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- PDB-7b96: NHL domain of human TRIM2 -

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Basic information

Entry
Database: PDB / ID: 7b96
TitleNHL domain of human TRIM2
ComponentsIsoform 2 of Tripartite motif-containing protein 2
KeywordsRNA BINDING PROTEIN / NHL domain / beta-propeller
Function / homology
Function and homology information


regulation of neuron apoptotic process / translation repressor activity / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / Interferon gamma signaling / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of translation / zinc ion binding / cytoplasm
Similarity search - Function
NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat ...NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
Tripartite motif-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWilliams, F.P. / Hennig, J. / Foot, J. / Murciano, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1935 Germany
CitationJournal: To Be Published
Title: NHL domain of human TRIM2
Authors: Williams, F.P. / Hennig, J. / Foot, J.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Tripartite motif-containing protein 2
B: Isoform 2 of Tripartite motif-containing protein 2


Theoretical massNumber of molelcules
Total (without water)60,2352
Polymers60,2352
Non-polymers00
Water6,792377
1
A: Isoform 2 of Tripartite motif-containing protein 2


Theoretical massNumber of molelcules
Total (without water)30,1181
Polymers30,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2 of Tripartite motif-containing protein 2


Theoretical massNumber of molelcules
Total (without water)30,1181
Polymers30,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.180, 83.200, 132.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 2 of Tripartite motif-containing protein 2 / E3 ubiquitin-protein ligase TRIM2 / RING finger protein 86 / RING-type E3 ubiquitin transferase TRIM2


Mass: 30117.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM2, KIAA0517, RNF86 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9C040, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mg/mL protein in 20mM Tris pH 7.5, 150mM NaCl, 20% (v/v) glycerol and 1mM DTT was added at a 1:1 ratio to the reservoir buffer: 0.2M potassium chloride and 24% (w/v) polyethylene glycol 3350 pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.8→39.7 Å / Num. obs: 46050 / % possible obs: 99.49 % / Redundancy: 4.5 % / Biso Wilson estimate: 25.43 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.1375 / Rpim(I) all: 0.07005 / Rrim(I) all: 0.1552 / Net I/σ(I): 6.72
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 4531 / CC1/2: 0.48 / CC star: 0.805 / Rpim(I) all: 0.5706 / Rrim(I) all: 1.24

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QF7

1qf7


Resolution: 1.8→39.7 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 1290 2.8 %
Rwork0.1771 44756 -
obs0.1782 46046 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 0 377 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124352
X-RAY DIFFRACTIONf_angle_d1.08215888
X-RAY DIFFRACTIONf_chiral_restr0.0849620
X-RAY DIFFRACTIONf_plane_restr0.0068802
X-RAY DIFFRACTIONf_dihedral_angle_d23.8459607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.36911410.32434900X-RAY DIFFRACTION99.6
1.87-1.960.34041410.28354901X-RAY DIFFRACTION99.43
1.96-2.060.23361410.22314887X-RAY DIFFRACTION99.33
2.06-2.190.2461420.19594923X-RAY DIFFRACTION99.55
2.19-2.360.2191420.18394929X-RAY DIFFRACTION99.33
2.36-2.60.23561440.18364973X-RAY DIFFRACTION99.71
2.6-2.970.2441430.17834985X-RAY DIFFRACTION99.77
2.97-3.740.20951450.15295026X-RAY DIFFRACTION99.5
3.74-39.70.16521510.14455232X-RAY DIFFRACTION99.28
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)
13.38695993179-0.947709499871-0.6204438271183.05518062350.5602501871061.431079398410.02128780843740.107662897037-0.2335698520940.0756967510986-0.1049092005920.2013945701050.106355475835-0.1300118399740.09971285700310.117538865468-0.017999768881-0.02467391949190.108045047085-0.01516388528730.149887034424-14.4283941391-27.659352849132.9506607717
25.7688041756-0.7879797084150.9143662268612.840392445840.3814795763752.635107822220.116920135034-0.302426684339-0.06632574912170.212181136434-0.1112045284750.2319982015610.180541998604-0.233750456866-0.005817476938150.137245855543-0.040359693640.03388630353660.123545561682-0.02450396873960.136578132-15.713002277-13.842648478543.7979833863
33.763970213580.6430384900510.2587139454823.90920609692-0.7695828558576.924309795880.117393641379-0.2296459211760.1711692738140.266416139125-0.130250534335-0.0393553342118-0.1231669364020.1215620300110.00495401431160.0958544574975-0.01882855250040.02355435623510.111730826982-0.021498766510.121800531636-3.41358011315-7.3007665723643.3092626635
42.269065078240.8050193627070.2190683563192.548254882181.100385365381.3727113881-0.06256762789740.2522629681240.0528047350954-0.310691090770.110555726458-0.112186759497-0.1866580841220.0855969660096-0.04967682922970.1308072804560.000602854833110.02591028855390.1433912097250.01304200175190.1109365397743.56314338066-14.391990148328.0338705469
50.3189272353320.9893546141460.1851680589123.94081347081-0.1899264332476.036763328620.0003785066724780.0298028793589-0.195946991149-0.01713581761940.00123349872169-0.3734699751540.1135527845090.1643367991750.007614309375320.092159484332-0.0007400319488320.01358134159730.0995505438047-0.03827100196710.166153050472-4.00904531393-28.852295096329.3732060364
67.31060217559-1.90784497783-0.00837758561425.745586309452.060479842325.334155447860.04801519310060.172292752377-1.013411832440.2172763963220.1092823435740.01235668691250.878761167958-0.363650169431-0.0326844395260.3715398369440.00447942630717-0.122251744640.241799909983-0.001367717684340.273396729286-16.4563268569-18.39797295045.98578709686
75.373915968750.4142149727970.3789770081146.613736275830.7738499335997.08800461582-0.03261589778210.693542947949-0.424360093371-0.6512581922690.314017302765-0.03571787055560.6477295389820.109574043777-0.2654078928650.3665614298650.0128281677959-0.05141193478980.423976554321-0.07358385460170.179091776143-13.4893847573-12.1030234026-4.01260577587
87.17123113149-2.741408376550.02472542459342.316141720710.179198657665.97023844741-0.154409834230.5041398442080.287605972777-0.3603713581090.0427189432185-0.5809046033060.1934234874881.003015142370.0131927408840.346943473188-0.01330092452520.005434544197330.5087266081470.02732558868650.310850846428-2.6558396242-6.23934440075-5.19848049037
94.02917543442-2.062495114610.3963192901286.37468974334-0.8620430787156.42835114117-0.1183541552580.6024759486520.166378779526-0.228425322789-0.121370720151-0.358500621235-0.544523431420.7084412765140.2374754425090.385200976986-0.09464787436520.00618438774610.5848854256110.04962906131110.232794307889-2.691803404610.748270946099-4.08302157093
101.74869311804-0.2311729503160.5667745787941.91071519752-0.4267595076364.1894082394-0.089846629619-0.02935669705320.286676344870.2549977519120.05979262717350.00866239942853-1.1195996445-0.08181457059110.002498683316980.484378160620.0753115826245-0.06493548766470.2528673492420.002818331432440.240280400134-11.80397237393.8581567091911.7517615519
113.631295267621.366655407541.150667632097.60124159595-0.2114237275574.04206325296-0.190800846794-0.1120160486130.222858592601-0.06098619793880.279090381150.519679152793-0.0298563384587-0.867240054047-0.06023517716250.1775890820180.0494249671815-0.0408916738750.379887300260.04449377070680.197118233401-20.9693120913-9.191295832876.35930176799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 465 through 523 )
2X-RAY DIFFRACTION2chain 'A' and (resid 524 through 570 )
3X-RAY DIFFRACTION3chain 'A' and (resid 571 through 612 )
4X-RAY DIFFRACTION4chain 'A' and (resid 613 through 718 )
5X-RAY DIFFRACTION5chain 'A' and (resid 719 through 744 )
6X-RAY DIFFRACTION6chain 'B' and (resid 465 through 491 )
7X-RAY DIFFRACTION7chain 'B' and (resid 492 through 523 )
8X-RAY DIFFRACTION8chain 'B' and (resid 524 through 551 )
9X-RAY DIFFRACTION9chain 'B' and (resid 552 through 593 )
10X-RAY DIFFRACTION10chain 'B' and (resid 594 through 718 )
11X-RAY DIFFRACTION11chain 'B' and (resid 719 through 744 )

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