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- PDB-3fn1: E2-RING expansion of the NEDD8 cascade confers specificity to cul... -

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Basic information

Entry
Database: PDB / ID: 3fn1
TitleE2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.
Components
  • NEDD8-activating enzyme E1 catalytic subunit
  • NEDD8-conjugating enzyme UBE2F
KeywordsLIGASE / ATP-binding / Cell cycle / Nucleotide-binding / Ubl conjugation pathway
Function / homology
Function and homology information


NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / NEDD8 ligase activity / post-translational protein modification / NIK-->noncanonical NF-kB signaling ...NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / NEDD8 ligase activity / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of cell cycle / protein heterodimerization activity / protein-containing complex / proteolysis / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme ...Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
NEDD8-activating enzyme E1 catalytic subunit / NEDD8-conjugating enzyme UBE2F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, D.T. / Ayrault, O. / Hunt, H.W. / Taherbhoy, A.M. / Duda, D.M. / Scott, D.C. / Borg, L.A. / Neale, G. / Murray, P.J. / Roussel, M.F. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2009
Title: E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification
Authors: Huang, D.T. / Ayrault, O. / Hunt, H.W. / Taherbhoy, A.M. / Duda, D.M. / Scott, D.C. / Borg, L.A. / Neale, G. / Murray, P.J. / Roussel, M.F. / Schulman, B.A.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD8-activating enzyme E1 catalytic subunit
B: NEDD8-conjugating enzyme UBE2F


Theoretical massNumber of molelcules
Total (without water)29,9622
Polymers29,9622
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-10 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.171, 81.171, 212.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein NEDD8-activating enzyme E1 catalytic subunit / Ubiquitin-like modifier-activating enzyme 3 / Ubiquitin-activating enzyme 3 / NEDD8-activating ...Ubiquitin-like modifier-activating enzyme 3 / Ubiquitin-activating enzyme 3 / NEDD8-activating enzyme E1C / Ubiquitin-activating enzyme E1C


Mass: 10856.974 Da / Num. of mol.: 1 / Fragment: UBIQUITIN-ACTIVATING ENZYME E1C, residue 368-463 / Mutation: L394M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E1C, UBA3, UBE1C / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8TBC4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein NEDD8-conjugating enzyme UBE2F / Ubiquitin-conjugating enzyme E2 F / NEDD8 protein ligase UBE2F / NEDD8 carrier protein UBE2F / ...Ubiquitin-conjugating enzyme E2 F / NEDD8 protein ligase UBE2F / NEDD8 carrier protein UBE2F / NEDD8-conjugating enzyme 2


Mass: 19104.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCE2, UBE2F / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q969M7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.7-0.8 M Na Citrate, 0.2 M NaC1, 0.1 M Bicine, 5 mM DTT, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 15203 / Num. obs: 13512 / % possible obs: 96.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.13
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y8X

1y8x


Resolution: 2.5→24.88 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.26 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.41 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26501 673 5 %RANDOM
Rwork0.22382 ---
obs0.22599 12839 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.941 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å21.63 Å20 Å2
2--3.27 Å20 Å2
3----4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 0 135 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9712767
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4865250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63324.94591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1091510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2906
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21362
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.51298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78622056
X-RAY DIFFRACTIONr_scbond_it0.9963824
X-RAY DIFFRACTIONr_scangle_it1.6044.5711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 41 -
Rwork0.324 798 -
obs--78.56 %
Refinement TLS params.Method: refined / Origin x: -16.5251 Å / Origin y: 5.2531 Å / Origin z: 12.9471 Å
111213212223313233
T-0.0357 Å20.0232 Å20.0302 Å2-0.1009 Å2-0.1056 Å2---0.0374 Å2
L0.921 °2-0.5979 °20.3759 °2-2.9917 °2-1.083 °2--4.2818 °2
S0.1305 Å °-0.2258 Å °0.0266 Å °0.2544 Å °-0.2016 Å °-0.0064 Å °-0.2445 Å °-1.1046 Å °0.0711 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B32 - 184
2X-RAY DIFFRACTION1A350 - 440

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