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- PDB-3tdu: N-terminal acetylation acts as an avidity enhancer within an inte... -

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Basic information

Entry
Database: PDB / ID: 3tdu
TitleN-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex
Components
  • Cullin-1
  • DCN1-like protein 1
  • NEDD8-conjugating enzyme Ubc12
KeywordsLigase/protein binding / E2:E3 / Ligase-protein binding complex
Function / homology
Function and homology information


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of protein neddylation / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of protein neddylation / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / ubiquitin conjugating enzyme binding / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / cullin family protein binding / regulation of protein ubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / post-translational protein modification / intrinsic apoptotic signaling pathway / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / animal organ morphogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Iron uptake and transport / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / protein modification process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / G1/S transition of mitotic cell cycle / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / protein-macromolecule adaptor activity / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / : / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NEDD8-conjugating enzyme Ubc12 / Cullin-1 / DCN1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsScott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A.
CitationJournal: Science / Year: 2011
Title: N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.
Authors: Scott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Mar 13, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DCN1-like protein 1
B: DCN1-like protein 1
C: Cullin-1
D: Cullin-1
E: NEDD8-conjugating enzyme Ubc12
F: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)68,3256
Polymers68,3256
Non-polymers00
Water10,611589
1
A: DCN1-like protein 1
C: Cullin-1
F: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)34,1623
Polymers34,1623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DCN1-like protein 1
D: Cullin-1
E: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)34,1623
Polymers34,1623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.431, 65.454, 64.182
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-145-

HOH

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Components

#1: Protein DCN1-like protein 1 / DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / ...DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / Squamous cell carcinoma-related oncogene


Mass: 23237.461 Da / Num. of mol.: 2 / Fragment: unp residues 62-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D1, DCUN1L1, RP42, SCCRO / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q96GG9
#2: Protein Cullin-1 / CUL-1


Mass: 9015.699 Da / Num. of mol.: 2 / Fragment: unp residues 702-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#3: Protein/peptide NEDD8-conjugating enzyme Ubc12 / NEDD8 carrier protein / NEDD8 protein ligase / Ubiquitin-conjugating enzyme E2 M


Mass: 1909.292 Da / Num. of mol.: 2 / Fragment: unp residues 2-15 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P61081, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationMonochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 86181 / Num. obs: 78739 / % possible obs: 96.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2.605 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.5-1.553.30.4132.60.413188
1.55-1.62195.4
1.69-1.92195.6
1.69-1.78196.1
1.78-1.89196.6
1.89-2.04197.1

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Processing

Software
NameVersionClassification
BSSdata collection
CCP4model building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LDJ

1ldj


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.716 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23249 4150 5 %RANDOM
Rwork0.20606 ---
obs0.20738 78739 96.08 %-
all-86181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0 Å20.39 Å2
2---1.48 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 0 589 5279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.9796561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2135589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22324.793242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34915975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4661530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213642
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_it1.621.52877
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.39924648
X-RAY DIFFRACTIONr_scbond_it4.67432003
X-RAY DIFFRACTIONr_scangle_it8.1374.51897
X-RAY DIFFRACTIONr_rigid_bond_restr2.45834880
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 261 -
Rwork0.326 5070 -
obs--84.32 %
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)
10.0639-0.00950.00440.0211-0.01570.00450.00790.0037-0.006-0.0128-0.00640.00160.00570.0036-0.00150.0256-0.0013-0.00650.02870.00090.031723.1649-4.3659-26.5951
20.0387-0.017-0.02270.0063-0.01480.06750.00010.0067-0.00260.0092-0.00030.0065-0.0283-0.01050.00020.0191-0.0024-0.0110.02990.00250.035714.888-7.10514.4874
30.11850.27730.10611.36210.22440.04560.0047-0.02030.0087-0.0208-0.0105-0.03450.0051-0.00770.00580.0056-0.0021-0.00360.03660.0070.017823.475926.0957-27.8761
40.0216-0.20950.16361.0133-0.5890.41320.02270.0054-0.00180.019-0.02870.04090.02670.02680.00610.02160.00190.00060.03060.00030.026213.9925-37.73524.9822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 252
2X-RAY DIFFRACTION1A60 - 252
3X-RAY DIFFRACTION2B60 - 253
4X-RAY DIFFRACTION2B60 - 253
5X-RAY DIFFRACTION3C702 - 776
6X-RAY DIFFRACTION3C24 - 547
7X-RAY DIFFRACTION4D701 - 776
8X-RAY DIFFRACTION4D48 - 597

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