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- PDB-5af6: Structure of Lys33-linked diUb bound to Trabid NZF1 -

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Basic information

Entry
Database: PDB / ID: 5af6
TitleStructure of Lys33-linked diUb bound to Trabid NZF1
Components
  • TRABID
  • UBIQUITIN
KeywordsSIGNALING PROTEIN / UBIQUITIN / UBIQUITIN TRABID
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 / regulation of cell morphogenesis / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of Wnt signaling pathway / polyubiquitin modification-dependent protein binding / protein deubiquitination ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / regulation of cell morphogenesis / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of Wnt signaling pathway / polyubiquitin modification-dependent protein binding / protein deubiquitination / cytoskeleton organization / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Hh mutants are degraded by ERAD / Stabilization of p53 / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome
Similarity search - Function
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. ...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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / UBC protein / Ubiquitin thioesterase ZRANB1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMichel, M.A. / Elliott, P.R. / Swatek, K.N. / Simicek, M. / Pruneda, J.N. / Wagstaff, J.L. / Freund, S.M.V. / Komander, D.
CitationJournal: Mol.Cell / Year: 2015
Title: Assembly and Specific Recognition of K29- and K33-Linked Polyubiquitin.
Authors: Michel, M.A. / Elliott, P.R. / Swatek, K.N. / Simicek, M. / Pruneda, J.N. / Wagstaff, J.L. / Freund, S.M.V. / Komander, D.
History
DepositionJan 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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
B: UBIQUITIN
C: UBIQUITIN
D: UBIQUITIN
E: UBIQUITIN
F: TRABID
G: TRABID
H: TRABID
I: TRABID
J: TRABID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,65015
Polymers63,32310
Non-polymers3275
Water00
1
A: UBIQUITIN
H: TRABID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,6652
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8.7 kcal/mol
Surface area7730 Å2
MethodPQS
2
B: UBIQUITIN
I: TRABID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,6652
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-7.9 kcal/mol
Surface area7450 Å2
MethodPQS
3
C: UBIQUITIN
G: TRABID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,6652
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7.2 kcal/mol
Surface area7860 Å2
MethodPQS
4
D: UBIQUITIN
F: TRABID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,6652
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-7.5 kcal/mol
Surface area7820 Å2
MethodPQS
5
E: UBIQUITIN
J: TRABID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,6652
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area7750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)98.384, 126.512, 78.092
Angle α, β, γ (deg.)90.00, 103.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
UBIQUITIN


Mass: 8604.845 Da / Num. of mol.: 5 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE BONDS ACROSS BETWEEN CHAINS, A76 C AND D33 NZ, B76 C AND A33 NZ, C76C AND B33 NZ, E76 C AND C33 NZ. ISOPEPTIDE BOND ACROSS THE ASU FOR, D76 C AND E33 NZ SYMM
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTAII / References: UniProt: Q96C32, UniProt: P0CG48*PLUS
#2: Protein/peptide
TRABID


Mass: 4059.696 Da / Num. of mol.: 5 / Fragment: NZF1, RESIDUES 1-33
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTAII / References: UniProt: Q9UGI0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
Sequence detailsQ96C32 REFERS TO POLYUB, WHICH IS SUBSEQUENTLY PROTEOLYSED TO THE MATURE FORM. CONTAINS ADDITIONAL ...Q96C32 REFERS TO POLYUB, WHICH IS SUBSEQUENTLY PROTEOLYSED TO THE MATURE FORM. CONTAINS ADDITIONAL GLYPRO AT N-TERMINUS FROM EXPRESSION.

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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: 3.99 Å3/Da / Density % sol: 69.15 % / Description: NONE
Crystal growpH: 6.5
Details: 20% PEG 550 MME, 10% PEG 20K, 0.12 M NA OXAMATE, 0.12 M NAF, 0.12 M NA CITRATE, 0.12 M NA/K TARTRATE 0.1 M MES/IMIDAZOLE PH 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.4→38.59 Å / Num. obs: 12855 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 83.17 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1UBQ AND 2WWZ

1ubq

2wwz


Resolution: 3.4→38.591 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 643 5 %
Rwork0.1803 --
obs0.1824 12783 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.53 Å2
Refinement stepCycle: LAST / Resolution: 3.4→38.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 5 0 4081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024145
X-RAY DIFFRACTIONf_angle_d0.6035602
X-RAY DIFFRACTIONf_dihedral_angle_d10.9761572
X-RAY DIFFRACTIONf_chiral_restr0.023638
X-RAY DIFFRACTIONf_plane_restr0.002711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.66260.32711380.27642387X-RAY DIFFRACTION99
3.6626-4.03080.2771160.24312399X-RAY DIFFRACTION99
4.0308-4.61320.19971210.16512449X-RAY DIFFRACTION100
4.6132-5.8090.22871330.16342429X-RAY DIFFRACTION100
5.809-38.59340.17841350.14862476X-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)
18.7662-2.56674.70718.23682.78945.0487-0.5139-0.5379-0.35260.3290.22690.2709-0.25410.40340.17430.74880.01040.21790.76730.08740.369511.4171-5.31910.9213
27.5570.51593.44977.1858-0.42936.7458-0.08480.10190.286-0.2115-0.13090.0748-0.3071-0.05990.15821.00960.04630.14530.58270.00920.2872-8.81170.354425.4469
38.84351.1306-2.35337.74161.5048.6625-0.32520.07090.499-0.1902-0.13030.2318-0.094-0.27650.51370.53650.1896-0.07440.6297-0.02280.3942-17.439914.36686.0526
48.4522-2.6911.71864.87660.08168.61310.1799-0.388-0.52860.66550.14750.95690.5546-0.5493-0.31211.218-0.00850.42010.65780.08921.16636.6201-29.906516.1865
59.7921-2.1323-1.70137.99820.11858.79390.1336-1.19780.07321.65750.5774-0.0562-0.13790.5621-0.5861.57060.0856-0.18670.7367-0.04240.6502-18.192932.829423.5951
67.5763-1.28472.85685.9309-4.41788.2665-1.1109-1.9304-1.98972.37950.83251.28460.4370.00170.26381.6531-0.02820.28731.15130.50751.448215.5686-39.009730.7251
79.3203-1.82275.85549.7386-4.49264.87130.18770.1291-0.87380.60250.26530.79511.6849-0.6047-0.27781.1253-0.1190.14160.792-0.10950.4735-20.1583-4.289511.3889
89.1637-1.97165.1216.8022-4.82295.95380.24450.8731-0.73940.4127-0.05280.94790.59830.4691-0.21671.163-0.11680.33040.9775-0.26390.761512.676-21.5950.623
94.1381-2.1518-3.29846.55324.86424.4584-0.417-1.3666-0.01490.26510.0938-0.45150.68831.21290.21350.9395-0.0685-0.01881.23370.13110.46619.9964-0.950228.8507
104.3596-2.0973-5.89462.61133.50058.2366-0.01890.76810.74510.04270.2594-0.7691-1.0858-0.2587-0.22811.0954-0.0018-0.20730.92810.11260.9771-5.116327.586410.4902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

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