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- PDB-4m3l: Crystal Structure of the coiled coil domain of MuRF1 -

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Basic information

Entry
Database: PDB / ID: 4m3l
TitleCrystal Structure of the coiled coil domain of MuRF1
ComponentsE3 ubiquitin-protein ligase TRIM63
KeywordsLIGASE / E3 ubiquitin ligase / titin / sarcoskeleton
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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 ...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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / E3 ubiquitin-protein ligase TRIM63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ARCIMBOLDO (fragment based ab initio) / Resolution: 2.1 Å
AuthorsMayans, O. / Franke, B.
CitationJournal: Open Biol / Year: 2014
Title: Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1.
Authors: Franke, B. / Gasch, A. / Rodriguez, D. / Chami, M. / Khan, M.M. / Rudolf, R. / Bibby, J. / Hanashima, A. / Bogomolovas, J. / von Castelmur, E. / Rigden, D.J. / Uson, I. / Labeit, S. / Mayans, O.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / 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 / _entity.formula_weight / _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
C: E3 ubiquitin-protein ligase TRIM63
B: E3 ubiquitin-protein ligase TRIM63
D: E3 ubiquitin-protein ligase TRIM63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,68225
Polymers28,0194
Non-polymers1,66321
Water99155
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-112 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.790, 24.410, 75.390
Angle α, β, γ (deg.)90.00, 107.65, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

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


Mass: 7004.825 Da / Num. of mol.: 4 / Fragment: unp residues 214-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF, MURF1, RNF28, SMRZ, TRIM63 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 35% MPD, 0.1M sodium acetate, 20% glycerol, 20mM sodium fluoride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14624 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.64 % / Rsym value: 0.027 / Net I/σ(I): 17.24
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.74 % / Mean I/σ(I) obs: 3.31 / Rsym value: 0.45 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Arcimboldophasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: ARCIMBOLDO (fragment based ab initio)
Resolution: 2.1→19.815 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 724 4.96 %
Rwork0.2118 --
obs0.2145 14598 97.81 %
all-14624 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0973 Å20 Å2-10.444 Å2
2--0.169 Å2-0 Å2
3----0.0717 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 110 55 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061954
X-RAY DIFFRACTIONf_angle_d0.8362595
X-RAY DIFFRACTIONf_dihedral_angle_d15.568761
X-RAY DIFFRACTIONf_chiral_restr0.051303
X-RAY DIFFRACTIONf_plane_restr0.003328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.26210.28881210.25282745X-RAY DIFFRACTION98
2.2621-2.48930.30251580.21462716X-RAY DIFFRACTION98
2.4893-2.84860.28011400.20442762X-RAY DIFFRACTION99
2.8486-3.58550.25591400.20172808X-RAY DIFFRACTION98
3.5855-19.81580.24181650.20962843X-RAY DIFFRACTION97
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)
15.3332-2.24255.23311.4801-2.50015.1214-0.2347-0.4652-0.3540.00850.40420.3269-0.221-0.5034-0.16370.21870.01610.00390.22640.00270.225629.69730.710370.5599
28.5649-7.82537.51867.4836-6.3657.24090.30290.55220.4547-0.347-0.4453-0.26710.26360.12050.15040.21770.00030.07190.43520.13760.34661.938723.370832.1602
36.5764-5.71946.54696.7445-6.71847.9482-0.0739-0.1801-0.0397-0.03030.09910.00720.0326-0.13630.01530.1126-0.01750.06690.103-0.01610.161141.5287-4.396871.9451
46.7224-3.00496.7712.2745-3.27928.8844-0.4489-0.24420.2960.15430.2364-0.1501-0.3642-0.73290.07840.2387-0.00990.01810.22230.03780.22424.142118.732244.7815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -3:270 )A-3 - 270
2X-RAY DIFFRACTION2( CHAIN B AND RESID -3:268 )B-3 - 268
3X-RAY DIFFRACTION3( CHAIN C AND RESID -2:268 )C-2 - 268
4X-RAY DIFFRACTION4( CHAIN D AND RESID 214:266 )D214 - 266

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