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- PDB-7qrz: Crystal structure of B30.2 PRYSPRY domain of MID2 -

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Basic information

Entry
Database: PDB / ID: 7qrz
TitleCrystal structure of B30.2 PRYSPRY domain of MID2
ComponentsProbable E3 ubiquitin-protein ligase MID2
KeywordsLIGASE / E3 / TRIM / MID2 / TRIM1 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


suppression of viral release by host / protein localization to microtubule / negative regulation of viral entry into host cell / negative regulation of viral transcription / positive regulation of autophagy / phosphoprotein binding / positive regulation of DNA-binding transcription factor activity / RING-type E3 ubiquitin transferase / positive regulation of NF-kappaB transcription factor activity / transferase activity ...suppression of viral release by host / protein localization to microtubule / negative regulation of viral entry into host cell / negative regulation of viral transcription / positive regulation of autophagy / phosphoprotein binding / positive regulation of DNA-binding transcription factor activity / RING-type E3 ubiquitin transferase / positive regulation of NF-kappaB transcription factor activity / transferase activity / microtubule binding / positive regulation of canonical NF-kappaB signal transduction / microtubule / transcription coactivator activity / 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. / Ring finger / Fibronectin type III domain / 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: 1.57 Å
AuthorsChaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of B30.2 PRYSPRY domain of MID2
Authors: Chaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,19010
Polymers21,5981
Non-polymers5939
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.921, 75.084, 78.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-807-

EDO

21A-807-

EDO

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID2, FXY2, RNF60, TRIM1 / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q9UJV3, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% High molecular weight PEG smears, 0.1M ADA pH 6.5, 0.2M ammonium sulfate

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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 EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→48.67 Å / Num. obs: 26626 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.066 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.57-1.6111.50.8892.819410.9050.2870.98199.8
7.02-48.6710.10.02834510.0090.02999.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jbm

6jbm


Resolution: 1.57→48.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.466 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1327 5 %RANDOM
Rwork0.1624 ---
obs0.1639 25278 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.13 Å2 / Biso mean: 24.777 Å2 / Biso min: 11.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2--0.91 Å20 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 1.57→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 41 134 1534
Biso mean--38.31 34.04 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171369
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.6451961
X-RAY DIFFRACTIONr_angle_other_deg1.381.5783165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9195177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37222.98567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.837155
X-RAY DIFFRACTIONr_chiral_restr0.1030.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021600
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02334
LS refinement shellResolution: 1.57→1.611 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 98 -
Rwork0.256 1841 -
all-1939 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3117-0.6170.53590.3113-0.20712.90250.02580.094-0.1186-0.01760.00180.04990.15930.2723-0.02760.0197-0.0030.00570.1018-0.01840.01513.919111.661622.6938
20.88910.27430.17740.27590.16050.8697-0.0152-0.04940.01090.0073-0.012-0.0165-0.0052-0.00640.02720.00170.0021-0.00240.029-0.00030.00457.629615.950635.0552
31.18980.7533-0.55161.1831.13973.3965-0.01140.19830.2946-0.1220.05830.2296-0.2356-0.2284-0.0470.02280.019-0.00680.06670.04740.08971.554319.754924.9456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A531 - 584
2X-RAY DIFFRACTION2A585 - 695
3X-RAY DIFFRACTION3A696 - 710

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