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- PDB-4zpz: Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 ... -

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Basic information

Entry
Database: PDB / ID: 4zpz
TitleCrystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys
ComponentsPolyubiquitin-B
KeywordsSIGNALING PROTEIN / chromosomal protein / cell signalling
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 / regulation of proteasomal protein catabolic process ...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 / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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 / neuron projection morphogenesis / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / 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 / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsHan, C. / Virdee, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Chembiochem / Year: 2015
Title: A Versatile Strategy for the Semisynthetic Production of Ser65 Phosphorylated Ubiquitin and Its Biochemical and Structural Characterisation.
Authors: Han, C. / Pao, K.C. / Kazlauskaite, A. / Muqit, M.M. / Virdee, S.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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: Polyubiquitin-B
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)17,3782
Polymers17,3782
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-9 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.699, 41.699, 69.831
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Polyubiquitin-B


Mass: 8688.876 Da / Num. of mol.: 2 / Fragment: ubiquitin, UNP residues 1-73 / Mutation: A46C, Phospho-Ser65
Source method: isolated from a genetically manipulated source
Details: ubiquitin 1-45 / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P0CG47
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 50 mM sodium cacodylate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11K, H, -L20.499
ReflectionResolution: 1.538→36.113 Å / Num. all: 20124 / Num. obs: 20124 / % possible obs: 99.7 % / Redundancy: 3.1 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.08 / Rsym value: 0.067 / Net I/av σ(I): 7 / Net I/σ(I): 10.2 / Num. measured all: 62396
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.538-1.622.80.3332.1808929100.2350.3333.298.8
1.62-1.723.10.2772.5867627860.1850.2774.299.8
1.72-1.843.10.1913.6798126040.1280.1915.899.8
1.84-1.993.20.1195.9770124390.0790.1198.799.8
1.99-2.183.10.0858.1702222540.0570.08511.699.8
2.18-2.433.20.0699.3639220160.0460.06913.299.9
2.43-2.813.20.0610.7579218050.0390.0615.799.9
2.81-3.443.30.04712.6488514990.0310.04719100
3.44-4.863.20.04313.3372011660.0280.04321.499.9
4.86-25.1023.30.04710.821386450.030.04720.799.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.54→25.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1414 / FOM work R set: 0.9085 / SU B: 1.67 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0144 / SU Rfree: 0.0152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1727 1035 5.2 %RANDOM
Rwork0.1386 ---
obs0.1403 19062 99.66 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 71.79 Å2 / Biso mean: 16.231 Å2 / Biso min: 7.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2--3.12 Å20 Å2
3----6.24 Å2
Refinement stepCycle: final / Resolution: 1.54→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 145 1311
Biso mean---19.84 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191217
X-RAY DIFFRACTIONr_bond_other_d0.0050.021228
X-RAY DIFFRACTIONr_angle_refined_deg1.8252.0061651
X-RAY DIFFRACTIONr_angle_other_deg1.24732847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.30326.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63115249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.52156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211344
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02242
X-RAY DIFFRACTIONr_mcbond_it2.5420.687594
X-RAY DIFFRACTIONr_mcbond_other2.5040.687593
X-RAY DIFFRACTIONr_mcangle_it2.9431.028744
LS refinement shellResolution: 1.538→1.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 99 -
Rwork0.182 1329 -
all-1428 -
obs--97.81 %
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)
11.81350.0010.13592.3464-0.02612.30060.014-0.027-0.0190.0479-0.001-0.00730.0211-0.0651-0.0130.011-0.0097-0.00250.01750.00210.053716.668-6.955.939
21.7161-0.2572-0.0292.12050.15081.8174-0.02390.0195-0.01960.01690.01730.0055-0.02270.02670.00660.0069-0.00830.00050.02430.00340.0559-2.441-18.01412.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 72
2X-RAY DIFFRACTION2B1 - 73

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