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- PDB-3lrq: Crystal structure of the U-box domain of human ubiquitin-protein ... -

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Basic information

Entry
Database: PDB / ID: 3lrq
TitleCrystal structure of the U-box domain of human ubiquitin-protein ligase (E3), NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR4604D.
ComponentsE3 ubiquitin-protein ligase TRIM37
KeywordsLIGASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Coiled coil / Metal-binding / Peroxisome / Phosphoprotein / Polymorphism / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


: / : / negative regulation of centriole replication / aggresome assembly / tumor necrosis factor receptor binding / aggresome / negative regulation of NF-kappaB transcription factor activity / protein autoubiquitination / RING-type E3 ubiquitin transferase / positive regulation of DNA-binding transcription factor activity ...: / : / negative regulation of centriole replication / aggresome assembly / tumor necrosis factor receptor binding / aggresome / negative regulation of NF-kappaB transcription factor activity / protein autoubiquitination / RING-type E3 ubiquitin transferase / positive regulation of DNA-binding transcription factor activity / ubiquitin-protein transferase activity / peroxisome / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of NF-kappaB transcription factor activity / ubiquitin protein ligase binding / chromatin binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
TRIM37, MATH domain / B-box, C-terminal / B-Box C-terminal domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / B-box zinc finger / B-Box-type zinc finger ...TRIM37, MATH domain / B-box, C-terminal / B-Box C-terminal domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 TRIM37
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.292 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: E3 UBIQUITIN-PROTEIN LIGASE RING DOMAIN FROM HUMAN TRIPARTITE MOTIF-CONTAINING PROTEIN 37 (TRIM37), NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR4604D.
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM37
B: E3 ubiquitin-protein ligase TRIM37
C: E3 ubiquitin-protein ligase TRIM37
D: E3 ubiquitin-protein ligase TRIM37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,75312
Polymers48,2304
Non-polymers5238
Water1,910106
1
A: E3 ubiquitin-protein ligase TRIM37
D: E3 ubiquitin-protein ligase TRIM37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3776
Polymers24,1152
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-24 kcal/mol
Surface area9990 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase TRIM37
C: E3 ubiquitin-protein ligase TRIM37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3776
Polymers24,1152
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-17 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.544, 34.922, 86.709
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211
Detailsdimer,24.59 kD,81.5%

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Components

#1: Protein
E3 ubiquitin-protein ligase TRIM37 / Tripartite motif-containing protein 37 / Mulibrey nanism protein


Mass: 12057.456 Da / Num. of mol.: 4 / Fragment: residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0898, MUL, POB1, TRIM37 / Plasmid: pET 14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: O94972, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1% w/v (+-)-2-methyl-2,4-pentanediol, 0.1% w/v 1,2,3-heptanetriol, 0.1% w/v ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1% w/v (+-)-2-methyl-2,4-pentanediol, 0.1% w/v 1,2,3-heptanetriol, 0.1% w/v dirthylenetriaminepentakis (methylphosphonic acid), 0.1% w/v D-Sorbitol, 0.1% w/v glycerol, 0.06M HEPES sodium, 12.5% PEG3350, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.292→30 Å / Num. obs: 38061 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 5.1 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.292→28.005 Å / SU ML: 0.27 / σ(F): 0.04 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 1843 5.09 %
Rwork0.1897 --
obs0.1925 36218 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.118 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 52.249 Å2
Refinement stepCycle: LAST / Resolution: 2.292→28.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 8 106 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092763
X-RAY DIFFRACTIONf_angle_d1.1493725
X-RAY DIFFRACTIONf_dihedral_angle_d19.5121081
X-RAY DIFFRACTIONf_chiral_restr0.076412
X-RAY DIFFRACTIONf_plane_restr0.004484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2922-2.35410.25071090.22312339X-RAY DIFFRACTION83
2.3541-2.42340.25861420.22122514X-RAY DIFFRACTION91
2.4234-2.50150.29391540.22922553X-RAY DIFFRACTION91
2.5015-2.59090.26341110.22652592X-RAY DIFFRACTION92
2.5909-2.69450.29321580.20472589X-RAY DIFFRACTION94
2.6945-2.8170.26041490.20812641X-RAY DIFFRACTION96
2.817-2.96540.25651460.20622700X-RAY DIFFRACTION97
2.9654-3.1510.20911690.20222728X-RAY DIFFRACTION97
3.151-3.39390.27491460.19042711X-RAY DIFFRACTION99
3.3939-3.73470.22131350.17742771X-RAY DIFFRACTION99
3.7347-4.27350.21651500.15572768X-RAY DIFFRACTION99
4.2735-5.37790.22291490.152766X-RAY DIFFRACTION100
5.3779-28.00740.21491250.17592703X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 48.6405 Å / Origin y: 22.7728 Å / Origin z: 31.7993 Å
111213212223313233
T0.1247 Å20.0552 Å20.0228 Å2-0.0662 Å2-0.0007 Å2--0.0889 Å2
L0.1316 °20.1545 °20.1476 °2-0.4187 °2-0.0085 °2--0.3104 °2
S0.073 Å °-0.0361 Å °-0.041 Å °-0.198 Å °-0.0645 Å °-0.1346 Å °0.0634 Å °-0.0231 Å °0.0037 Å °
Refinement TLS groupSelection details: all

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