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- PDB-3q1d: The B-box domain of Trim54 -

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Basic information

Entry
Database: PDB / ID: 3q1d
TitleThe B-box domain of Trim54
ComponentsTripartite motif-containing protein 54
KeywordsLIGASE / ZINC-BINDING MOTIF / RING-LIKE FOLD / METAL-BINDING / MUSCLE PROTEIN / NUCLEUS / UBL CONJUGATION PATHWAY / ZINC-FINGER
Function / homology
Function and homology information


multicellular organism development / negative regulation of microtubule depolymerization / microtubule associated complex / microtubule-based process / Z disc / ubiquitin protein ligase activity / microtubule binding / microtubule / cell differentiation / protein ubiquitination ...multicellular organism development / negative regulation of microtubule depolymerization / microtubule associated complex / microtubule-based process / Z disc / ubiquitin protein ligase activity / microtubule binding / microtubule / cell differentiation / protein ubiquitination / signal transduction / zinc ion binding / cytoplasm
Similarity search - Function
TRIM54, 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 ...TRIM54, 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
Tripartite motif-containing protein 54
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Mackenzie, F. / Dong, A. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S.
CitationJournal: To be Published
Title: The B-Box Domain of Trim54
Authors: Walker, J.R. / Yermekbayeva, L. / Mackenzie, F. / Dong, A. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Tripartite motif-containing protein 54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5213
Polymers5,3901
Non-polymers1312
Water57632
1
A: Tripartite motif-containing protein 54
hetero molecules

A: Tripartite motif-containing protein 54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0426
Polymers10,7812
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area1340 Å2
ΔGint-10 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.276, 47.276, 87.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein/peptide Tripartite motif-containing protein 54 / Muscle-specific RING finger protein / MuRF / Muscle-specific RING finger protein 3 / MuRF-3 / MuRF3 ...Muscle-specific RING finger protein / MuRF / Muscle-specific RING finger protein 3 / MuRF-3 / MuRF3 / RING finger protein 30


Mass: 5390.276 Da / Num. of mol.: 1 / Fragment: B-Box domain, UNP residues 122-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MURF, MURF3, RNF30, TRIM54 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9BYV2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE PUT IN FOR CRYSTALLIZATION IS ...THE SEQUENCE PUT IN FOR CRYSTALLIZATION IS MHHHHHHSSGRENLYFQGQESSRPLHSKAEQHLMCEEHEEEKINIYCLSCEVPTCSLCKVFGAHKDCEVAPLPTIYKRQK AND IN SITU PROTEOLYSIS HAS BEEN CARRIED OUT DURING CRYSTALLIZATION

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M SODIUM CITRATE, 0.1M HEPES PH 7.5, 5% MPD, 0.57 MICROMOLAR TRYPSIN, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 3560 / Num. obs: 3560 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 23.6 % / Rsym value: 0.131 / Net I/σ(I): 32.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.569 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DDT

3ddt


Resolution: 2.15→29.823 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.524 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25343 148 4.3 %RANDOM
Rwork0.18198 ---
obs0.18518 3297 99.11 %-
all-3560 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.228 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms364 0 2 32 398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022387
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.987520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.805548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41125.71414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6241568
X-RAY DIFFRACTIONr_chiral_restr0.0870.259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021277
X-RAY DIFFRACTIONr_mcbond_it0.4541.5242
X-RAY DIFFRACTIONr_mcangle_it0.8752395
X-RAY DIFFRACTIONr_scbond_it2.8433145
X-RAY DIFFRACTIONr_scangle_it3.5844.5125
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 6 -
Rwork0.182 230 -
obs--99.16 %
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)
129.9619-10.896710.798215.0728-5.037722.70870.5157-0.794-1.2503-0.13480.42580.39111.3049-0.3697-0.94150.1204-0.0754-0.07390.10040.06380.077120.86778.59029.6691
216.3714-9.1763-1.663513.8175-3.62473.36210.24740.5132-1.013-0.4851-0.15490.55920.3107-0.1847-0.09240.1079-0.0436-0.08590.2059-0.00250.1316.016211.42923.5639
37.4752-0.5072-0.79076.66-0.00134.48550.05-0.5503-0.4324-0.47630.0266-0.3333-0.1158-0.0227-0.07660.0408-0.0220.02510.16330.04130.048825.216316.5829.152
43.5023-2.18461.16518.2582-4.94032.9627-0.0723-1.10210.1570.4282-0.0395-0.23-0.26250.06410.11190.0864-0.0286-0.00960.5044-0.08940.114623.180523.678314.7455
56.3319-0.88295.16538.6208-3.58938.26420.1693-0.2133-0.0414-0.0381-0.0310.05950.1957-0.036-0.13830.0329-0.0190.00860.12730.00940.025120.875819.2254.3376
63.5157-0.79290.64398.933812.411519.8874-0.1033-0.1269-0.0501-0.1731-0.09160.2307-0.4523-0.73190.19490.02070.05380.00140.1790.00090.100717.570223.66282.9841
735.5361-13.0259-1.717213.55715.20982.47270.3835-0.23752.3241-0.1558-0.4355-0.5509-0.0235-0.25550.0520.0627-0.00140.02990.1885-0.04560.163825.753326.1627.6566
825.90284.3338-9.17895.374-3.725418.22670.08540.1586-0.9727-0.3027-0.332-0.56371.1365-0.03790.24660.1216-0.0242-0.01840.12990.06280.095534.02513.83037.2466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A122 - 127
2X-RAY DIFFRACTION2A128 - 132
3X-RAY DIFFRACTION3A133 - 138
4X-RAY DIFFRACTION4A139 - 144
5X-RAY DIFFRACTION5A145 - 150
6X-RAY DIFFRACTION6A151 - 156
7X-RAY DIFFRACTION7A157 - 162
8X-RAY DIFFRACTION8A163 - 168

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