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- PDB-6yxe: Structure of the Trim69 RING domain -

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Basic information

Entry
Database: PDB / ID: 6yxe
TitleStructure of the Trim69 RING domain
ComponentsE3 ubiquitin-protein ligase TRIM69
KeywordsANTIVIRAL PROTEIN / Trim69 / tripartite motif / Trim protein
Function / homology
Function and homology information


RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / nuclear speck / apoptotic process / identical protein binding / metal ion binding / nucleus ...RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / nuclear speck / apoptotic process / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily ...zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / 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 TRIM69
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKeown, J.R. / Goldstone, D.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden Fund New Zealand
Royal Society of New Zealand New Zealand
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: The RING domain of TRIM69 promotes higher-order assembly.
Authors: Keown, J.R. / Yang, J. / Black, M.M. / Goldstone, D.C.
History
DepositionMay 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM69
B: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7446
Polymers29,4822
Non-polymers2624
Water54030
1
A: E3 ubiquitin-protein ligase TRIM69
hetero molecules

A: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7446
Polymers29,4822
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area2520 Å2
ΔGint-25 kcal/mol
Surface area10360 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM69
hetero molecules

B: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7446
Polymers29,4822
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area1310 Å2
ΔGint-15 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.965, 109.965, 90.135
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A33 - 103
2010B33 - 103

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM69 / RFP-like domain-containing protein trimless / RING finger protein 36 / RING-type E3 ubiquitin ...RFP-like domain-containing protein trimless / RING finger protein 36 / RING-type E3 ubiquitin transferase TRIM69 / Tripartite motif-containing protein 69


Mass: 14741.005 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM69, RNF36, HSD-34, HSD34 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86WT6, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.03 Å3/Da / Density % sol: 39.5 % / Description: hexagonal plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.26 M NH4SO4, 0.2 M LiSO4, and 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.2524 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2524 Å / Relative weight: 1
ReflectionResolution: 2.1→65.46 Å / Num. obs: 12387 / % possible obs: 100 % / Redundancy: 21.5 % / CC1/2: 1 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.024 / Rrim(I) all: 0.113 / Net I/σ(I): 27.4
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
2.1-2.1615.32.145152469990.5080.5582.2191.5100
8.91-42.119.10.042348418210.010.044107.199.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
SHELXDEphasing
REFMAC5.0.32refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→65.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.518 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.172
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 643 5.2 %RANDOM
Rwork0.1977 ---
obs0.1999 11743 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.68 Å2 / Biso mean: 52.317 Å2 / Biso min: 28.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.22 Å20 Å2
2---0.44 Å20 Å2
3---1.44 Å2
Refinement stepCycle: final / Resolution: 2.1→65.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 4 30 1323
Biso mean--44.88 42.57 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191331
X-RAY DIFFRACTIONr_bond_other_d0.0020.021189
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9591808
X-RAY DIFFRACTIONr_angle_other_deg1.01432788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.43225.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81315233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.564152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
Refine LS restraints NCS

Ens-ID: 1 / Number: 4184 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 44 -
Rwork0.315 865 -
all-909 -
obs--100 %
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)
15.6642.62122.4053.47291.64193.97480.1077-0.3684-0.11520.1863-0.0060.00420.4753-0.4838-0.10170.137-0.0021-0.01110.2903-0.01740.012723.62823.8627.402
23.4825-0.01040.2657.17821.05998.3147-0.1085-0.2954-0.31070.15560.1255-0.23080.51651.1529-0.0170.2480.0219-0.04560.31040.04420.126922.9950.5610.017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 110
2X-RAY DIFFRACTION1C1
3X-RAY DIFFRACTION1C2
4X-RAY DIFFRACTION2B33 - 104
5X-RAY DIFFRACTION2C3
6X-RAY DIFFRACTION2C4

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