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- PDB-8a5l: TRIM7 PRYSPRY in complex with a 2BC peptide TIEALFQ -

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Basic information

Entry
Database: PDB / ID: 8a5l
TitleTRIM7 PRYSPRY in complex with a 2BC peptide TIEALFQ
Components
  • 2BC peptide TIEALFQ
  • E3 ubiquitin-protein ligase TRIM7
KeywordsPROTEIN BINDING / E3 ligase / PRYSPRY / TRIM
Function / homology
Function and homology information


antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / Golgi apparatus / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger, B-box, chordata / zinc finger of C3HC4-type, RING / 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, B-box, chordata / zinc finger of C3HC4-type, RING / 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
D(-)-TARTARIC ACID / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.622 Å
AuthorsLuptak, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Viruses / Year: 2022
Title: TRIM7 Restricts Coxsackievirus and Norovirus Infection by Detecting the C-Terminal Glutamine Generated by 3C Protease Processing.
Authors: Luptak, J. / Mallery, D.L. / Jahun, A.S. / Albecka, A. / Clift, D. / Ather, O. / Slodkowicz, G. / Goodfellow, I. / James, L.C.
History
DepositionJun 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 10, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM7
B: 2BC peptide TIEALFQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3063
Polymers21,1562
Non-polymers1501
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.887, 79.887, 53.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM7 / Glycogenin-interacting protein / RING finger protein 90 / Tripartite motif-containing protein 7


Mass: 20335.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q9C029, RING-type E3 ubiquitin transferase
#2: Protein/peptide 2BC peptide TIEALFQ


Mass: 820.929 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterovirus A71
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.32 Å3/Da / Density % sol: 46.9 % / Description: rods
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1 M Sodium Potassium Tartrate, 0.1 M HEPES pH 6.8 (adjusted with HCl)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→29.02 Å / Num. obs: 24565 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.99 / Net I/σ(I): 11.1
Reflection shellResolution: 1.62→1.66 Å / Num. unique obs: 1780 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2FastDPdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OW2

7ow2


Resolution: 1.622→29.018 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.853 / SU ML: 0.061 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1884 1286 5.239 %
Rwork0.156 23260 -
all0.158 --
obs-24546 99.752 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.412 Å2
Baniso -1Baniso -2Baniso -3
1-0.385 Å20.193 Å20 Å2
2--0.385 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.622→29.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 10 152 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141351
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.6442013
X-RAY DIFFRACTIONr_angle_other_deg1.4671.5763099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8925180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47919.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26115227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3891516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_nbd_refined0.1890.2230
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21268
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2705
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.210
X-RAY DIFFRACTIONr_nbd_other0.2040.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.227
X-RAY DIFFRACTIONr_mcbond_it1.641.606714
X-RAY DIFFRACTIONr_mcbond_other1.6411.606713
X-RAY DIFFRACTIONr_mcangle_it2.4872.406890
X-RAY DIFFRACTIONr_mcangle_other2.4862.406891
X-RAY DIFFRACTIONr_scbond_it2.5881.943765
X-RAY DIFFRACTIONr_scbond_other2.5671.941764
X-RAY DIFFRACTIONr_scangle_it3.8622.8051121
X-RAY DIFFRACTIONr_scangle_other3.8492.8061121
X-RAY DIFFRACTIONr_lrange_it5.31719.6231598
X-RAY DIFFRACTIONr_lrange_other5.31619.651599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.622-1.6640.298760.2721721X-RAY DIFFRACTION97.8225
1.664-1.7090.289560.2381666X-RAY DIFFRACTION100
1.709-1.7590.251720.2211630X-RAY DIFFRACTION100
1.759-1.8130.238930.1991582X-RAY DIFFRACTION99.9403
1.813-1.8730.183780.1741543X-RAY DIFFRACTION100
1.873-1.9380.201870.1621465X-RAY DIFFRACTION99.9356
1.938-2.0110.194650.1511462X-RAY DIFFRACTION99.9346
2.011-2.0930.179980.1421347X-RAY DIFFRACTION99.8618
2.093-2.1860.192970.151298X-RAY DIFFRACTION100
2.186-2.2930.174790.151262X-RAY DIFFRACTION100
2.293-2.4170.19710.1451201X-RAY DIFFRACTION99.9214
2.417-2.5630.182850.151112X-RAY DIFFRACTION100
2.563-2.740.187530.1531085X-RAY DIFFRACTION100
2.74-2.9590.196510.1431013X-RAY DIFFRACTION100
2.959-3.2410.166620.136896X-RAY DIFFRACTION100
3.241-3.6220.147460.138839X-RAY DIFFRACTION99.8871
3.622-4.1810.142440.123742X-RAY DIFFRACTION99.8729
4.181-5.1160.173250.123634X-RAY DIFFRACTION99.5468
5.116-7.2150.235310.172484X-RAY DIFFRACTION100

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