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- PDB-7qs1: Crystal structure of B30.2 PRYSPRY domain of TRIM11 -

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Basic information

Entry
Database: PDB / ID: 7qs1
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM11
ComponentsE3 ubiquitin-protein ligase TRIM11
KeywordsLIGASE / E3 / TRIM / TRIM11 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / RING-type E3 ubiquitin transferase / negative regulation of neurogenesis / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / positive regulation of viral entry into host cell / protein ubiquitination ...suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / RING-type E3 ubiquitin transferase / negative regulation of neurogenesis / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / positive regulation of viral entry into host cell / protein ubiquitination / protein domain specific binding / innate immune response / negative regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
SPRY-associated domain / SPRY-associated / PRY / 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 ...SPRY-associated domain / SPRY-associated / PRY / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 TRIM11
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 TRIM11
B: E3 ubiquitin-protein ligase TRIM11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75816
Polymers41,7872
Non-polymers97114
Water2,360131
1
A: E3 ubiquitin-protein ligase TRIM11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2726
Polymers20,8941
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase TRIM11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,48610
Polymers20,8941
Non-polymers5939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.636, 42.018, 68.584
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 276 - 459 / Label seq-ID: 2 - 185

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM11 / Protein BIA1 / RING finger protein 92 / RING-type E3 ubiquitin transferase TRIM11 / Tripartite ...Protein BIA1 / RING finger protein 92 / RING-type E3 ubiquitin transferase TRIM11 / Tripartite motif-containing protein 11


Mass: 20893.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM11, RNF92 / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q96F44, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 10% ethylene glycol, 0.2M sodium 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: 1.93→43.36 Å / Num. obs: 27861 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.032 / Rrim(I) all: 0.078 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1 / % possible all: 99.4

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.93-26.10.764227300.7940.3690.921
7.47-43.365.60.0385330.9980.0170.042

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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: 2iwg

2iwg


Resolution: 1.93→43.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.779 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1523 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1407 5.1 %RANDOM
Rwork0.1683 ---
obs0.1702 26443 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.75 Å2 / Biso mean: 44.167 Å2 / Biso min: 25.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.56 Å2
2--1.33 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 1.93→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 59 131 3019
Biso mean--61.19 48.73 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172759
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6643997
X-RAY DIFFRACTIONr_angle_other_deg1.2511.5766352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2475360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17219.318176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6761537
X-RAY DIFFRACTIONr_chiral_restr0.0710.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023302
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02728
Refine LS restraints NCS

Ens-ID: 1 / Number: 5076 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 114 -
Rwork0.236 1932 -
all-2046 -
obs--99.22 %
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)
10.3744-0.0685-0.90320.84971.19053.5277-0.03390.0458-0.0346-0.0731-0.09080.063-0.0885-0.25210.12470.096-0.0162-0.00990.16610.00980.057673.55792.828951.6436
24.7378-1.47672.97152.01431.07585.5174-0.1516-0.26420.40440.06430.12560.0192-0.24540.16960.0260.0987-0.06730.01870.1332-0.08380.238446.955810.588748.287
32.0922-0.5806-1.0141.16360.55953.0133-0.01480.1046-0.04290.1089-0.19960.0930.0303-0.43650.21440.0533-0.0437-0.00350.2499-0.01690.024267.5324.613758.1332
40.7012-0.1074-0.37570.5912-0.19981.48670.0488-0.02170.0673-0.0056-0.03570.03470.04970.0255-0.01310.0621-0.01050.01160.11750.0090.035636.8741-4.976144.1073
57.997-2.9991-3.9061.61812.53614.5097-0.29610.6179-0.17150.14580.02170.22760.20950.38720.27440.1117-0.02240.01330.30580.01450.161754.4738-1.440940.2194
61.3356-0.1003-0.31541.18970.10611.6999-0.0114-0.10450.0270.1381-0.02790.01980.03490.1080.03930.0679-0.03530.00690.1444-0.00420.012540.8914-3.190551.9966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A276 - 381
2X-RAY DIFFRACTION2A382 - 400
3X-RAY DIFFRACTION3A401 - 459
4X-RAY DIFFRACTION4B276 - 380
5X-RAY DIFFRACTION5B381 - 398
6X-RAY DIFFRACTION6B399 - 459

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