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- PDB-8r5d: Crystal structure of human TRIM7 PRYSPRY domain -

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Basic information

Entry
Database: PDB / ID: 8r5d
TitleCrystal structure of human TRIM7 PRYSPRY domain
ComponentsE3 ubiquitin-protein ligase TRIM7
KeywordsLIGASE / TRIM7 / E3-Ligase / Structural Genomics / Structural Genomics Consortium / SGC
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
MALONIC ACID / E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMunoz Sosa, C.J. / Kraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of human TRIM7 PRYSPRY domain
Authors: Munoz Sosa, C.J. / Kraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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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)40,67419
Polymers39,4932
Non-polymers1,18117
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint30 kcal/mol
Surface area14330 Å2
Unit cell
Length a, b, c (Å)61.258, 70.905, 85.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM7


Mass: 19746.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C029
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium malonate dibasic monohydrate pH 7.0, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→46.35 Å / Num. obs: 35213 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.047 / Rrim(I) all: 0.122 / Χ2: 0.9 / Net I/σ(I): 7.2 / Num. measured all: 237490
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.898 / Num. measured all: 13884 / Num. unique obs: 2068 / CC1/2: 0.884 / Rpim(I) all: 0.371 / Rrim(I) all: 0.973 / Χ2: 0.88 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.93 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1726 4.9 %RANDOM
Rwork0.20419 ---
obs0.20589 33425 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.946 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å2-0 Å2-0 Å2
2--2.44 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.8→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 77 216 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122843
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162632
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6613856
X-RAY DIFFRACTIONr_angle_other_deg0.5091.5776023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5985352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.844530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1410421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0861.0661384
X-RAY DIFFRACTIONr_mcbond_other1.0861.0661384
X-RAY DIFFRACTIONr_mcangle_it1.7011.9021729
X-RAY DIFFRACTIONr_mcangle_other1.7011.9031730
X-RAY DIFFRACTIONr_scbond_it1.8351.3381459
X-RAY DIFFRACTIONr_scbond_other1.8361.3411460
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.792.3152123
X-RAY DIFFRACTIONr_long_range_B_refined6.1112.823072
X-RAY DIFFRACTIONr_long_range_B_other6.06211.953037
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 129 -
Rwork0.272 2423 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6338-0.3441.00121.46450.01162.0753-0.06350.02980.14140.0022-0.02910.0196-0.11680.01460.09260.1189-0.0108-0.00180.00180.00480.13117.829715.19717.8017
23.50780.39751.09911.46020.04862.3316-0.03820.00710.13760.0071-0.0099-0.035-0.11850.02880.04810.11810.00970.0010.00160.00320.137927.500315.092735.0433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A340 - 605
2X-RAY DIFFRACTION2B340 - 609

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