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- PDB-8a5m: TRIM7 PRYSPRY in complex with a MNV1-NS6 peptide LEALEFQ -

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Basic information

Entry
Database: PDB / ID: 8a5m
TitleTRIM7 PRYSPRY in complex with a MNV1-NS6 peptide LEALEFQ
Components
  • E3 ubiquitin-protein ligase TRIM7
  • MNV1-NS6 peptide LEALEFQ
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
PHOSPHATE ION / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
Murine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.918 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: E3 ubiquitin-protein ligase TRIM7
C: MNV1-NS6 peptide LEALEFQ
E: MNV1-NS6 peptide LEALEFQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6537
Polymers42,3684
Non-polymers2853
Water43224
1
A: E3 ubiquitin-protein ligase TRIM7
C: MNV1-NS6 peptide LEALEFQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3744
Polymers21,1842
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area8250 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM7
E: MNV1-NS6 peptide LEALEFQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2793
Polymers21,1842
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-11 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.919, 112.972, 53.036
Angle α, β, γ (deg.)90.000, 102.928, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2
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 MNV1-NS6 peptide LEALEFQ


Mass: 848.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Murine norovirus 1
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.82 Å3/Da / Density % sol: 56.38 % / Description: small rods
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1 M Sodium Potassium Phosphate pH 5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.918→112.97 Å / Num. obs: 10246 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.96 / Net I/σ(I): 24.4
Reflection shellResolution: 2.92→3.1 Å / Num. unique obs: 524 / CC1/2: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2dialsdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OW2

7ow2


Resolution: 2.918→56.55 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.861 / SU B: 23.235 / SU ML: 0.404 / Cross valid method: FREE R-VALUE / ESU R Free: 0.443
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2746 524 5.125 %
Rwork0.1931 9700 -
all0.197 --
obs-10224 99.873 %
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: 54.013 Å2
Baniso -1Baniso -2Baniso -3
1--3.679 Å2-0 Å2-2.008 Å2
2--1.848 Å20 Å2
3---2.491 Å2
Refinement stepCycle: LAST / Resolution: 2.918→56.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 15 24 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142668
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.6443947
X-RAY DIFFRACTIONr_angle_other_deg1.1661.5766114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.985352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15619.885174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31815452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8591532
X-RAY DIFFRACTIONr_chiral_restr0.0550.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023305
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02743
X-RAY DIFFRACTIONr_nbd_refined0.1850.2524
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22605
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21302
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.27
X-RAY DIFFRACTIONr_nbd_other0.2360.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0550.22
X-RAY DIFFRACTIONr_mcbond_it3.6615.5041408
X-RAY DIFFRACTIONr_mcbond_other3.6615.5041407
X-RAY DIFFRACTIONr_mcangle_it5.9928.2421754
X-RAY DIFFRACTIONr_mcangle_other5.9918.2421755
X-RAY DIFFRACTIONr_scbond_it4.1276.041494
X-RAY DIFFRACTIONr_scbond_other4.0776.0141482
X-RAY DIFFRACTIONr_scangle_it6.5718.882191
X-RAY DIFFRACTIONr_scangle_other6.5478.8432173
X-RAY DIFFRACTIONr_lrange_it9.70262.1153027
X-RAY DIFFRACTIONr_lrange_other9.70162.1183028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.918-2.9940.357430.31675X-RAY DIFFRACTION99.1713
2.994-3.0760.336370.308694X-RAY DIFFRACTION99.5913
3.076-3.1650.376390.293689X-RAY DIFFRACTION100
3.165-3.2620.264340.269644X-RAY DIFFRACTION99.8527
3.262-3.3690.298390.24649X-RAY DIFFRACTION99.8549
3.369-3.4880.305320.219620X-RAY DIFFRACTION100
3.488-3.6190.224200.189599X-RAY DIFFRACTION100
3.619-3.7670.297360.219593X-RAY DIFFRACTION100
3.767-3.9340.333240.2532X-RAY DIFFRACTION100
3.934-4.1260.33260.193546X-RAY DIFFRACTION100
4.126-4.3490.216290.171499X-RAY DIFFRACTION100
4.349-4.6120.291240.135480X-RAY DIFFRACTION99.802
4.612-4.930.146180.129453X-RAY DIFFRACTION100
4.93-5.3240.246230.124416X-RAY DIFFRACTION100
5.324-5.8310.216240.156382X-RAY DIFFRACTION100
5.831-6.5170.301240.16334X-RAY DIFFRACTION99.7215
6.517-7.5210.327130.182320X-RAY DIFFRACTION100
7.521-9.2010.259180.162252X-RAY DIFFRACTION100
9.201-12.9690.19170.135204X-RAY DIFFRACTION100

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