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- PDB-4gao: DCNL complex with N-terminally acetylated NEDD8 E2 peptide -

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Basic information

Entry
Database: PDB / ID: 4gao
TitleDCNL complex with N-terminally acetylated NEDD8 E2 peptide
Components
  • DCN1-like protein 2
  • NEDD8-conjugating enzyme Ubc12
KeywordsLIGASE/PEPTIDE / E3 ligase / LIGASE-PEPTIDE complex
Function / homology
Function and homology information


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / TGF-beta receptor signaling activates SMADs / cullin family protein binding ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / TGF-beta receptor signaling activates SMADs / cullin family protein binding / regulation of postsynapse assembly / ubiquitin ligase complex / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / Neddylation / postsynapse / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / : / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site ...Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / : / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / NEDD8-conjugating enzyme Ubc12 / DCN1-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsMonda, J.K. / Scott, D.C. / Miller, D.J. / Harper, J.W. / Bennett, E.J. / Schulman, B.A.
CitationJournal: Structure / Year: 2013
Title: Structural Conservation of Distinctive N-terminal Acetylation-Dependent Interactions across a Family of Mammalian NEDD8 Ligation Enzymes.
Authors: Monda, J.K. / Scott, D.C. / Miller, D.J. / Lydeard, J. / King, D. / Harper, J.W. / Bennett, E.J. / Schulman, B.A.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 2.0Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: DCN1-like protein 2
B: DCN1-like protein 2
C: NEDD8-conjugating enzyme Ubc12
D: DCN1-like protein 2
E: NEDD8-conjugating enzyme Ubc12
F: NEDD8-conjugating enzyme Ubc12
G: DCN1-like protein 2
H: NEDD8-conjugating enzyme Ubc12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,13810
Polymers98,9788
Non-polymers1602
Water00
1
A: DCN1-like protein 2
F: NEDD8-conjugating enzyme Ubc12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8243
Polymers24,7452
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-15 kcal/mol
Surface area10300 Å2
MethodPISA
2
B: DCN1-like protein 2
C: NEDD8-conjugating enzyme Ubc12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8243
Polymers24,7452
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-14 kcal/mol
Surface area10210 Å2
MethodPISA
3
D: DCN1-like protein 2
E: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)24,7452
Polymers24,7452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-16 kcal/mol
Surface area10340 Å2
MethodPISA
4
G: DCN1-like protein 2
H: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)24,7452
Polymers24,7452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-14 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.567, 190.151, 49.072
Angle α, β, γ (deg.)90.00, 101.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22G

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA60 - 2491 - 190
21LYSLYSPROPRODD62 - 2493 - 190
12GLYGLYVALVALBB60 - 2511 - 192
22GLYGLYVALVALGG60 - 2511 - 192

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
DCN1-like protein 2 / DCUN1 domain-containing protein 2 / Defective in cullin neddylation protein 1-like protein 2


Mass: 23206.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D2, C13orf17, DCUN1L2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PH85
#2: Protein/peptide
NEDD8-conjugating enzyme Ubc12


Mass: 1537.950 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61081
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20% PEG2000 MME, 0.1M NaBr, 3% sorbitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2010
RadiationMonochromator: single crystal, side bounce horizontal offset Silicon 220 monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.28→40 Å / Num. all: 13036 / Num. obs: 12366 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.28-3.42180
3.42-3.55189.3
3.55-3.72194.5
3.72-3.91196.6
3.91-4.16197.8
4.16-4.48197.5
4.48-4.93197.8
4.93-5.64197.7
5.64-7.1197.5
7.1-40197.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→40 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.783 / SU B: 77.659 / SU ML: 0.595 / Cross valid method: THROUGHOUT / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29631 643 4.9 %RANDOM
Rwork0.25162 ---
obs0.25376 12366 98.1 %-
all-13036 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-1.13 Å2
2--2.34 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 3.28→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6297 0 2 0 6299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9511.968731
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2965795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49925.017297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8881520
X-RAY DIFFRACTIONr_chiral_restr0.070.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214936
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.54016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0326354
X-RAY DIFFRACTIONr_scbond_it0.72532429
X-RAY DIFFRACTIONr_scangle_it1.3344.52377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
111445medium positional0.280.5
221425medium positional0.30.5
111445medium thermal2.822
221425medium thermal1.82
LS refinement shellResolution: 3.28→3.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 43 -
Rwork0.303 743 -
obs--83 %
Refinement TLS params.Method: refined / Origin x: 11.7702 Å / Origin y: 42.8478 Å / Origin z: -1.6495 Å
111213212223313233
T0.0317 Å2-0.0373 Å2-0.0114 Å2-0.1246 Å20.0132 Å2--0.0022 Å2
L0.0989 °20.035 °20.0987 °2-0.8711 °20.3252 °2--0.2126 °2
S0 Å °0.0365 Å °-0.01 Å °0.0848 Å °-0.0051 Å °-0.0015 Å °0.0138 Å °-0.0368 Å °0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 252
2X-RAY DIFFRACTION1B60 - 251
3X-RAY DIFFRACTION1C1 - 10
4X-RAY DIFFRACTION1D62 - 249
5X-RAY DIFFRACTION1E1 - 10
6X-RAY DIFFRACTION1F1 - 11
7X-RAY DIFFRACTION1G60 - 252
8X-RAY DIFFRACTION1H1 - 10

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