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- PDB-7y3a: Crystal structure of TRIM7 bound to 2C -

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Basic information

Entry
Database: PDB / ID: 7y3a
TitleCrystal structure of TRIM7 bound to 2C
ComponentsE3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C
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: 1.7 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C
C: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C
B: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C


Theoretical massNumber of molelcules
Total (without water)63,7593
Polymers63,7593
Non-polymers00
Water12,881715
1
A: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C
B: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C


Theoretical massNumber of molelcules
Total (without water)42,5062
Polymers42,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C


Theoretical massNumber of molelcules
Total (without water)21,2531
Polymers21,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.228, 53.644, 80.999
Angle α, β, γ (deg.)90.000, 119.210, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-2C / Glycogenin-interacting protein / RING finger protein 90 / Tripartite motif-containing protein 7


Mass: 21252.924 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium formate pH 7.0 20%3350 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.97918 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→70.7 Å / Num. obs: 61973 / % possible obs: 99.4 % / Redundancy: 12.1 % / Biso Wilson estimate: 10.71 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.73
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.14 / Num. unique obs: 3432

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UMA

6uma


Resolution: 1.7→29.04 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1751 2927 4.72 %
Rwork0.1484 59046 -
obs0.1496 61973 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.07 Å2 / Biso mean: 14.6624 Å2 / Biso min: 4.35 Å2
Refinement stepCycle: final / Resolution: 1.7→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 0 715 4974
Biso mean---26.97 -
Num. residues----540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.18831070.16551602170954
1.73-1.760.23631730.16628763049100
1.76-1.790.18851440.159829713115100
1.79-1.820.21941320.157729263058100
1.82-1.860.18731710.149429503121100
1.86-1.90.181480.149429853133100
1.9-1.950.19761160.155530033119100
1.95-1.990.2021480.154529273075100
1.99-2.050.18111800.146929083088100
2.05-2.110.17491320.14829903122100
2.11-2.180.18971830.148829293112100
2.18-2.250.16731520.150629853137100
2.25-2.340.2093860.148529923078100
2.34-2.450.18921260.150730023128100
2.45-2.580.15771610.155729603121100
2.58-2.740.16651090.15261824193362
2.74-2.950.20171310.151129853116100
2.95-3.250.15461930.142929373130100
3.25-3.720.15291470.13462321246878
3.72-4.680.1355770.1282834291192
4.68-29.040.16411110.160431393250100
Refinement TLS params.Method: refined / Origin x: 19.4011 Å / Origin y: 11.6751 Å / Origin z: 11.7783 Å
111213212223313233
T0.057 Å2-0.0033 Å20.0024 Å2-0.049 Å20.007 Å2--0.0521 Å2
L0.1243 °20.0063 °20.0298 °2-0.0689 °20.0375 °2--0.0955 °2
S-0.0026 Å °-0.0083 Å °-0.0124 Å °-0.0038 Å °0.0126 Å °-0.0096 Å °-0.0133 Å °0.0121 Å °-0.0083 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA342 - 530
2X-RAY DIFFRACTION1allC342 - 530
3X-RAY DIFFRACTION1allB342 - 530
4X-RAY DIFFRACTION1allS1 - 748

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