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- PDB-4ksk: Gumby/Fam105B in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4ksk
TitleGumby/Fam105B in complex with ubiquitin
Components
  • Polyubiquitin-C
  • Protein FAM105B
KeywordsHYDROLASE/protein binding / OTU domain / deubiquitinase / ubiquitin / HYDROLASE / HYDROLASE-protein binding complex
Function / homology
Function and homology information


protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E ...protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / 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 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Degradation of AXIN / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Stabilization of p53 / Termination of translesion DNA synthesis
Similarity search - Function
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin thioesterase otulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCeccarelli, D.F. / Juang, Y.-C. / Sicheri, F.
CitationJournal: Nature / Year: 2013
Title: The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.
Authors: Rivkin, E. / Almeida, S.M. / Ceccarelli, D.F. / Juang, Y.C. / MacLean, T.A. / Srikumar, T. / Huang, H. / Dunham, W.H. / Fukumura, R. / Xie, G. / Gondo, Y. / Raught, B. / Gingras, A.C. / ...Authors: Rivkin, E. / Almeida, S.M. / Ceccarelli, D.F. / Juang, Y.C. / MacLean, T.A. / Srikumar, T. / Huang, H. / Dunham, W.H. / Fukumura, R. / Xie, G. / Gondo, Y. / Raught, B. / Gingras, A.C. / Sicheri, F. / Cordes, S.P.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Protein FAM105B
B: Protein FAM105B
C: Polyubiquitin-C
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6025
Polymers87,5064
Non-polymers961
Water2,918162
1
A: Protein FAM105B
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8493
Polymers43,7532
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-30 kcal/mol
Surface area15410 Å2
MethodPISA
2
B: Protein FAM105B
C: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)43,7532
Polymers43,7532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-10 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.273, 43.309, 113.918
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein FAM105B


Mass: 34859.871 Da / Num. of mol.: 2 / Fragment: OTU domain (unp residues 55-352) / Mutation: C129S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM105B / Plasmid: pRoEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96BN8
#2: Protein Polyubiquitin-C / Ubiquitin


Mass: 8893.206 Da / Num. of mol.: 2 / Fragment: unp residues 76-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pETm30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 20, 2012
RadiationMonochromator: VariMax VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 31314 / Num. obs: 28755 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.443.80.6192.2176.1
2.44-2.49191.5
2.49-2.53193.3

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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: 4KSJ

4ksj


Resolution: 2.4→24.43 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 24.893 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.477 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26764 1533 5.1 %RANDOM
Rwork0.21425 ---
obs0.21702 28755 97.34 %-
all-31314 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.72 Å2
2--0.33 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 5 162 5501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225446
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9687382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17624.228246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20815964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7451536
X-RAY DIFFRACTIONr_chiral_restr0.1060.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214058
X-RAY DIFFRACTIONr_mcbond_it0.7341.53346
X-RAY DIFFRACTIONr_mcangle_it1.31725393
X-RAY DIFFRACTIONr_scbond_it2.25532100
X-RAY DIFFRACTIONr_scangle_it3.3334.51989
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 112 -
Rwork0.263 1926 -
obs--90.98 %
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)
12.41010.0776-1.8142.07320.45693.5597-0.02980.3150.0467-0.34130.0311-0.0144-0.01080.0421-0.00130.30180.00790.21710.0780.01830.1895-9.5931.3738.449
22.168-0.3933-1.21312.5663-0.86962.8252-0.0894-0.42460.03290.52320.17730.1842-0.06840.0918-0.08780.3150.01290.2340.0951-0.01780.205-48.522-19.73816.433
33.6326-0.48821.11098.8506-2.32735.25050.01120.44680.2429-0.7560.30681.6117-0.1769-0.8801-0.31810.41610.03280.17970.42910.0620.7718-72.368-13.1931.971
46.4771.93414.28635.69172.483910.96630.1193-0.30990.26170.7073-0.1802-0.0231-0.68781.80030.0610.5244-0.15860.22960.75590.06720.229912.5966.8455.508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A78 - 346
2X-RAY DIFFRACTION2B78 - 346
3X-RAY DIFFRACTION3C1 - 73
4X-RAY DIFFRACTION4D1 - 73

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