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- PDB-7qs4: Crystal structure of B30.2 PRYSPRY domain of TRIM36 -

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Basic information

Entry
Database: PDB / ID: 7qs4
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM36
ComponentsHAPRIN-a2
KeywordsLIGASE / E3 / TRIM / TRIM36 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


ubiquitin-protein transferase activity / regulation of cell cycle / zinc ion binding
Similarity search - Function
E3 ubiquitin-protein ligase Trim36 / TRIM36, PRY/SPRY domain / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / Butyrophylin-like, SPRY domain / B-box-type zinc finger / Zinc finger B-box type profile. / B30.2/SPRY domain ...E3 ubiquitin-protein ligase Trim36 / TRIM36, PRY/SPRY domain / Midline-1, COS domain / TRIM C-terminal subgroup One Signature domain / COS domain / COS domain profile. / Butyrophylin-like, SPRY domain / B-box-type zinc finger / Zinc finger B-box type profile. / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 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 TRIM36
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAPRIN-a2
B: HAPRIN-a2
C: HAPRIN-a2
D: HAPRIN-a2


Theoretical massNumber of molelcules
Total (without water)104,8544
Polymers104,8544
Non-polymers00
Water1,74797
1
A: HAPRIN-a2


Theoretical massNumber of molelcules
Total (without water)26,2141
Polymers26,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HAPRIN-a2


Theoretical massNumber of molelcules
Total (without water)26,2141
Polymers26,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HAPRIN-a2


Theoretical massNumber of molelcules
Total (without water)26,2141
Polymers26,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HAPRIN-a2


Theoretical massNumber of molelcules
Total (without water)26,2141
Polymers26,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.736, 93.064, 103.850
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
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A510 - 723
2010B510 - 723
1020A510 - 723
2020C510 - 723
1030A507 - 714
2030D507 - 714
1040B510 - 724
2040C510 - 724
1050B510 - 715
2050D510 - 715
1060C510 - 714
2060D510 - 714

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
HAPRIN-a2


Mass: 26213.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNIC-CTH0 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: Q4R1Q4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 24% PEG 3350, 0.15M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.25→46.53 Å / Num. obs: 42900 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.339.40.927241390.8610.3351.04100
8.71-46.538.50.0348400.9990.0120.03699.6

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→46.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 21.632 / SU ML: 0.228 / SU R Cruickshank DPI: 0.2909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 2169 5.1 %RANDOM
Rwork0.2026 ---
obs0.2049 40675 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.05 Å2 / Biso mean: 69.725 Å2 / Biso min: 38.81 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å2-0 Å2
2---4.26 Å20 Å2
3---7.38 Å2
Refinement stepCycle: final / Resolution: 2.25→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 0 97 6183
Biso mean---59.33 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175887
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.6488491
X-RAY DIFFRACTIONr_angle_other_deg1.1251.57913584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11322.322323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2231534
X-RAY DIFFRACTIONr_chiral_restr0.0530.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027033
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021483
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A52490.13
12B52490.13
21A52670.1
22C52670.1
31A51340.1
32D51340.1
41B53440.09
42C53440.09
51B49680.1
52D49680.1
61C50960.08
62D50960.08
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 150 -
Rwork0.334 2962 -
all-3112 -
obs--100 %
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)
15.2116-1.1129-0.89693.98941.00611.7467-0.03990.40360.3646-0.16250.1407-0.6913-0.05190.2531-0.10080.2213-0.07880.04130.2437-0.00550.13433.008735.9471-14.5884
25.0615-1.1512-1.26214.5750.53383.3136-0.08950.6975-0.5797-0.48050.1144-0.10770.30490.1528-0.02480.2270.00160.00820.2355-0.09980.091-0.102320.9084-16.3825
35.94455.11924.82878.64065.91736.4513-0.0794-0.04980.1026-0.0839-0.04660.0413-0.1905-0.08870.1260.15170.0440.02470.10140.01220.162223.583827.54176.1252
43.6599-0.558-0.9513.29450.98152.1198-0.03570.23710.1108-0.0166-0.04840.30970.1145-0.17390.08410.1246-0.0074-0.0220.04940.02160.0527-21.487534.9499-4.6765
55.4944-0.2691-0.213.10850.732.03240.0199-0.01530.614-0.07430.0230.2915-0.4096-0.082-0.04290.20260.02860.03130.01280.02230.1568-18.790750.43310.8334
62.8872-0.0585-0.33474.0042-2.38233.4738-0.0008-0.22270.55710.1616-0.1231-0.5728-0.270.4070.12390.2007-0.04470.02020.1306-0.06780.207318.533750.05335.8095
74.7891.16630.49733.3474-1.17732.871-0.13960.61750.6271-0.23580.1636-0.0081-0.28620.0527-0.02390.2635-0.0410.09940.11880.01290.228611.511157.5876-3.4657
83.20930.89620.12785.1133-1.07582.06670.0258-0.39890.15490.33740.10330.6875-0.0071-0.0788-0.1290.20410.02180.07680.26150.00820.0984-0.661935.7916.6188
94.40860.7672-1.51595.2934-0.51982.721-0.0209-0.7254-0.27130.71320.088-0.09170.20490.0059-0.0670.25630.0158-0.02310.26580.05880.02917.158224.409219.262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A507 - 574
2X-RAY DIFFRACTION2A575 - 715
3X-RAY DIFFRACTION3A716 - 735
4X-RAY DIFFRACTION4B510 - 570
5X-RAY DIFFRACTION5B571 - 724
6X-RAY DIFFRACTION6C510 - 655
7X-RAY DIFFRACTION7C656 - 724
8X-RAY DIFFRACTION8D507 - 573
9X-RAY DIFFRACTION9D574 - 715

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