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- PDB-3zrh: Crystal structure of the Lys29, Lys33-linkage-specific TRABID OTU... -

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Basic information

Entry
Database: PDB / ID: 3zrh
TitleCrystal structure of the Lys29, Lys33-linkage-specific TRABID OTU deubiquitinase domain reveals an Ankyrin-repeat ubiquitin binding domain (AnkUBD)
ComponentsUBIQUITIN THIOESTERASE ZRANB1
KeywordsHYDROLASE / DEUBIQUITINATING ENZYME / WNT SIGNALING / OVARIAN TUMOR DOMAIN
Function / homology
Function and homology information


protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / protein K63-linked deubiquitination / regulation of cell morphogenesis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of Wnt signaling pathway / polyubiquitin modification-dependent protein binding / cytoskeleton organization ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / protein K63-linked deubiquitination / regulation of cell morphogenesis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of Wnt signaling pathway / polyubiquitin modification-dependent protein binding / cytoskeleton organization / Degradation of beta-catenin by the destruction complex / Wnt signaling pathway / Ovarian tumor domain proteases / cell migration / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / intracellular membrane-bounded organelle / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #560 / Ankyrin ubiquitin-binding domain / Ankyrin ubiquitin-binding domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #560 / Ankyrin ubiquitin-binding domain / Ankyrin ubiquitin-binding domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin thioesterase ZRANB1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.23 Å
AuthorsLicchesi, J.D.F. / Akutsu, M. / Komander, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: An Ankyrin-Repeat Ubiquitin-Binding Domain Determines Trabid'S Specificity for Atypical Ubiquitin Chains.
Authors: Licchesi, J.D.F. / Mieszczanek, J. / Mevissen, T.E.T. / Rutherford, T.J. / Akutsu, M. / Virdee, S. / Oualid, F.E. / Chin, J.W. / Ovaa, H. / Bienz, M. / Komander, D.
History
DepositionJun 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: UBIQUITIN THIOESTERASE ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5444
Polymers52,3851
Non-polymers1603
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 72.150, 133.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN THIOESTERASE ZRANB1 / TRABID / ZINC FINGER RAN-BINDING DOMAIN-CONTAINING PROTEIN 1 / HTRABID


Mass: 52384.559 Da / Num. of mol.: 1 / Fragment: ANKUBD, OTU, RESIUDES 245-697
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: ARCTICEXPRESS COMPETENT CELLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UGI0, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.77 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 5.9
Details: 150 MM NACL, 100 MM NAOAC, 5 MM MGCL2, 50 MM MES [PH 5.9]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorDetector: CCD / Date: Nov 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.23→46.32 Å / Num. obs: 29095 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 34.45 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_764)refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.23→44.712 Å / SU ML: 0.85 / σ(F): 0.8 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 3741 6.8 %
Rwork0.2001 --
obs0.2035 54669 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.619 Å2 / ksol: 0.327 e/Å3
Refinement stepCycle: LAST / Resolution: 2.23→44.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 9 188 3608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133520
X-RAY DIFFRACTIONf_angle_d1.4134787
X-RAY DIFFRACTIONf_dihedral_angle_d18.1021261
X-RAY DIFFRACTIONf_chiral_restr0.099535
X-RAY DIFFRACTIONf_plane_restr0.006610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.30970.37343680.31435062X-RAY DIFFRACTION100
2.3097-2.40220.34163840.25585103X-RAY DIFFRACTION100
2.4022-2.51150.3153650.25025111X-RAY DIFFRACTION100
2.5115-2.64390.32133700.22965067X-RAY DIFFRACTION100
2.6439-2.80950.2813820.20635140X-RAY DIFFRACTION100
2.8095-3.02640.2333790.18055104X-RAY DIFFRACTION100
3.0264-3.33090.25923690.19655064X-RAY DIFFRACTION100
3.3309-3.81260.23153770.19595101X-RAY DIFFRACTION100
3.8126-4.80260.19793720.16385083X-RAY DIFFRACTION100
4.8026-44.72110.21933750.19225093X-RAY DIFFRACTION100
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)
12.79980.84360.9131.8027-0.59741.9007-0.3837-0.1741-0.0987-0.44110.17120.02350.1316-0.2210.15820.25930.01690.05450.17450.04260.109555.587470.073515.1967
21.0336-0.3020.13191.3377-0.05981.44720.11710.1237-0.0732-0.2195-0.10310.08250.1613-0.06120.01770.1339-0.0017-0.03610.1022-0.00110.067721.281650.089718.3257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 244:340))
2X-RAY DIFFRACTION2CHAIN A AND ((RESSEQ 341:692))

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