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- PDB-4nqj: Structure of coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 4nqj
TitleStructure of coiled-coil domain
ComponentsE3 ubiquitin-protein ligase TRIM69
KeywordsLIGASE / coiled-coil domain / oligomerization
Function / homology
Function and homology information


protein localization to centrosome / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / nuclear speck / centrosome / apoptotic process / identical protein binding ...protein localization to centrosome / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / nuclear speck / centrosome / apoptotic process / identical protein binding / nucleus / metal ion binding / 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. / 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. / 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
E3 ubiquitin-protein ligase TRIM69
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.152 Å
AuthorsYang, M. / Li, Y.
CitationJournal: Cell Res. / Year: 2014
Title: Structural insights into the TRIM family of ubiquitin E3 ligases.
Authors: Li, Y. / Wu, H. / Wu, W. / Zhuo, W. / Liu, W. / Zhang, Y. / Cheng, M. / Chen, Y.G. / Gao, N. / Yu, H. / Wang, L. / Li, W. / Yang, M.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: 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 TRIM69
B: E3 ubiquitin-protein ligase TRIM69
C: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0228
Polymers62,4693
Non-polymers2,5535
Water3,531196
1
A: E3 ubiquitin-protein ligase TRIM69
B: E3 ubiquitin-protein ligase TRIM69
C: E3 ubiquitin-protein ligase TRIM69
hetero molecules

A: E3 ubiquitin-protein ligase TRIM69
B: E3 ubiquitin-protein ligase TRIM69
C: E3 ubiquitin-protein ligase TRIM69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,04416
Polymers124,9386
Non-polymers5,10610
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area42660 Å2
ΔGint-341 kcal/mol
Surface area59870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.097, 101.064, 233.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20822.973 Da / Num. of mol.: 3 / Fragment: UNP residues 143-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM69 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86WT6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUESE IS NATURAL VARIANT, RS3100139

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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: 3.92 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 6, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 52974 / Num. obs: 52974 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35 / Biso Wilson estimate: 40.67 Å2
Reflection shellHighest resolution: 2.15 Å / % possible all: 98.72

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: SAD

Resolution: 2.152→39.139 Å / FOM work R set: 0.7787 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2691 5.08 %
Rwork0.2162 50284 -
obs0.2179 52974 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.84 Å2 / Biso mean: 64.82 Å2 / Biso min: 33.43 Å2
Refinement stepCycle: LAST / Resolution: 2.152→39.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 175 196 4697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084585
X-RAY DIFFRACTIONf_angle_d1.0386142
X-RAY DIFFRACTIONf_chiral_restr0.063720
X-RAY DIFFRACTIONf_plane_restr0.004760
X-RAY DIFFRACTIONf_dihedral_angle_d18.041777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1516-2.19070.27291180.26182420253890
2.1907-2.23280.2751380.24862481261995
2.2328-2.27840.33041520.2572597274998
2.2784-2.32790.26681270.25072645277299
2.3279-2.38210.331360.245326222758100
2.3821-2.44160.29281600.231726452805100
2.4416-2.50760.24671340.224126592793100
2.5076-2.58140.27341490.22926322781100
2.5814-2.66470.29561400.23272652279299
2.6647-2.75990.31021340.224326572791100
2.7599-2.87040.26691490.229626712820100
2.8704-3.0010.27091470.235426482795100
3.001-3.15910.24311490.244426642813100
3.1591-3.3570.26931390.233726862825100
3.357-3.6160.25191370.210627142851100
3.616-3.97960.24221460.195126792825100
3.9796-4.55470.21210.183927312852100
4.5547-5.73550.22261590.194327312890100
5.7355-39.14540.24031560.22172750290696
Refinement TLS params.Method: refined / Origin x: -4.9701 Å / Origin y: -23.4267 Å / Origin z: 49.2064 Å
111213212223313233
T0.4749 Å2-0.007 Å20.1551 Å2-0.3752 Å20.0059 Å2--0.4698 Å2
L0.0836 °20.1032 °2-0.0196 °2--0.1159 °2-0.1361 °2--0.1515 °2
S-0.0255 Å °0.0902 Å °-0.0203 Å °0.0466 Å °0.0003 Å °-0.0029 Å °-0.0327 Å °-0.0671 Å °0.0221 Å °
Refinement TLS groupSelection details: ALL

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