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- PDB-3ddt: Crystal structure of the B2 box from MuRF1 in dimeric state -

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Basic information

Entry
Database: PDB / ID: 3ddt
TitleCrystal structure of the B2 box from MuRF1 in dimeric state
ComponentsE3 ubiquitin-protein ligase TRIM63
KeywordsLIGASE / zinc-binding motif / RING-like fold / Coiled coil / Cytoplasm / Metal-binding / Muscle protein / Nucleus / Polymorphism / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / negative regulation of cardiac muscle hypertrophy / M band / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucocorticoid / titin binding / response to interleukin-1 / muscle contraction / RING-type E3 ubiquitin transferase ...response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / negative regulation of cardiac muscle hypertrophy / M band / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucocorticoid / titin binding / response to interleukin-1 / muscle contraction / RING-type E3 ubiquitin transferase / Z disc / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / microtubule / protein ubiquitination / signal transduction / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase TRIM63, RING finger, HC subclass / COS domain / COS domain profile. / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger ...E3 ubiquitin-protein ligase TRIM63, RING finger, HC subclass / COS domain / COS domain profile. / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger / Double Stranded RNA Binding Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsMayans, O. / Mrosek, M.
CitationJournal: Biochemistry / Year: 2008
Title: Structural analysis of B-Box 2 from MuRF1: identification of a novel self-association pattern in a RING-like fold
Authors: Mrosek, M. / Meier, S. / Ucurum-Fotiadis, Z. / von Castelmur, E. / Hedbom, E. / Lustig, A. / Grzesiek, S. / Labeit, D. / Labeit, S. / Mayans, O.
History
DepositionJun 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM63
B: E3 ubiquitin-protein ligase TRIM63
C: E3 ubiquitin-protein ligase TRIM63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2249
Polymers15,8323
Non-polymers3926
Water2,846158
1
A: E3 ubiquitin-protein ligase TRIM63
B: E3 ubiquitin-protein ligase TRIM63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8166
Polymers10,5542
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-15 kcal/mol
Surface area6280 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase TRIM63
hetero molecules

C: E3 ubiquitin-protein ligase TRIM63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8166
Polymers10,5542
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area900 Å2
ΔGint-8 kcal/mol
Surface area5780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.220, 76.220, 146.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-71-

HOH

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase TRIM63 / Tripartite motif-containing protein 63 / Muscle-specific RING finger protein 1 / MuRF1 / MURF-1 / ...Tripartite motif-containing protein 63 / Muscle-specific RING finger protein 1 / MuRF1 / MURF-1 / RING finger protein 28 / Striated muscle RING zinc finger protein / Iris RING finger protein


Mass: 5277.209 Da / Num. of mol.: 3 / Fragment: B2-box
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q969Q1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8M ammonium sulfate, 0.1M Tris pH 8.5, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.992
SYNCHROTRONESRF ID23-121.254743, 1.28332, 1.215686
Detector
TypeIDDetector
MARMOSAIC 225 mm CCD1CCD
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9921
21.2547431
31.283321
41.2156861
ReflectionResolution: 1.9→18 Å / Num. obs: 20520 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 28.35 Å2 / Rsym value: 0.071 / Net I/σ(I): 20.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 2802 / Rsym value: 0.386 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→17.694 Å / SU ML: 0.25 / Cross valid method: Rfree / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 853 4.16 %XDSCONV
Rwork0.199 19667 --
obs0.201 20520 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.298 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 15.59 Å2 / Biso mean: 35.01 Å2 / Biso min: 74.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.959 Å20 Å2-0 Å2
2--0.959 Å20 Å2
3----1.917 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 6 158 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121072
X-RAY DIFFRACTIONf_angle_d1.3581441
X-RAY DIFFRACTIONf_chiral_restr0.088161
X-RAY DIFFRACTIONf_plane_restr0.005184
X-RAY DIFFRACTIONf_dihedral_angle_d14.887401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.0190.261490.23331863335100
2.019-2.1750.31390.22132183357100
2.175-2.3930.2641730.2231933366100
2.393-2.7380.241330.2173270340399.97
2.738-3.4450.2681320.20433243456100
3.445-17.6950.2271270.1763476360398.36

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