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- PDB-7w0s: TRIM7 in complex with C-terminal peptide of 2C -

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Basic information

Entry
Database: PDB / ID: 7w0s
TitleTRIM7 in complex with C-terminal peptide of 2C
Components
  • E3 ubiquitin-protein ligase TRIM7
  • peptide
KeywordsANTIVIRAL PROTEIN
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
NITRATE ION / DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhang, H. / Liang, X. / Li, X.Z.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.
Authors: Liang, X. / Xiao, J. / Li, X. / Liu, Y. / Lu, Y. / Wen, Y. / Li, Z. / Che, X. / Ma, Y. / Zhang, X. / Zhang, Y. / Jian, D. / Wang, P. / Xuan, C. / Yu, G. / Li, L. / Zhang, H.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase TRIM7
A: peptide
C: E3 ubiquitin-protein ligase TRIM7
D: peptide
E: E3 ubiquitin-protein ligase TRIM7
F: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27319
Polymers62,3036
Non-polymers97113
Water12,106672
1
B: E3 ubiquitin-protein ligase TRIM7
A: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9845
Polymers20,7682
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint1 kcal/mol
Surface area8430 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase TRIM7
D: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1227
Polymers20,7682
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-0 kcal/mol
Surface area8400 Å2
MethodPISA
3
E: E3 ubiquitin-protein ligase TRIM7
F: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1687
Polymers20,7682
Non-polymers4005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-3 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.131, 53.479, 80.873
Angle α, β, γ (deg.)90.000, 118.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Protein/peptide , 2 types, 6 molecules BCEADF

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


Mass: 19689.295 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C029, RING-type E3 ubiquitin transferase
#2: Protein/peptide peptide /


Mass: 1078.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus

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Non-polymers , 4 types, 685 molecules

#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion / Details: PEG 3350, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→42.68 Å / Num. obs: 107169 / % possible obs: 91.58 % / Redundancy: 6.2 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.89
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 6515 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6uma

6uma


Resolution: 1.4→42.34 Å / SU ML: 0.1189 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.7155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1685 5112 4.77 %
Rwork0.1512 102047 -
obs0.152 107159 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.12 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 63 672 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944311
X-RAY DIFFRACTIONf_angle_d1.08725846
X-RAY DIFFRACTIONf_chiral_restr0.0869624
X-RAY DIFFRACTIONf_plane_restr0.0111765
X-RAY DIFFRACTIONf_dihedral_angle_d7.8586592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.410.2057680.2291861X-RAY DIFFRACTION49.4
1.41-1.430.2734790.20312065X-RAY DIFFRACTION54.93
1.43-1.450.219980.19492289X-RAY DIFFRACTION60.92
1.45-1.470.21461210.18332504X-RAY DIFFRACTION68.45
1.47-1.480.20381270.17962689X-RAY DIFFRACTION72.76
1.48-1.510.19751730.17752954X-RAY DIFFRACTION80.49
1.51-1.530.2041620.17133203X-RAY DIFFRACTION85.69
1.53-1.550.18251540.16633351X-RAY DIFFRACTION90.66
1.55-1.570.19181690.16423490X-RAY DIFFRACTION94.23
1.57-1.60.17131820.16973662X-RAY DIFFRACTION98.44
1.6-1.630.19262050.16763666X-RAY DIFFRACTION99.56
1.63-1.660.19261930.18563676X-RAY DIFFRACTION99.15
1.66-1.690.20052420.18063615X-RAY DIFFRACTION99.02
1.69-1.720.18312330.16813656X-RAY DIFFRACTION99.34
1.72-1.760.19312130.16623649X-RAY DIFFRACTION99.28
1.76-1.80.17941640.15863708X-RAY DIFFRACTION98.62
1.8-1.850.16592100.14653625X-RAY DIFFRACTION98.54
1.85-1.90.15781920.14293674X-RAY DIFFRACTION99.54
1.9-1.950.16541410.14113722X-RAY DIFFRACTION99.38
1.95-2.020.15752160.14513666X-RAY DIFFRACTION99.41
2.02-2.090.1741770.1433709X-RAY DIFFRACTION99.11
2.09-2.170.15812130.13823657X-RAY DIFFRACTION98.98
2.17-2.270.15911830.13753690X-RAY DIFFRACTION98.9
2.27-2.390.17231090.13683794X-RAY DIFFRACTION99.46
2.39-2.540.16451950.14093723X-RAY DIFFRACTION99.64
2.54-2.730.16131830.14583692X-RAY DIFFRACTION98.83
2.74-3.010.17241780.14723711X-RAY DIFFRACTION98.73
3.01-3.450.15572120.14233724X-RAY DIFFRACTION99.57
3.45-4.340.13752010.1373715X-RAY DIFFRACTION98.69
4.34-42.340.19531190.17033907X-RAY DIFFRACTION98.97
Refinement TLS params.Method: refined / Origin x: 6.77917058983 Å / Origin y: -16.8107987031 Å / Origin z: 20.2705303866 Å
111213212223313233
T0.118420026458 Å20.00772141227143 Å20.000275178130204 Å2-0.0953910124642 Å2-0.00250439094405 Å2--0.113287598775 Å2
L0.195512177504 °20.0271464044481 °2-0.0321949421508 °2-0.0939847785896 °2-0.0407526765126 °2--0.183435129263 °2
S-0.0142789572141 Å °0.0272106084141 Å °-0.00271459212043 Å °0.00442115464971 Å °0.0125027129903 Å °-0.00980199697408 Å °-0.012137509187 Å °0.00141782632471 Å °-0.000449398977722 Å °
Refinement TLS groupSelection details: all

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