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- PDB-7qs0: Crystal structure of B30.2 PRYSPRY domain of TRIM10 -

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Basic information

Entry
Database: PDB / ID: 7qs0
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM10
ComponentsTripartite motif-containing protein 10
KeywordsLIGASE / E3 / TRIM / TRIM10 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


host-mediated suppression of symbiont invasion / erythrocyte differentiation / Interferon gamma signaling / ubiquitin protein ligase activity / protein ubiquitination / innate immune response / zinc ion binding / cytoplasm
Similarity search - Function
TRIM10, RING-HC finger / 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 ...TRIM10, RING-HC finger / 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. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tripartite motif-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 TRIM10
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: Tripartite motif-containing protein 10
B: Tripartite motif-containing protein 10
C: Tripartite motif-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4277
Polymers60,1793
Non-polymers2484
Water1,36976
1
A: Tripartite motif-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2464
Polymers20,0601
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1222
Polymers20,0601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tripartite motif-containing protein 10


Theoretical massNumber of molelcules
Total (without water)20,0601
Polymers20,0601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.991, 65.991, 103.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA306 - 4803 - 177
21BB306 - 4803 - 177
12AA306 - 4803 - 177
22CC306 - 4803 - 177
13BB306 - 4813 - 178
23CC306 - 4813 - 178

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Tripartite motif-containing protein 10 / B30-RING finger protein / RING finger protein 9


Mass: 20059.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM10, RFB30, RNF9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: Q9UDY6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% ethylene glycol

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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 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.3→38.32 Å / Num. obs: 22199 / % possible obs: 99.2 % / Redundancy: 8.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.034 / Rrim(I) all: 0.101 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.3890.3511.821740.9860.1330.401100
8.91-38.329.20.0623850.9970.0220.06697.6

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6umb

6umb


Resolution: 2.3→38.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 20.474 / SU ML: 0.236 / SU R Cruickshank DPI: 0.5129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.513 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1155 5.2 %RANDOM
Rwork0.2038 ---
obs0.2065 21014 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.72 Å2 / Biso mean: 50.251 Å2 / Biso min: 25.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.65 Å20 Å2
2--1.31 Å20 Å2
3----4.25 Å2
Refinement stepCycle: final / Resolution: 2.3→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 16 76 4306
Biso mean--58.02 48.22 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134359
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173998
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.6475931
X-RAY DIFFRACTIONr_angle_other_deg1.1481.5759173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7885529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.27820.04247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3581542
X-RAY DIFFRACTIONr_chiral_restr0.0550.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021117
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53260.09
12B53260.09
21A51600.11
22C51600.11
31B51730.12
32C51730.12
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 76 -
Rwork0.237 1581 -
all-1657 -
obs--99.88 %
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)
12.90650.3402-0.57832.4412-1.54575.7898-0.01770.2286-0.139-0.2787-0.0524-0.22210.46470.50030.07010.07060.0347-0.00430.0741-0.00140.103748.2903-24.9849-4.401
21.73680.1735-1.47572.3079-0.75424.27840.01070.09790.04820.00680.06690.12440.0017-0.1219-0.07760.00130.0025-0.00060.0202-0.00130.011437.4226-19.77212.5741
33.2025-0.0702-1.59692.96520.42285.1069-0.2803-0.2881-0.13970.24660.15010.10950.46570.16470.13020.14740.02030.02120.05560.02810.032356.794-42.03428.4604
41.8995-0.9976-0.87562.45330.70594.857-0.11740.00870.1793-0.00820.1695-0.13020.00850.3124-0.05210.066-0.0564-0.01160.09230.01890.03661.6847-35.133520.0604
54.17020.5239-0.64213.7503-1.28640.5402-0.21840.5932-0.1083-0.44650.18940.12180.1817-0.24290.02910.4371-0.02920.03470.4297-0.02250.309552.3015-9.431825.13
62.8073-1.1227-0.80133.57250.42443.8679-0.0758-0.29770.1357-0.10330.1075-0.1152-0.0797-0.1573-0.03170.4329-0.06940.00660.1988-0.03350.114161.4503-1.986924.6819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 344
2X-RAY DIFFRACTION2A345 - 481
3X-RAY DIFFRACTION3B306 - 409
4X-RAY DIFFRACTION4B410 - 481
5X-RAY DIFFRACTION5C306 - 331
6X-RAY DIFFRACTION6C332 - 481

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