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- PDB-4wzp: Ser65 phosphorylated ubiquitin, major conformation -

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Basic information

Entry
Database: PDB / ID: 4wzp
TitleSer65 phosphorylated ubiquitin, major conformation
Componentsubiquitin
KeywordsSIGNALING PROTEIN / posttranslational modification / phosphorylation / mitophagy / Parkin / PINK1
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / 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) / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / neuron projection morphogenesis / 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) / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / 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 / Degradation of DVL / 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 / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWauer, T. / Wagstaff, J. / Freund, S.M.V. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council309756 United Kingdom
CitationJournal: Embo J. / Year: 2015
Title: Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis.
Authors: Wauer, T. / Swatek, K.N. / Wagstaff, J.L. / Gladkova, C. / Pruneda, J.N. / Michel, M.A. / Gersch, M. / Johnson, C.M. / Freund, S.M. / Komander, D.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: ubiquitin
G: ubiquitin
H: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92715
Polymers69,2548
Non-polymers6727
Water6,413356
1
A: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8493
Polymers8,6571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6571
Polymers8,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7532
Polymers8,6571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7532
Polymers8,6571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6571
Polymers8,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8493
Polymers8,6571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7532
Polymers8,6571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6571
Polymers8,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.563, 53.285, 56.866
Angle α, β, γ (deg.)96.86, 104.94, 110.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ubiquitin


Mass: 8656.811 Da / Num. of mol.: 8 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Details: phosphorylation at Ser65 / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 30% (w/v) PEG 8000, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→32.28 Å / Num. obs: 39104 / % possible obs: 97.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 4.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.1 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ubq

1ubq


Resolution: 1.9→32.28 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1904 4.87 %random
Rwork0.1934 ---
obs0.1956 39071 97.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 35 356 4950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064657
X-RAY DIFFRACTIONf_angle_d0.9976313
X-RAY DIFFRACTIONf_dihedral_angle_d13.4081765
X-RAY DIFFRACTIONf_chiral_restr0.036753
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.27181330.23092577X-RAY DIFFRACTION96
1.9476-2.00020.29361470.21552630X-RAY DIFFRACTION96
2.0002-2.05910.26531150.20552655X-RAY DIFFRACTION96
2.0591-2.12550.26991350.2182616X-RAY DIFFRACTION96
2.1255-2.20150.26751500.19692608X-RAY DIFFRACTION96
2.2015-2.28960.23711310.20762705X-RAY DIFFRACTION97
2.2896-2.39380.26671140.20132663X-RAY DIFFRACTION97
2.3938-2.51990.27331510.20252649X-RAY DIFFRACTION98
2.5199-2.67770.25291250.20382676X-RAY DIFFRACTION97
2.6777-2.88440.25741240.20122676X-RAY DIFFRACTION97
2.8844-3.17440.25611390.20012670X-RAY DIFFRACTION97
3.1744-3.63320.23451480.18292661X-RAY DIFFRACTION98
3.6332-4.57540.19531430.16522681X-RAY DIFFRACTION98
4.5754-32.28530.19831490.18792700X-RAY DIFFRACTION99
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)
12.132-0.59820.71432.8470.31892.36750.0485-0.21380.0530.10710.08170.15320.1038-0.191-0.09890.0607-0.01990.00450.09220.01090.126-16.8804-27.684761.9789
22.02010.55590.34742.8095-0.67152.94290.0441-0.1068-0.048-0.1709-0.0134-0.16460.09030.2302-0.04740.0760.02980.01160.0837-0.00520.1275.6046-27.716562.9191
32.0253-0.08880.11982.298-0.24763.6037-0.0367-0.15180.10730.31080.02810.2827-0.0422-0.47750.00470.16350.0190.00940.2862-0.00540.16-34.2454-22.510735.5135
42.4988-0.26491.28083.3934-1.09251.7960.07280.42130.0911-0.3568-0.2266-0.26270.10220.61450.05050.17050.00470.02490.35970.05080.1578-11.8358-21.330736.2158
51.9640.0987-0.69932.13290.48752.10380.0085-0.02030.09420.0579-0.00560.1674-0.0999-0.25390.03170.13850.0152-0.00030.1084-0.0180.1469-16.131-3.246262.5146
61.92760.58580.04381.9966-0.89841.31530.0366-0.14840.12020.15070.00390.0087-0.15960.0021-0.03970.12260.01890.00880.0959-0.02390.10243.873-5.749273.2684
71.1695-0.0287-0.40851.93610.33532.2562-0.05750.1623-0.1819-0.30490.05340.00060.1271-0.07820.00050.2099-0.05210.02270.2448-0.02780.174212.63311.600848.3617
81.56320.6109-0.03232.2486-0.50322.39720.04820.0153-0.01880.09-0.0816-0.0913-0.2049-0.1077-0.01650.36970.0334-0.0020.36880.00220.22-10.09085.021935.6072
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

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