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- PDB-7b2r: Crystal structure of NHL domain of TRIM2 -

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Basic information

Entry
Database: PDB / ID: 7b2r
TitleCrystal structure of NHL domain of TRIM2
ComponentsTripartite motif-containing protein 2
KeywordsLIGASE / E3 ligase / NHL domain / TRIM / protein-protein interaction / beta propeller / Structural Genomics / Structural Genomics Consortium / SGC
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: 1.6 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of NHL domain of TRIM2
Authors: Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionNov 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif-containing protein 2
B: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,07111
Polymers59,5122
Non-polymers5599
Water7,656425
1
A: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8803
Polymers29,7561
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1918
Polymers29,7561
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.620, 44.223, 68.230
Angle α, β, γ (deg.)74.060, 86.930, 62.380
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 468 - 739 / Label seq-ID: 5 - 276

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 29756.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM2, KIAA0517, RNF86 / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q9C040, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% Medium molecular weight PEG Smears, 0.1M MES pH 6.5

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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 EIGER2 X 16M / Detector: PIXEL / Date: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.6→38.5 Å / Num. obs: 52021 / % possible obs: 91.1 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.026 / Rrim(I) all: 0.058 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.644.90.2275.138880.9620.1310.29392.1
7.16-38.54.60.0586060.9970.0280.06494.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6d69

6d69


Resolution: 1.6→38.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.377 / SU ML: 0.059 / SU R Cruickshank DPI: 0.1021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 2555 4.9 %RANDOM
Rwork0.1558 ---
obs0.1576 49455 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.55 Å2 / Biso mean: 22.533 Å2 / Biso min: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.28 Å20.71 Å2
2---0.4 Å2-0.32 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.6→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 0 40 425 4624
Biso mean--36.88 33.61 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134351
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184056
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6325882
X-RAY DIFFRACTIONr_angle_other_deg1.4251.5879319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.52123.391233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91515687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6681522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021087
Refine LS restraints NCS

Ens-ID: 1 / Number: 8470 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 174 -
Rwork0.2 3707 -
all-3881 -
obs--92.1 %
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)
12.51720.37091.01471.51130.21071.2869-0.02460.12670.1349-0.1102-0.01380.1170.0047-0.07910.03850.05830.00830.03670.02810.01670.0558-0.432723.7128.075
21.4373-0.3230.94134.1156-2.54413.6297-0.01110.1509-0.0305-0.4068-0.0058-0.00290.1414-0.13940.01690.131-0.01740.03940.09-0.01210.0708-3.39195.299324.0653
31.79970.37840.26033.38260.67220.94190.01080.1086-0.1347-0.0149-0.0274-0.1960.18130.05920.01660.04920.01190.02580.03660.02120.062911.11589.477232.6064
41.58580.2135-0.01592.2893-0.2330.9419-0.0018-0.1445-0.09180.1382-0.0246-0.13740.00980.04840.02630.0177-0.00290.00670.03890.01120.03826.83578.731965.3587
53.47290.33381.7342.4602-0.32894.64390.0152-0.287-0.17390.1257-0.11060.00350.1546-0.21890.09540.0305-0.01320.03080.02980.0020.0796-5.5967-5.90360.4658
61.99450.77780.14391.9428-0.00220.7082-0.0467-0.04410.0484-0.00030.02730.1674-0.0211-0.12750.01940.00660.00760.00920.02580.00510.0329-9.315510.73454.6366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A465 - 578
2X-RAY DIFFRACTION2A579 - 627
3X-RAY DIFFRACTION3A628 - 740
4X-RAY DIFFRACTION4B468 - 573
5X-RAY DIFFRACTION5B574 - 625
6X-RAY DIFFRACTION6B626 - 740

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