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- PDB-7qry: Crystal structure of B30.2 PRYSPRY domain of MID1 -

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Basic information

Entry
Database: PDB / ID: 7qry
TitleCrystal structure of B30.2 PRYSPRY domain of MID1
ComponentsE3 ubiquitin-protein ligase Midline-1
KeywordsLIGASE / E3 / TRIM / MID1 TRIM18 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


protein localization to microtubule / positive regulation of stress-activated MAPK cascade / negative regulation of microtubule depolymerization / pattern specification process / microtubule associated complex / centriolar satellite / regulation of microtubule cytoskeleton organization / phosphoprotein binding / RING-type E3 ubiquitin transferase / microtubule cytoskeleton organization ...protein localization to microtubule / positive regulation of stress-activated MAPK cascade / negative regulation of microtubule depolymerization / pattern specification process / microtubule associated complex / centriolar satellite / regulation of microtubule cytoskeleton organization / phosphoprotein binding / RING-type E3 ubiquitin transferase / microtubule cytoskeleton organization / spindle / Interferon gamma signaling / transferase activity / microtubule binding / microtubule / ubiquitin protein ligase binding / enzyme binding / Golgi apparatus / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Midline-1 / : / 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 ...Midline-1 / : / 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 / SPRY domain / 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 domain profile. / 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 / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Midline-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsChaikuad, A. / 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 MID1
Authors: Chaikuad, A. / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Midline-1
B: E3 ubiquitin-protein ligase Midline-1
C: E3 ubiquitin-protein ligase Midline-1
D: E3 ubiquitin-protein ligase Midline-1


Theoretical massNumber of molelcules
Total (without water)84,8564
Polymers84,8564
Non-polymers00
Water2,108117
1
A: E3 ubiquitin-protein ligase Midline-1


Theoretical massNumber of molelcules
Total (without water)21,2141
Polymers21,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase Midline-1


Theoretical massNumber of molelcules
Total (without water)21,2141
Polymers21,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase Midline-1


Theoretical massNumber of molelcules
Total (without water)21,2141
Polymers21,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase Midline-1


Theoretical massNumber of molelcules
Total (without water)21,2141
Polymers21,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.863, 51.763, 80.380
Angle α, β, γ (deg.)103.760, 92.640, 94.330
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 482 - 661 / Label seq-ID: 3 - 182

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
E3 ubiquitin-protein ligase Midline-1 / Midin / Putative transcription factor XPRF / RING finger protein 59 / RING finger protein Midline-1 ...Midin / Putative transcription factor XPRF / RING finger protein 59 / RING finger protein Midline-1 / RING-type E3 ubiquitin transferase Midline-1 / Tripartite motif-containing protein 18


Mass: 21213.943 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID1, FXY, RNF59, TRIM18, XPRF / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O15344, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.25 / Details: 1.1M sodium citrate, 0.1M HEPES 7.25

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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: 2.07→47.71 Å / Num. obs: 35045 / % possible obs: 95 % / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.07 / Rrim(I) all: 0.146 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.07-2.1440.472234310.8670.3030.62594.6
8.02-47.714.30.0926280.980.0470.10398.7

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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: 2.07→47.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.399 / SU ML: 0.243 / SU R Cruickshank DPI: 0.3279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 1721 4.9 %RANDOM
Rwork0.227 ---
obs0.2291 33313 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.73 Å2 / Biso mean: 49.382 Å2 / Biso min: 26.73 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å2-0.48 Å21.24 Å2
2--2.1 Å24.62 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 2.07→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 0 117 5376
Biso mean---48.46 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135423
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174961
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.6317400
X-RAY DIFFRACTIONr_angle_other_deg1.1431.5811416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7335652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36422.058277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29915825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8761528
X-RAY DIFFRACTIONr_chiral_restr0.0540.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021296
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53050.07
12B53050.07
21A53390.06
22C53390.06
31A53350.07
32D53350.07
41B53060.07
42C53060.07
51B52980.07
52D52980.07
61C53770.06
62D53770.06
LS refinement shellResolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 115 -
Rwork0.32 2409 -
all-2524 -
obs--94.57 %
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)
11.0633-0.2756-0.18680.6223-0.25250.6194-0.0219-0.09970.01850.0409-0.00080.0222-0.03990.05560.02270.02020.0085-0.0250.130.02420.055139.71141.165369.1924
21.42441.0225-0.88931.1453-0.33620.93920.0751-0.1843-0.2128-0.0708-0.2673-0.1327-0.08060.16780.19220.07510.0706-0.0280.22710.08490.088151.4265-3.220868.0289
30.69330.26621.03370.65670.67841.6917-0.05120.03690.01460.06620.0142-0.0181-0.04180.07950.03690.0365-0.0037-0.02750.12130.08320.084644.3717-1.705865.1228
44.06470.8472-0.79922.0261-1.37250.94810.035-0.01470.242-0.10110.02920.03640.061-0.0193-0.06420.0338-0.0326-0.00420.06910.01580.120544.8256-3.633728.5054
50.99060.31570.02540.8321-0.25351.1924-0.10280.0321-0.0669-0.0810.1005-0.00640.05360.0150.00230.0239-0.0215-0.00980.03680.03110.114535.6629-12.67634.9638
68.69982.3554-0.78157.2767-4.05257.25490.04280.3246-0.5570.09140.1238-0.061-0.2383-0.6281-0.16660.01420.01580.0290.1005-0.01640.179922.3086-1.727737.8308
71.0976-0.0676-0.16362.25180.39663.69840.1667-0.0517-0.00670.1089-0.1152-0.02960.0683-0.2158-0.05150.0372-0.0262-0.01950.07060.00820.081418.07941.68320.7095
81.43040.1796-0.67370.8715-0.05750.8976-0.05290.08820.0255-0.037-0.01260.03560.02210.03150.06550.0311-0.0348-0.03160.08910.03620.043828.32648.411412.8005
93.35070.50295.07114.6367-0.7218.1629-0.0177-0.4458-0.419-0.88070.489-0.57130.256-0.8248-0.47120.1702-0.11540.10580.27980.00090.208543.012410.281421.1857
101.7522-0.03840.42141.0657-0.53120.5847-0.1132-0.08490.12240.070.08010.0114-0.07430.03910.03310.02150.0026-0.03730.05270.00490.107355.260918.61249.4199
111.9646-0.446-1.40160.8774-0.60433.0632-0.0101-0.04840.0225-0.0010.11260.103-0.0440.0121-0.10240.0371-0.0114-0.05530.02540.02560.122845.915917.132742.9162
121.58070.7333-0.24483.47992.432.303-0.14820.0059-0.02580.22390.14940.13760.149-0.0279-0.00120.12710.07670.03470.12590.12060.169949.228913.573251.6843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A482 - 601
2X-RAY DIFFRACTION2A602 - 629
3X-RAY DIFFRACTION3A630 - 661
4X-RAY DIFFRACTION4B482 - 507
5X-RAY DIFFRACTION5B508 - 654
6X-RAY DIFFRACTION6B655 - 661
7X-RAY DIFFRACTION7C482 - 527
8X-RAY DIFFRACTION8C528 - 656
9X-RAY DIFFRACTION9C657 - 661
10X-RAY DIFFRACTION10D481 - 601
11X-RAY DIFFRACTION11D602 - 638
12X-RAY DIFFRACTION12D639 - 661

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