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- PDB-7y3b: Crystal structure of TRIM7 bound to GN1 -

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Basic information

Entry
Database: PDB / ID: 7y3b
TitleCrystal structure of TRIM7 bound to GN1
ComponentsE3 ubiquitin-protein ligase TRIM7,TRIM7-GN1
KeywordsCYTOSOLIC PROTEIN / E3 ligase
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
E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDong, C. / Yan, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32071193 China
National Natural Science Foundation of China (NSFC)81874039 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: C-terminal glutamine acts as a C-degron targeted by E3 ubiquitin ligase TRIM7.
Authors: Ru, Y. / Yan, X. / Zhang, B. / Song, L. / Feng, Q. / Ye, C. / Zhou, Z. / Yang, Z. / Li, Y. / Zhang, Z. / Li, Q. / Mi, W. / Dong, C.
History
DepositionJun 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM7,TRIM7-GN1


Theoretical massNumber of molelcules
Total (without water)21,1971
Polymers21,1971
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.768, 79.768, 52.229
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM7,TRIM7-GN1 / Glycogenin-interacting protein / RING finger protein 90 / Tripartite motif-containing protein 7


Mass: 21196.881 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 (E. coli)
References: UniProt: Q9C029, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.76→41.66 Å / Num. obs: 18832 / % possible obs: 99.87 % / Redundancy: 18.1 % / Biso Wilson estimate: 19.17 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 20.08
Reflection shellResolution: 1.761→1.824 Å / Rmerge(I) obs: 1.229 / Num. unique obs: 1870

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UMA

6uma


Resolution: 1.76→41.66 Å / SU ML: 0.1903 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7851
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 1894 10.06 %
Rwork0.1629 16936 -
obs0.1655 18830 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 1.76→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 0 180 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781462
X-RAY DIFFRACTIONf_angle_d1.02781993
X-RAY DIFFRACTIONf_chiral_restr0.0595217
X-RAY DIFFRACTIONf_plane_restr0.0088259
X-RAY DIFFRACTIONf_dihedral_angle_d6.8357203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.31211340.24581186X-RAY DIFFRACTION98.65
1.81-1.850.23351310.22591198X-RAY DIFFRACTION99.92
1.85-1.910.26131370.20731206X-RAY DIFFRACTION100
1.91-1.970.25731350.20141185X-RAY DIFFRACTION100
1.97-2.040.18931340.16711212X-RAY DIFFRACTION100
2.04-2.120.20691360.15881211X-RAY DIFFRACTION100
2.12-2.220.19821350.14881213X-RAY DIFFRACTION99.93
2.22-2.340.18991380.15891208X-RAY DIFFRACTION99.93
2.34-2.480.17471360.1511206X-RAY DIFFRACTION100
2.48-2.670.21751300.15561205X-RAY DIFFRACTION100
2.67-2.940.18861390.15371209X-RAY DIFFRACTION100
2.94-3.370.15381370.1381220X-RAY DIFFRACTION100
3.37-4.240.15031350.14181221X-RAY DIFFRACTION100
4.24-41.660.18221370.17891256X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 21.0926592365 Å / Origin y: -24.0045882374 Å / Origin z: 1.61724684178 Å
111213212223313233
T0.134735356912 Å2-0.0107463636788 Å2-0.00598240406263 Å2-0.137879950423 Å20.00592581867983 Å2--0.138892484962 Å2
L1.57126027528 °20.0689904572826 °2-0.331333895336 °2-1.25928777221 °20.300097291419 °2--1.3033743353 °2
S-0.00215240991977 Å °0.0114498821476 Å °0.0968725977931 Å °-0.00516591173654 Å °-0.0166350545591 Å °0.0632358334668 Å °-0.0692889560997 Å °0.00873331212803 Å °0.0223368304473 Å °
Refinement TLS groupSelection details: all

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