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- PDB-6uma: Crystal structure of the TRIM7 B30.2 domain at 1.6 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6uma
TitleCrystal structure of the TRIM7 B30.2 domain at 1.6 angstrom resolution
ComponentsE3 ubiquitin-protein ligase TRIM7
KeywordsLIGASE / B30.2 / E3 ubiquitin ligase / PRY/SPRY / TRIM7
Function / homology
Function and homology information


antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / innate immune response / Golgi apparatus / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / Zinc finger, B-box, chordata / : / 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 of C3HC4-type, RING / Zinc finger, B-box, chordata / : / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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
MALONATE ION / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMunoz Sosa, C.J. / Carrizo, M.E.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1.
Authors: Munoz Sosa, C.J. / Issoglio, F.M. / Carrizo, M.E.
History
DepositionOct 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1418
Polymers40,5482
Non-polymers5926
Water3,639202
1
A: E3 ubiquitin-protein ligase TRIM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6625
Polymers20,2741
Non-polymers3884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4783
Polymers20,2741
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.940, 62.070, 128.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 20274.066 Da / Num. of mol.: 2 / Fragment: B30.2 domain
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: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Sodium malonate pH 6.0, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.6→20.69 Å / Num. obs: 44099 / % possible obs: 97.6 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.019 / Rrim(I) all: 0.046 / Net I/σ(I): 11.3 / Num. measured all: 237684 / Scaling rejects: 95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.635.30.3371086120550.9590.1520.3711.790.5
8.62-20.695.70.02718613270.9990.0120.0325.393.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7I

4n7i


Resolution: 1.6→20.69 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.079 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 2238 5.1 %RANDOM
Rwork0.1741 ---
obs0.1757 41804 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.48 Å2 / Biso mean: 26.102 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--1.23 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 1.6→20.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 40 202 3043
Biso mean--40.45 34.37 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132938
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172674
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6473984
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5726179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.935358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.88119.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39415452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9811532
X-RAY DIFFRACTIONr_chiral_restr0.0870.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 142 -
Rwork0.286 2840 -
all-2982 -
obs--91.11 %

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