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- PDB-6jbm: Crystal structure of the TRIM14 PRYSPRY domain -

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Basic information

Entry
Database: PDB / ID: 6jbm
TitleCrystal structure of the TRIM14 PRYSPRY domain
ComponentsTripartite motif-containing protein 14
KeywordsPROTEIN BINDING / TRIM / protein interaction domain
Function / homology
Function and homology information


negative regulation of viral transcription / positive regulation of DNA-binding transcription factor activity / phagocytic vesicle / positive regulation of NF-kappaB transcription factor activity / Interferon gamma signaling / ubiquitin protein ligase activity / molecular adaptor activity / mitochondrial outer membrane / transcription coactivator activity / protein ubiquitination ...negative regulation of viral transcription / positive regulation of DNA-binding transcription factor activity / phagocytic vesicle / positive regulation of NF-kappaB transcription factor activity / Interferon gamma signaling / ubiquitin protein ligase activity / molecular adaptor activity / mitochondrial outer membrane / transcription coactivator activity / protein ubiquitination / inflammatory response / innate immune response / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
TRIM14, PRY/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. ...TRIM14, PRY/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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Tripartite motif-containing protein 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYin, Y.X. / Yu, Y. / Liang, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81430056 China
National Natural Science Foundation of China31420103905 China
National Natural Science Foundation of China31800626 China
CitationJournal: Febs Lett. / Year: 2019
Title: The TRIM14 PRYSPRY domain mediates protein interaction via its basic interface.
Authors: Yu, Y. / Liang, L. / Jin, Y. / Yin, Y.
History
DepositionJan 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tripartite motif-containing protein 14
A: Tripartite motif-containing protein 14
C: Tripartite motif-containing protein 14
D: Tripartite motif-containing protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,72916
Polymers91,5774
Non-polymers1,15312
Water5,044280
1
A: Tripartite motif-containing protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1824
Polymers22,8941
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2785
Polymers22,8941
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tripartite motif-containing protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9902
Polymers22,8941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tripartite motif-containing protein 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2785
Polymers22,8941
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.326, 104.020, 93.381
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tripartite motif-containing protein 14 / TRIM14


Mass: 22894.139 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM14, KIAA0129 / Plasmid: pet28a+ / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha] / References: UniProt: Q14142
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Ammonium sulfate, PEG8000 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46284 / % possible obs: 99.4 % / Redundancy: 3.3 % / Net I/σ(I): 9.39
Reflection shellResolution: 2.1→2.15 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7I

4n7i


Resolution: 2.1→35.396 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2425 2294 4.96 %
Rwork0.2132 --
obs0.2146 46284 85.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 60 280 6296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016169
X-RAY DIFFRACTIONf_angle_d1.2118376
X-RAY DIFFRACTIONf_dihedral_angle_d22.3622213
X-RAY DIFFRACTIONf_chiral_restr0.193861
X-RAY DIFFRACTIONf_plane_restr0.0061067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14560.25951050.24491645X-RAY DIFFRACTION53
2.1456-2.19560.291870.23771917X-RAY DIFFRACTION59
2.1956-2.25050.2674920.23552025X-RAY DIFFRACTION63
2.2505-2.31130.29311280.23432191X-RAY DIFFRACTION69
2.3113-2.37930.27681330.23382327X-RAY DIFFRACTION74
2.3793-2.45610.30271400.2422502X-RAY DIFFRACTION79
2.4561-2.54380.29641650.24362749X-RAY DIFFRACTION86
2.5438-2.64560.28421330.25142975X-RAY DIFFRACTION94
2.6456-2.7660.2791550.24663174X-RAY DIFFRACTION99
2.766-2.91180.27481740.22953185X-RAY DIFFRACTION100
2.9118-3.09410.27651750.22643192X-RAY DIFFRACTION100
3.0941-3.33280.26311610.22213209X-RAY DIFFRACTION100
3.3328-3.66790.211730.19853194X-RAY DIFFRACTION100
3.6679-4.19790.20341580.19093200X-RAY DIFFRACTION100
4.1979-5.28610.191740.17193216X-RAY DIFFRACTION100
5.2861-35.40110.2311410.21263289X-RAY DIFFRACTION100

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