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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 / protein K63-linked deubiquitination / regulation of cell morphogenesis / K63-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / positive regulation of Wnt signaling pathway / 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 / polyubiquitin modification-dependent protein binding / positive regulation of Wnt signaling pathway / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling
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. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily ...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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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
Water0
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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