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- PDB-7qrv: Crystal structure of NHL domain of TRIM2 (full C-terminal) -

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Basic information

Entry
Database: PDB / ID: 7qrv
TitleCrystal structure of NHL domain of TRIM2 (full C-terminal)
ComponentsTripartite motif-containing protein 2
KeywordsLIGASE / E3 / TRIM / TRIM2 / NHL domain
Function / homology
Function and homology information


regulation of neuron apoptotic process / cellular response to leukemia inhibitory factor / RING-type E3 ubiquitin transferase / protein polyubiquitination / Interferon gamma signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 ...: / 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: 1.45 Å
AuthorsChaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2022
Title: Comparative structural analyses of the NHL domains from the human E3 ligase TRIM-NHL family.
Authors: Chaikuad, A. / Zhubi, R. / Tredup, C. / Knapp, S.
History
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
C: Tripartite motif-containing protein 2
D: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,88530
Polymers121,2714
Non-polymers1,61426
Water22,8611269
1
A: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,87610
Polymers30,3181
Non-polymers5599
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5665
Polymers30,3181
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6907
Polymers30,3181
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tripartite motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7528
Polymers30,3181
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.669, 89.242, 86.725
Angle α, β, γ (deg.)90.000, 106.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA469 - 7436 - 280
21GLUGLULEULEUBB469 - 7436 - 280
12PROPROGLNGLNAA467 - 7444 - 281
22PROPROGLNGLNCC467 - 7444 - 281
13PROPROLEULEUAA467 - 7434 - 280
23PROPROLEULEUDD467 - 7434 - 280
14GLUGLULEULEUBB469 - 7436 - 280
24GLUGLULEULEUCC469 - 7436 - 280
15GLUGLULEULEUBB469 - 7436 - 280
25GLUGLULEULEUDD469 - 7436 - 280
16PROPROLEULEUCC467 - 7434 - 280
26PROPROLEULEUDD467 - 7434 - 280

NCS ensembles :
ID
1
2
3
4
5
6

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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: 30317.811 Da / Num. of mol.: 4
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


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1269 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% w/v PEG 5000 MME, 0.2 M Ammonium sulfate, 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: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.45→45.47 Å / Num. obs: 175817 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.45-1.496.70.4113.8126840.9220.1860.48897.4
6.48-45.436.90.04320650.9980.0170.04699.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B2R

7b2r


Resolution: 1.45→45.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.037 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0629 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 8686 4.9 %RANDOM
Rwork0.1518 ---
obs0.1531 167100 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.35 Å2 / Biso mean: 16.27 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.24 Å2
2---0.08 Å20 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 1.45→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8467 0 108 1269 9844
Biso mean--30.51 28.64 -
Num. residues----1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0138915
X-RAY DIFFRACTIONr_bond_other_d0.0020.0188386
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.63512034
X-RAY DIFFRACTIONr_angle_other_deg1.451.58719275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97851176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20823.098481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.266151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0321549
X-RAY DIFFRACTIONr_chiral_restr0.1040.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210580
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022242
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89770.08
12B89770.08
21A91100.08
22C91100.08
31A89910.1
32D89910.1
41B90010.07
42C90010.07
51B89740.08
52D89740.08
61C91500.09
62D91500.09
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 599 -
Rwork0.189 12083 -
all-12682 -
obs--97.19 %
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)
10.2267-0.08660.15590.5101-0.00510.25060.0129-0.00930.00510.02220.01080.02080.0003-0.0147-0.02370.0391-0.00250.00960.00560.0010.032730.50179.90485.1995
20.63820.07750.28760.5804-0.1530.2141-0.0305-0.08160.0033-0.01960.0184-0.0677-0.012-0.05080.01220.00260.00680.00320.0735-0.00970.014546.022325.908742.9876
30.4573-0.11620.07840.45750.11830.3702-0.0443-0.0157-0.01420.00040.02840.0829-0.01-0.00350.01590.0149-0.0142-0.01270.02570.02410.030313.460224.710643.6885
40.22090.06590.11460.3158-0.04440.27430.001-0.0024-0.0307-0.0316-0.0251-0.0542-0.00160.01150.02420.03890.00730.00470.0080.00460.036463.01619.857284.4782
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A467 - 744
2X-RAY DIFFRACTION2B469 - 744
3X-RAY DIFFRACTION3C467 - 744
4X-RAY DIFFRACTION4D464 - 744

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