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- PDB-5v88: Structure of DCN1 bound to NAcM-COV -

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Basic information

Entry
Database: PDB / ID: 5v88
TitleStructure of DCN1 bound to NAcM-COV
ComponentsLysozyme,DCN1-like protein 1
KeywordsLigase / protein binding / E3 Ligase / HYDROLASE / Ligase - protein binding complex
Function / homology
Function and homology information


positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process ...positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / defense response to bacterium / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Lysozyme - #40 / Endolysin T4 type ...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 / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Recoverin; domain 1 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8ZD / Endolysin / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsGuy, R.K. / Schulman, B.A. / Scott, D.C. / Hammill, J.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM069530 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.
Authors: Scott, D.C. / Hammill, J.T. / Min, J. / Rhee, D.Y. / Connelly, M. / Sviderskiy, V.O. / Bhasin, D. / Chen, Y. / Ong, S.S. / Chai, S.C. / Goktug, A.N. / Huang, G. / Monda, J.K. / Low, J. / ...Authors: Scott, D.C. / Hammill, J.T. / Min, J. / Rhee, D.Y. / Connelly, M. / Sviderskiy, V.O. / Bhasin, D. / Chen, Y. / Ong, S.S. / Chai, S.C. / Goktug, A.N. / Huang, G. / Monda, J.K. / Low, J. / Kim, H.S. / Paulo, J.A. / Cannon, J.R. / Shelat, A.A. / Chen, T. / Kelsall, I.R. / Alpi, A.F. / Pagala, V. / Wang, X. / Peng, J. / Singh, B. / Harper, J.W. / Schulman, B.A. / Guy, R.K.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme,DCN1-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6962
Polymers44,1771
Non-polymers5191
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.392, 98.677, 59.181
Angle α, β, γ (deg.)90.000, 104.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme,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: 44177.227 Da / Num. of mol.: 1 / Mutation: D127A, R154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, DCUN1D1, DCUN1L1, RP42, SCCRO / Plasmid: pRSF DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D9IEF7, UniProt: Q96GG9, UniProt: P00720*PLUS, lysozyme
#2: Chemical ChemComp-8ZD / N-{2-[({1-[(2R)-pentan-2-yl]piperidin-4-yl}{[3-(trifluoromethyl)phenyl]carbamoyl}amino)methyl]phenyl}propanamide


Mass: 518.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37F3N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 6% PEG3350, 0.2M NH4Br

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 48294 / % possible obs: 93.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.032 / Rrim(I) all: 0.047 / Χ2: 1.381 / Net I/σ(I): 18.5 / Num. measured all: 87116
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.661.70.2830.8170.2610.3860.71883.7
1.66-1.721.70.210.8910.1910.2850.78690.1
1.72-1.81.80.1510.9440.1360.2040.92297.3
1.8-1.91.80.1030.9720.0930.1391.12297.5
1.9-2.021.80.0740.9820.0670.1011.55697.7
2.02-2.171.80.0550.990.050.0751.96297.8
2.17-2.391.80.0430.9930.0380.0571.40797.2
2.39-2.741.80.040.9930.0360.0541.75396.2
2.74-3.451.80.0410.9930.0360.0552.22194.7
3.45-501.90.0240.9970.0220.0331.03786.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: residues 65-250 of Chain A from 3TDU and residues 6-158 from 2LZM

3tdu

2lzm


Resolution: 1.601→28.515 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1885 2465 5.11 %
Rwork0.1593 --
obs0.1608 48262 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.71 Å2 / Biso mean: 35.9045 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: final / Resolution: 1.601→28.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 37 472 3442
Biso mean--28.9 43.87 -
Num. residues----363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113056
X-RAY DIFFRACTIONf_angle_d1.3244125
X-RAY DIFFRACTIONf_chiral_restr0.052440
X-RAY DIFFRACTIONf_plane_restr0.006530
X-RAY DIFFRACTIONf_dihedral_angle_d15.9821169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.601-1.63180.25621150.21822049216477
1.6318-1.66510.23171430.20752328247186
1.6651-1.70130.25161290.21632408253789
1.7013-1.74090.2661480.19732556270495
1.7409-1.78440.22581580.19142628278697
1.7844-1.83260.19161340.1842635276998
1.8326-1.88660.25241080.18222677278597
1.8866-1.94740.22121270.18322675280298
1.9474-2.0170.21831550.17132632278798
2.017-2.09780.21311550.16742667282298
2.0978-2.19320.18331360.16012662279898
2.1932-2.30880.19061570.14932598275597
2.3088-2.45340.22151340.15462643277797
2.4534-2.64270.18221630.16442617278096
2.6427-2.90840.19551310.16322612274396
2.9084-3.32870.17941350.15942572270794
3.3287-4.19160.14961180.13432547266593
4.1916-28.51980.16751190.15132291241082
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)
11.1876-0.0444-0.28731.5460.39582.161-0.09360.28390.0953-0.0795-0.15160.1273-0.2351-0.75870.00320.17310.0427-0.030.3454-0.06190.2321-4.332819.4082-0.7862
21.2745-1.0291-0.48782.4621.26051.2102-0.0492-0.0788-0.0210.0825-0.0028-0.01330.153-0.12430.00270.1853-0.04420.01890.19820.01420.16887.0251.6031-5.8507
32.8964-0.42770.46840.35130.21981.78480.10540.0876-0.3804-0.3072-0.0902-0.32220.53320.2380.070.3850.01090.02470.18910.0040.353915.9195-18.4869-17.4672
43.55360.4194-1.04910.8317-0.09970.6133-0.1678-0.0795-0.0576-0.11320.06840.1391-0.006-0.1121-0.00450.17430.0125-0.00470.2348-0.00340.2029-7.988210.427124.7117
50.8729-0.8395-0.38343.04820.23071.65350.06370.1208-0.1623-0.5414-0.1653-0.24950.4916-0.0964-0.00130.4031-0.01650.00070.2074-0.0380.2469-0.0101-6.22817.0335
60.7070.2263-0.09711.10080.32431.87080.0471-0.0515-0.06440.0253-0.04530.0295-0.0563-0.1408-0.00790.1575-0.0037-0.00220.1680.01180.18590.50057.506133.3553
71.0056-0.1129-0.03221.11120.20781.33370.0079-0.08450.06970.1175-0.0301-0.0898-0.23450.2188-0.00460.1889-0.0225-0.00810.18370.00510.18269.377819.120528.7138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1062 through 1092 )A1062 - 1092
2X-RAY DIFFRACTION2chain 'A' and (resid 1093 through 1222 )A1093 - 1222
3X-RAY DIFFRACTION3chain 'A' and (resid 1223 through 1252 )A1223 - 1252
4X-RAY DIFFRACTION4chain 'A' and (resid -11 through 10 )A-11 - 10
5X-RAY DIFFRACTION5chain 'A' and (resid 11 through 59 )A11 - 59
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 92 )A60 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 164 )A93 - 164

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