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- PDB-3u30: Crystal structure of a linear-specific Ubiquitin fab bound to lin... -

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Basic information

Entry
Database: PDB / ID: 3u30
TitleCrystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin
Components
  • Heavy chain Fab
  • Light chain Fab
  • linear di-ubiquitin
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


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 ...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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / 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 / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / 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 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Assembly Of The HIV Virion
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.428 Å
AuthorsMatsumoto, M.L. / Dong, K.C. / Yu, C. / Phu, L. / Gao, X. / Hannoush, R.N. / Hymowitz, S.G. / Kirkpatrick, D.S. / Dixit, V.M. / Kelley, R.F.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Engineering and structural characterization of a linear polyubiquitin-specific antibody.
Authors: Matsumoto, M.L. / Dong, K.C. / Yu, C. / Phu, L. / Gao, X. / Hannoush, R.N. / Hymowitz, S.G. / Kirkpatrick, D.S. / Dixit, V.M. / Kelley, R.F.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: linear di-ubiquitin
B: Light chain Fab
C: Heavy chain Fab
D: linear di-ubiquitin
E: Light chain Fab
F: Heavy chain Fab


Theoretical massNumber of molelcules
Total (without water)133,3586
Polymers133,3586
Non-polymers00
Water3,495194
1
A: linear di-ubiquitin
B: Light chain Fab
C: Heavy chain Fab


Theoretical massNumber of molelcules
Total (without water)66,6793
Polymers66,6793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-35 kcal/mol
Surface area25090 Å2
MethodPISA
2
D: linear di-ubiquitin
E: Light chain Fab
F: Heavy chain Fab


Theoretical massNumber of molelcules
Total (without water)66,6793
Polymers66,6793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-34 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.322, 59.767, 96.033
Angle α, β, γ (deg.)87.08, 76.77, 71.70
Int Tables number1
Space group name H-MP1
DetailsChain A, B, C / Chain D, E, F

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Components

#1: Protein linear di-ubiquitin / Ubiquitin


Mass: 19307.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Antibody Light chain Fab


Mass: 23329.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Heavy chain Fab


Mass: 24041.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 18% isopropanol, 0.09 M MES, 19.8% PEG 2K MME, 10 mM sodium bromide., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.428→50 Å / Num. all: 39225 / Num. obs: 39225 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.07 / % possible all: 92.6

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1UBQ

1ubq


Resolution: 2.428→49.331 Å / SU ML: 0.37 / σ(F): 0.13 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1853 5 %
Rwork0.2291 --
obs0.2306 37043 89.61 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.825 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3981 Å2-2.9364 Å2-2.6787 Å2
2--8.6386 Å23.8945 Å2
3----7.2405 Å2
Refinement stepCycle: LAST / Resolution: 2.428→49.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8804 0 0 194 8998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038989
X-RAY DIFFRACTIONf_angle_d0.81612204
X-RAY DIFFRACTIONf_dihedral_angle_d12.0733278
X-RAY DIFFRACTIONf_chiral_restr0.0481419
X-RAY DIFFRACTIONf_plane_restr0.0071555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4283-2.4940.3681320.31922196X-RAY DIFFRACTION74
2.494-2.56740.34151260.30072432X-RAY DIFFRACTION81
2.5674-2.65020.36761340.30422578X-RAY DIFFRACTION85
2.6502-2.74490.3431450.28652629X-RAY DIFFRACTION87
2.7449-2.85480.34891220.27512712X-RAY DIFFRACTION89
2.8548-2.98480.30651320.272798X-RAY DIFFRACTION92
2.9848-3.14210.30881530.25292796X-RAY DIFFRACTION93
3.1421-3.33890.2691540.24452844X-RAY DIFFRACTION94
3.3389-3.59660.26491370.22882823X-RAY DIFFRACTION94
3.5966-3.95840.22621510.2122822X-RAY DIFFRACTION93
3.9584-4.53090.2081520.1872815X-RAY DIFFRACTION93
4.5309-5.70710.21261380.18792812X-RAY DIFFRACTION93
5.7071-49.34110.20781770.1972933X-RAY DIFFRACTION98

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