[English] 日本語
Yorodumi
- PDB-5v83: Structure of DCN1 bound to NAcM-HIT -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / UBA-like superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 ...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 / Lysozyme domain superfamily / Phage lysozyme / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more