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

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Entry
Database: PDB / ID: 3tdz
TitleN-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex
Components
  • Cullin-1
  • DCN1-like protein 1
  • STAPLED PEPTIDE
KeywordsPROTEIN BINDING/INHIBITOR / E2:E3 / PROTEIN BINDING-INHIBITOR 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 / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / cullin family protein binding / regulation of protein ubiquitination / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / ubiquitin ligase complex / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / post-translational protein modification / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / animal organ morphogenesis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of beta-catenin by the destruction complex / protein modification process / 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 / G1/S transition of mitotic cell cycle / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of neuron apoptotic process / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / protein-macromolecule adaptor activity / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 ...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 / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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
Cul1WHB-Dcn1P-stapled acetylated / NEDD8-conjugating enzyme Ubc12 / Cullin-1 / DCN1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Dec 12, 2012Group: Other
Revision 1.3Apr 17, 2013Group: Other
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.6Dec 6, 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: DCN1-like protein 1
C: Cullin-1
B: DCN1-like protein 1
D: Cullin-1
E: STAPLED PEPTIDE
F: STAPLED PEPTIDE


Theoretical massNumber of molelcules
Total (without water)67,6026
Polymers67,6026
Non-polymers00
Water8,737485
1
A: DCN1-like protein 1
C: Cullin-1
E: STAPLED PEPTIDE


Theoretical massNumber of molelcules
Total (without water)33,8013
Polymers33,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DCN1-like protein 1
D: Cullin-1
F: STAPLED PEPTIDE


Theoretical massNumber of molelcules
Total (without water)33,8013
Polymers33,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.790, 190.210, 67.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#3: Protein/peptide STAPLED PEPTIDE / NEDD8-conjugating enzyme Ubc12 / NEDD8 carrier protein / NEDD8 protein ligase / Ubiquitin- ...NEDD8-conjugating enzyme Ubc12 / NEDD8 carrier protein / NEDD8 protein ligase / Ubiquitin-conjugating enzyme E2 M


Type: Oligopeptide / Class: Inhibitor / Mass: 1547.910 Da / Num. of mol.: 2 / Fragment: unp residues 2-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P61081, Cul1WHB-Dcn1P-stapled acetylated, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SIDE CHAINS OF MK8 RESIDUE OF CHAIN E/F AND NUMBERS 5 AND 9 ARE LINKED BY A DOUBLE BOND AT THE CE ATOMS

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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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 21% PEG3350, 0.2M KCl, pH Unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 277K
PH range: Unbuffered

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2011
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 57893 / Num. obs: 53080 / % possible obs: 96.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2.474 / Redundancy: 6.6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 24.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2-2.073.50.4392.50.439177.2
2.07-2.15191.5
2.15-2.25198.3
2.25-2.37199.7
2.37-2.521100

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
CCP4model building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3TDU

3tdu


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.87 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22352 2840 5.1 %RANDOM
Rwork0.19567 ---
obs0.19706 53080 96.58 %-
all-57893 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.86 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 0 485 5078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9821.9846331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5885550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1624.978231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11815922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4411526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213472
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_it0.4171.52810
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80924511
X-RAY DIFFRACTIONr_scbond_it1.25531923
X-RAY DIFFRACTIONr_scangle_it2.1624.51819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 147 -
Rwork0.254 2963 -
obs--74.03 %
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)
13.2920.3959-1.09910.3953-0.09320.60750.07990.26230.18220.03480.03770.0764-0.09450.0208-0.11760.064-0.01560.0080.20260.04060.0718-2.45149.5971.469
24.05413.1061-0.49845.8977-1.30043.1003-0.17520.7432-0.0328-0.14820.43380.04890.14540.1729-0.25870.01850.0053-0.00560.32850.01920.0471-28.06237.158-7.729
30.2608-0.19290.08884.18191.2921.5003-0.01160.0541-0.0107-0.10620.1447-0.204-0.43080.1839-0.13310.2380.00320.06370.103-0.00760.0376-21.58191.978-18.323
43.61052.52110.45274.7095-0.68673.71830.09410.1243-0.01730.35610.08970.0588-0.2396-0.2203-0.18380.10720.09290.02180.1346-0.00690.0389-33.92766.376-8.727
59.1336-6.08115.82913.1383-9.389516.55870.1360.3182-0.1443-0.53850.17640.10740.45880.3578-0.31240.0776-0.03350.00670.266-0.07120.12437.74641.19211.127
69.2569-3.53725.82110.2455-8.411212.9210.1524-0.55770.02970.29350.25510.6451-0.3627-0.5453-0.40750.53870.01120.10790.1293-0.0070.1712-29.92103.194-27.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 151
2X-RAY DIFFRACTION1A152 - 220
3X-RAY DIFFRACTION1A221 - 250
4X-RAY DIFFRACTION2C702 - 722
5X-RAY DIFFRACTION2C723 - 740
6X-RAY DIFFRACTION2C741 - 776
7X-RAY DIFFRACTION3B61 - 151
8X-RAY DIFFRACTION3B152 - 220
9X-RAY DIFFRACTION3B221 - 250
10X-RAY DIFFRACTION4D701 - 722
11X-RAY DIFFRACTION4D723 - 740
12X-RAY DIFFRACTION4D741 - 775
13X-RAY DIFFRACTION5E1 - 11
14X-RAY DIFFRACTION6F1 - 11

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