocaine / DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / establishment of protein localization / CLEC7A (Dectin-1) signaling / cellular response to gamma radiation / protein destabilization / FCERI mediated NF-kB activation / protein modification process / 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 / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / p53 binding / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / negative regulation of neuron projection development / 5S rRNA binding
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMagnussen, H.M. / Huang, D.T.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKA17196 United Kingdom
Cancer Research UKA29256 United Kingdom
European Research Council (ERC)647849 United Kingdom
CitationJournal: 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
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 2.0Jan 27, 2021Group: Atomic model / Database references / Category: atom_site / 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 2.1Feb 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.2May 1, 2024Group: Data collection / Database references ...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
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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: E3 ubiquitin-protein ligase Mdm2
BBB: Ubiquitin-conjugating enzyme E2 D2
CCC: Polyubiquitin-B
DDD: E3 ubiquitin-protein ligase Mdm2
EEE: Ubiquitin-conjugating enzyme E2 D2
FFF: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,66414
Polymers68,2076
Non-polymers4578
Water5,008278
1
AAA: E3 ubiquitin-protein ligase Mdm2
DDD: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9928
Polymers16,6602
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: E3 ubiquitin-protein ligase Mdm2
BBB: Ubiquitin-conjugating enzyme E2 D2
CCC: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3948
Polymers34,1033
Non-polymers2905
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
DDD: E3 ubiquitin-protein ligase Mdm2
EEE: Ubiquitin-conjugating enzyme E2 D2
FFF: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2706
Polymers34,1033
Non-polymers1663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.267, 80.687, 135.909
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
11Chains A D
22Chains B E
33Chains C F

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 3 types, 6 molecules AAADDDBBBEEECCCFFF

#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: 8329.913 Da / Num. of mol.: 2 / Mutation: G443T
Source method: isolated from a genetically manipulated source
Details: G417, S418: Expression tag / Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16851.381 Da / Num. of mol.: 2 / Mutation: S22R, C85K
Source method: isolated from a genetically manipulated source
Details: C85K is covalently linked to G76 (Molecule 3). / Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Protein Polyubiquitin-B


Mass: 8922.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G-4,S-3,G-2,G-1,S0: Expression tag G76 is covalently linked to C85K (Molecule 2).
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

-
Non-polymers , 4 types, 286 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.07→135.91 Å / Num. obs: 38548 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 1861 / CC1/2: 0.584

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MDM2-E2-Ub

Resolution: 2.07→69.478 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.191 / SU B: 6.44 / SU ML: 0.165 / Average fsc free: 0.8728 / Average fsc work: 0.8939 / Cross valid method: FREE R-VALUE / ESU R: 0.234 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.266 1887 4.925 %
Rwork0.2121 36425 -
all0.215 --
obs-38312 99.517 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.177 Å2-0 Å2-0 Å2
2---0.078 Å20 Å2
3---1.255 Å2
Refinement stepCycle: LAST / Resolution: 2.07→69.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 14 278 4750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134587
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174346
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.666225
X-RAY DIFFRACTIONr_angle_other_deg1.261.57710138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4815567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60122.347213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0851527
X-RAY DIFFRACTIONr_chiral_restr0.0680.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_nbd_refined0.1910.2880
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24043
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22175
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.210
X-RAY DIFFRACTIONr_nbd_other0.1680.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.214
X-RAY DIFFRACTIONr_mcbond_it2.5743.3642274
X-RAY DIFFRACTIONr_mcbond_other2.5743.3632272
X-RAY DIFFRACTIONr_mcangle_it3.7945.0352833
X-RAY DIFFRACTIONr_mcangle_other3.7945.0352833
X-RAY DIFFRACTIONr_scbond_it3.0223.692313
X-RAY DIFFRACTIONr_scbond_other3.0213.692314
X-RAY DIFFRACTIONr_scangle_it4.6825.4053390
X-RAY DIFFRACTIONr_scangle_other4.6815.4053391
X-RAY DIFFRACTIONr_lrange_it6.6140.2855036
X-RAY DIFFRACTIONr_lrange_other6.60940.2875037
X-RAY DIFFRACTIONr_ncsr_local_group_10.1180.051645
X-RAY DIFFRACTIONr_ncsr_local_group_20.1040.054508
X-RAY DIFFRACTIONr_ncsr_local_group_30.0760.052254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.1240.3581290.3282614X-RAY DIFFRACTION98.4919
2.124-2.1820.3371610.322561X-RAY DIFFRACTION99.3068
2.182-2.2450.3551570.2942486X-RAY DIFFRACTION99.4731
2.245-2.3140.3021340.2652419X-RAY DIFFRACTION99.4546
2.314-2.390.3071070.2622400X-RAY DIFFRACTION99.3658
2.39-2.4740.3161020.2552305X-RAY DIFFRACTION99.5039
2.474-2.5670.3141160.2472242X-RAY DIFFRACTION99.7462
2.567-2.6720.3151100.2372154X-RAY DIFFRACTION99.4728
2.672-2.7910.294950.2322052X-RAY DIFFRACTION99.4903
2.791-2.9270.282870.2181988X-RAY DIFFRACTION99.7596
2.927-3.0850.2591020.2071897X-RAY DIFFRACTION99.7008
3.085-3.2720.316680.2041802X-RAY DIFFRACTION99.7866
3.272-3.4980.2491020.2031681X-RAY DIFFRACTION99.832
3.498-3.7780.239690.21588X-RAY DIFFRACTION99.8193
3.778-4.1380.226730.1581444X-RAY DIFFRACTION99.8026
4.138-4.6260.186780.1461327X-RAY DIFFRACTION99.6454
4.626-5.3410.228570.1611185X-RAY DIFFRACTION99.8392
5.341-6.5390.288640.201997X-RAY DIFFRACTION99.6244
6.539-9.2370.194460.171811X-RAY DIFFRACTION99.6512
9.237-69.4780.2300.162472X-RAY DIFFRACTION99.6032

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more