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- PDB-9r11: Structure of the PRYSPRY domain of human MID2, crystal form II -

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Basic information

Entry
Database: PDB / ID: 9r11
TitleStructure of the PRYSPRY domain of human MID2, crystal form II
ComponentsProbable E3 ubiquitin-protein ligase MID2
KeywordsLIGASE / TRIM family / MID2 / TRIM1 / B30.2 DOMAIN / SPRY DOMAIN / PRYSPRY DOMAIN / E3 ubiquitin ligase
Function / homology
Function and homology information


suppression of viral release by host / protein localization to microtubule / host-mediated suppression of symbiont invasion / negative regulation of viral transcription / positive regulation of DNA-binding transcription factor activity / positive regulation of autophagy / phosphoprotein binding / positive regulation of NF-kappaB transcription factor activity / RING-type E3 ubiquitin transferase / transferase activity ...suppression of viral release by host / protein localization to microtubule / host-mediated suppression of symbiont invasion / negative regulation of viral transcription / positive regulation of DNA-binding transcription factor activity / positive regulation of autophagy / phosphoprotein binding / positive regulation of NF-kappaB transcription factor activity / RING-type E3 ubiquitin transferase / transferase activity / microtubule binding / microtubule / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / innate immune response / enzyme binding / protein homodimerization activity / extracellular exosome / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Probable E3 ubiquitin-protein ligase MID2 / TRIM1, PRY/SPRY domain / : / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / : / ANCHR-like B-box zinc-binding domain ...Probable E3 ubiquitin-protein ligase MID2 / TRIM1, PRY/SPRY domain / : / : / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / : / ANCHR-like B-box zinc-binding domain / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Fibronectin type III domain / Ring finger / Fibronectin type 3 domain / Fibronectin type III / Fibronectin type III superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
Probable E3 ubiquitin-protein ligase MID2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMunoz Sosa, C.J. / Zhubi, R. / Chaikuad, A. / Knapp, S. / Joerger, A.C. / Structural Genomics Consortium (SGC)
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEUbOPEN grant 875510European Union
CitationJournal: J Struct Biol X / Year: 2025
Title: Structural analysis of TRIM family PRYSPRY domains and its implications for E3-ligand design.
Authors: Zhubi, R. / Chaikuad, A. / Munoz Sosa, C.J. / Joerger, A.C. / Knapp, S.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable E3 ubiquitin-protein ligase MID2
A: Probable E3 ubiquitin-protein ligase MID2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4385
Polymers43,1952
Non-polymers2423
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-5 kcal/mol
Surface area14600 Å2
Unit cell
Length a, b, c (Å)53.406, 60.919, 118.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable E3 ubiquitin-protein ligase MID2 / Midin-2 / Midline defect 2 / Midline-2 / RING finger protein 60 / RING-type E3 ubiquitin ...Midin-2 / Midline defect 2 / Midline-2 / RING finger protein 60 / RING-type E3 ubiquitin transferase MID2 / Tripartite motif-containing protein 1


Mass: 21597.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID2, FXY2, RNF60, TRIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UJV3, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 9 mg/ml MID2 PRYSPRY in 20 mM HEPES pH 7.5, 100 mM NaCl, and 0.5 mM TCEP. Reservoir solution: 7% PEG 6000, 5% MPD, 0.1 M HEPES, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→48.7 Å / Num. obs: 48227 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 22.7557474007 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2354 / CC1/2: 0.812

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→48.7 Å / SU ML: 0.185461799681 / Cross valid method: FREE R-VALUE / σ(F): 1.34369245418 / Phase error: 19.6979183357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205686183562 2433 5.05295950156 %
Rwork0.155347201058 45717 -
obs0.157888917472 48150 99.8569028806 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.7612985504 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 16 297 2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005533160830352705
X-RAY DIFFRACTIONf_angle_d0.8234017796943687
X-RAY DIFFRACTIONf_chiral_restr0.05529598515395
X-RAY DIFFRACTIONf_plane_restr0.00445604726674469
X-RAY DIFFRACTIONf_dihedral_angle_d10.85611805591579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.67350.2783546568091380.2125708030622654X-RAY DIFFRACTION99.9641962048
1.6735-1.70990.2753982519531380.2020678514182661X-RAY DIFFRACTION99.9285969297
1.7099-1.74960.265434557371540.1798635963642629X-RAY DIFFRACTION99.9640804598
1.7496-1.79340.2413296452491580.1673879684322657X-RAY DIFFRACTION99.9290024849
1.7934-1.84190.2271420107521450.1546245088132662X-RAY DIFFRACTION99.7512437811
1.8419-1.89610.2255603399141450.1559968931082627X-RAY DIFFRACTION99.9279019466
1.8961-1.95730.1955966059971330.1494508081612669X-RAY DIFFRACTION99.8930481283
1.9573-2.02730.2147659119351420.1363594821112666X-RAY DIFFRACTION99.9288256228
2.0273-2.10840.1840421359831350.13606323992659X-RAY DIFFRACTION99.5723449751
2.1084-2.20440.1884622557741440.1366274494032660X-RAY DIFFRACTION99.6800568788
2.2044-2.32060.2118497863391320.1389986857732727X-RAY DIFFRACTION100
2.3206-2.4660.2146201143111290.1520723388552681X-RAY DIFFRACTION100
2.466-2.65640.1894682464261380.1630996660812714X-RAY DIFFRACTION100
2.6564-2.92370.2129034682721520.1629571955672690X-RAY DIFFRACTION100
2.9237-3.34660.2055702411851500.1623095665982739X-RAY DIFFRACTION100
3.3466-4.2160.189531991121450.1480093508282726X-RAY DIFFRACTION99.2738589212
4.216-48.70.2024514598361550.1594614401382896X-RAY DIFFRACTION99.8037291462

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