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- PDB-1ogw: Synthetic Ubiquitin with fluoro-Leu at 50 and 67 -

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Entry
Database: PDB / ID: 1ogw
TitleSynthetic Ubiquitin with fluoro-Leu at 50 and 67
ComponentsUBIQUITIN
KeywordsCELL CYCLE / CHROMOSOMAL PROTEIN
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 / 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 ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Stabilization of p53 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis / Assembly of the pre-replicative complex / EGFR downregulation / Vpu mediated degradation of CD4 / Regulation of TNFR1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Assembly Of The HIV Virion / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / Spry regulation of FGF signaling / Late endosomal microautophagy / Hh mutants are degraded by ERAD / Iron uptake and transport / Activation of NF-kappaB in B cells / NOD1/2 Signaling Pathway / G2/M Checkpoints
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsAlexeev, D. / Ramage, R. / Young, D.W. / Sawyer, L.
Citation
Journal: Chembiochem / Year: 2003
Title: Synthesis, Structural and Biological Studies of Ubiquitin Mutants Containing (2S, 4S)-5-Fluoroleucine Residues Strategically Placed in the Hydrophobic Core
Authors: Alexeev, D. / Barlow, P.N. / Bury, S.M. / Charrier, J.-D. / Cooper, A. / Hadfield, D. / Jamieson, C. / Kelly, S.M. / Layfield, R. / Mayer, R.J. / Mcsparran, H. / Price, N.C. / Ramage, R. / ...Authors: Alexeev, D. / Barlow, P.N. / Bury, S.M. / Charrier, J.-D. / Cooper, A. / Hadfield, D. / Jamieson, C. / Kelly, S.M. / Layfield, R. / Mayer, R.J. / Mcsparran, H. / Price, N.C. / Ramage, R. / Sawyer, L. / Starkmann, B.A. / Uhrin, D. / Willken, J. / Young, D.W.
#1: Journal: Biochem.J. / Year: 1994
Title: Synthetic, Structural and Biological Studies of the Ubiquitin System
Authors: Alexeev, D. / Bury, S.M. / Turner, M.A. / Ogunjobi, O.M. / Muir, T.W. / Ramage, R. / Sawyer, L.
#2: Journal: Biochem.J. / Year: 1997
Title: Synthetic, Structural and Biological Studies of the Ubiquitin System: The Synthesis and Crystal Structu of an Analogue Containing Unnatural Amino Acids
Authors: Love, S.G. / Muir, T.W. / Ramage, R. / Shaw, K.T. / Alexeev, D. / Sawyer, L. / Kelly, S.M. / Price, N.C. / Arnold, J.E. / Lee, M.P. / Mayer, R.J.
#3: Journal: J Mol Biol / Year: 1987
Title: Structure of ubiquitin refined at 1.8 A resolution.
Abstract: The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond ...The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.5 degrees, respectively. A total of 58 water molecules per molecule of ubiquitin are included in the final model. The last four residues in the molecule appear to have partial occupancy or large thermal motion. The overall structure of ubiquitin is extremely compact and tightly hydrogen-bonded; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns.
History
DepositionMay 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: 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_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN


Theoretical massNumber of molelcules
Total (without water)8,6131
Polymers8,6131
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.840, 42.770, 28.950
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


Mass: 8612.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-76 / Source method: isolated from a natural source / Details: LEF IS (4S)-5-FLUORO-L-LEUCINE / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P0CG48
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Compound detailsLEU (50) AND LEU (67) ARE MODIFIED RESIDUES
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: 1.8 Å3/Da / Density % sol: 32.68 %
Crystal growpH: 5.6
Details: SEEDED FROM DROP CONTAINING CONTAINING 5 MUL 20MG/ML UBIQUITIN AND 5 MUL 30% PEG 4000 IN 50MM CACODYLATE-HCL PH 5.6. STORED IN 38% PEG 4000.
Crystal grow
*PLUS
Method: other / Details: Love, S.G., (1997) Biochem. J., 323, 727.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.32→6 Å / Num. obs: 13828 / % possible obs: 89.9 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 1.31→1.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 81.4
Reflection
*PLUS
Num. obs: 14305 / Num. measured all: 157103

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBI

1ubi


Resolution: 1.32→8 Å / Num. parameters: 2814 / Num. restraintsaints: 2521 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
all0.222 14305 -
obs0.222 -89.9 %
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 3212 / Occupancy sum non hydrogen: 2736
Refinement stepCycle: LAST / Resolution: 1.32→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms604 0 0 114 718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.1
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.4
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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