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- PDB-4f8c: Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 4f8c
TitleStructure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8
Components
  • Cycle Inhibiting Factor
  • NEDD8
KeywordsCELL CYCLE/PROTEIN BINDING / Effector-Host target complex / Glutamine deamidase / Deamidation / BACTERIAL EFFECTOR / CELL CYCLE-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / protein localization / modification-dependent protein catabolic process / protein tag activity / UCH proteinases ...regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / protein localization / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / 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 ...Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / 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
Uncharacterized protein / Uncharacterized protein / NEDD8
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCrow, A. / Banfield, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The molecular basis of Nedd8 deamidation by the bacterial effector protein Cif
Authors: Crow, A. / Hughes, R.K. / Taieb, F. / Oswald, E. / Banfield, M.J.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: Cycle Inhibiting Factor
B: NEDD8
C: Cycle Inhibiting Factor
D: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9568
Polymers81,7084
Non-polymers2484
Water5,729318
1
A: Cycle Inhibiting Factor
B: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9784
Polymers40,8542
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-3 kcal/mol
Surface area14140 Å2
MethodPISA
2
C: Cycle Inhibiting Factor
D: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9784
Polymers40,8542
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-6 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.359, 125.359, 169.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Cycle Inhibiting Factor


Mass: 30809.465 Da / Num. of mol.: 2 / Fragment: Effector domain, UNP residues 33-288 / Mutation: C117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: YPIII / Gene: YPK_1971 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: B1JJZ9, UniProt: A0A0H3B1Q8*PLUS
#2: Protein NEDD8 / / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 10044.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rossetta / References: UniProt: Q15843
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.2M sodium malonate, 44mM bis-tris propane (pH 7.0), 66mM bis-tris propane (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.0072 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 1.95→66.9 Å / Num. all: 57931 / Num. obs: 57931 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.1 % / Rsym value: 0.079 / Net I/σ(I): 18.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.463 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
REFMAC5.7.0025refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FBJ

4fbj


Resolution: 1.95→58.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23479 2938 5.1 %RANDOM
Rwork0.18681 ---
obs0.18923 54900 99.83 %-
all-54900 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→58.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 0 16 318 5431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0195543
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9587530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58725.169267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.039151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.771532
X-RAY DIFFRACTIONr_chiral_restr0.1520.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214220
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 221 -
Rwork0.223 3972 -
obs--99.81 %

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