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- PDB-5v83: Structure of DCN1 bound to NAcM-HIT -

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Basic information

Entry
Database: PDB / ID: 5v83
TitleStructure of DCN1 bound to NAcM-HIT
ComponentsLysozyme,DCN1-like protein 1 chimera
KeywordsLIGASE / E3 Ligase / HYDROLASE
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
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / : ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-8Z7 / Endolysin / Endolysin / DCN1-like protein 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,6852
Polymers44,3071
Non-polymers3771
Water5,278293
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 area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.966, 97.280, 58.148
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme,DCN1-like protein 1 chimera / 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: 44307.352 Da / Num. of mol.: 1
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-8Z7 / N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea


Mass: 377.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22F3N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
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: 2→50 Å / Num. obs: 25413 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.045 / Rrim(I) all: 0.088 / Χ2: 1.489 / Net I/σ(I): 9.7 / Num. measured all: 95803
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2-2.073.70.61525530.4560.370.7192.138
2.07-2.153.80.38625310.8780.230.450.702
2.15-2.253.80.35725000.5550.2130.4162.574
2.25-2.373.80.19725300.9660.1170.230.735
2.37-2.523.80.15425470.9770.0920.180.744
2.52-2.713.80.11725370.9840.070.1370.898
2.71-2.993.80.0825290.9930.0470.0931.062
2.99-3.423.80.0725510.9920.0420.0822.026
3.42-4.313.70.0625420.9920.0360.072.49
4.31-503.70.03725930.9790.0220.0431.561

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
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: 2.002→48.743 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1294 5.1 %
Rwork0.1713 24089 -
obs0.1743 25383 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.91 Å2 / Biso mean: 38.8967 Å2 / Biso min: 14.71 Å2
Refinement stepCycle: final / Resolution: 2.002→48.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 27 293 3245
Biso mean--47 43.59 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113015
X-RAY DIFFRACTIONf_angle_d1.2684068
X-RAY DIFFRACTIONf_chiral_restr0.051435
X-RAY DIFFRACTIONf_plane_restr0.006523
X-RAY DIFFRACTIONf_dihedral_angle_d13.3691127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0016-2.08170.26741400.21832675281599
2.0817-2.17650.27591370.19626532790100
2.1765-2.29120.23791220.189226802802100
2.2912-2.43480.25641380.189426582796100
2.4348-2.62280.28371580.192626752833100
2.6228-2.88670.23351560.191226762832100
2.8867-3.30430.23771410.181826732814100
3.3043-4.16270.22371440.145626912835100
4.1627-48.75730.19111580.155127082866100
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)
10.3428-0.63080.92771.2695-1.82042.961-0.31570.19130.39830.3748-0.16560.515-1.0782-1.3337-0.12560.13770.0799-0.02780.4896-0.06540.3077-6.205519.96921.9748
20.3629-0.3398-0.42710.44080.34670.41260.07930.13740.2788-0.1605-0.08780.11150.0169-0.3574-00.2773-0.03390.02420.3855-0.02210.24792.594311.6765-5.03
30.153-0.1983-0.22680.17710.26180.3458-0.1689-0.46360.45060.5770.05630.14440.333-0.1876-0.00410.32890.0345-0.02310.4391-0.06190.28441.867814.29956.9746
40.4538-0.2284-0.67421.19721.12881.6847-0.2204-0.59240.15830.5548-0.13540.12760.55140.3824-0.24540.27960.04780.02110.4290.02690.293810.73334.468-0.6074
50.27230.0136-0.03910.96210.15140.6164-0.0839-0.0317-0.22-0.1284-0.18770.24180.0580.1086-0.02570.32980.01150.07120.2323-0.02810.27467.6664-3.9948-16.1186
60.4396-0.2451-0.58471.53371.1011.232-0.45850.1428-0.73750.4083-0.17640.4990.5948-0.0939-0.53940.3605-0.0440.19790.22180.02780.40176.6981-11.1491-11.5001
70.8765-0.4543-0.54380.45630.41530.3594-0.5379-0.0152-1.2572-0.3662-0.2471-0.4960.48990.2058-0.43930.56430.06030.24390.3040.11430.594715.1946-17.4367-17.3071
80.08250.0340.0550.1760.33890.5519-0.2354-0.1448-0.331-0.2693-0.01020.2495-0.13520.0088-0.03230.18550.0196-0.04070.2475-0.00040.3576-7.879110.598724.2009
90.369-0.5665-0.18361.03730.21240.7459-0.00390.0612-0.2576-0.5262-0.0456-0.11770.3816-0.0754-0.00130.4199-0.02270.01950.234-0.04970.28770.2019-5.842716.6516
100.06360.0165-0.06560.73640.09860.16540.011-0.1706-0.28520.13620.0090.10680.0272-0.4248-0.00010.2543-0.0106-0.04960.24150.00170.1768-2.33733.866328.6709
110.18930.0777-0.33320.2893-0.22070.3801-0.0184-0.04760.04780.3168-0.2001-0.0024-0.21180.1747-0.00570.2037-0.0279-0.0260.20720.0170.19166.958613.16333.9129
120.24750.1193-0.23880.1441-0.4231.3303-0.0777-0.30660.75860.7171-0.3144-0.2469-0.12930.5521-0.08940.3635-0.1213-0.09870.36430.01310.35412.443122.120737.6904
130.2530.13550.57720.70680.07250.83490.13280.17640.2957-0.1167-0.0862-0.1234-0.29830.1772-0.00060.2318-0.0373-0.03190.21470.04360.28629.344621.646924.0192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1062 through 1082 )A1062 - 1082
2X-RAY DIFFRACTION2chain 'A' and (resid 1083 through 1118 )A1083 - 1118
3X-RAY DIFFRACTION3chain 'A' and (resid 1119 through 1133 )A1119 - 1133
4X-RAY DIFFRACTION4chain 'A' and (resid 1134 through 1165 )A1134 - 1165
5X-RAY DIFFRACTION5chain 'A' and (resid 1166 through 1202 )A1166 - 1202
6X-RAY DIFFRACTION6chain 'A' and (resid 1203 through 1222 )A1203 - 1222
7X-RAY DIFFRACTION7chain 'A' and (resid 1223 through 1252 )A1223 - 1252
8X-RAY DIFFRACTION8chain 'A' and (resid -11 through 10 )A-11 - 10
9X-RAY DIFFRACTION9chain 'A' and (resid 11 through 59 )A11 - 59
10X-RAY DIFFRACTION10chain 'A' and (resid 60 through 80 )A60 - 80
11X-RAY DIFFRACTION11chain 'A' and (resid 81 through 113 )A81 - 113
12X-RAY DIFFRACTION12chain 'A' and (resid 114 through 125 )A114 - 125
13X-RAY DIFFRACTION13chain 'A' and (resid 126 through 164 )A126 - 164

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