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- PDB-6d4p: Ube2D1 in complex with ubiquitin variant Ubv.D1.1 -

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Basic information

Entry
Database: PDB / ID: 6d4p
TitleUbe2D1 in complex with ubiquitin variant Ubv.D1.1
Components
  • Ubiquitin Variant Ubv.D1.1
  • Ubiquitin-conjugating enzyme E2 D1
KeywordsTRANSFERASE / Ubiquitin / Ubiquitin conjugating enzyme / Ubiquitin variant
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / negative regulation of BMP signaling pathway / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / negative regulation of TORC1 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Negative regulators of DDX58/IFIH1 signaling / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ubiquitin conserved site ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D1 / Ubiquitin C variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsCeccarelli, D.F. / Garg, P. / Sidhu, S. / Sicheri, F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-136956 Canada
Canadian Institutes of Health Research (CIHR)MOP-126129 Canada
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes.
Authors: Garg, P. / Ceccarelli, D.F. / Keszei, A.F.A. / Kurinov, I. / Sicheri, F. / Sidhu, S.S.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D1
C: Ubiquitin Variant Ubv.D1.1


Theoretical massNumber of molelcules
Total (without water)26,7342
Polymers26,7342
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: competitive ELISA assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-11 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.120, 52.565, 96.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D1 / (E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-protein ligase D1


Mass: 16750.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51668, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin Variant Ubv.D1.1


Mass: 9984.271 Da / Num. of mol.: 1
Mutation: T7K, L8F, T9W, E64K, S65F, H68Y, V70A, L71Y, R72G, G75A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59EM9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG2000-MME, 0.2M trimethylamine N-oxide, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15572 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 41.91 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.047 / Rrim(I) all: 0.112 / Χ2: 1.829 / Net I/σ(I): 30.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.186.711.4614980.610.57311.07999.6
2.18-2.267.2115260.7960.41911.15199.7
2.26-2.377.40.85315390.8570.3350.9171.161100
2.37-2.497.40.63315350.9210.2470.681.197100
2.49-2.657.40.41615250.9590.1630.4471.272100
2.65-2.857.40.27315500.980.1070.2941.368100
2.85-3.147.40.15215470.9920.060.1641.467100
3.14-3.597.40.09715630.9960.0380.1052100
3.59-4.527.20.08815950.9930.0350.0944.896100
4.52-506.80.0516940.9980.0210.0542.56899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.13_2998refinement
DENZOdata reduction
HKL-20002.3.12data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PTF

3ptf


Resolution: 2.11→48.37 Å / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.2422
RfactorNum. reflection% reflection
Rfree0.231 787 5.07 %
Rwork0.2142 --
obs0.2151 15521 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.99 Å2
Refinement stepCycle: LAST / Resolution: 2.11→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 24 1750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231783
X-RAY DIFFRACTIONf_angle_d0.59882435
X-RAY DIFFRACTIONf_chiral_restr0.0442269
X-RAY DIFFRACTIONf_plane_restr0.0034316
X-RAY DIFFRACTIONf_dihedral_angle_d11.38781068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.240.30891200.30812357X-RAY DIFFRACTION97.75
2.24-2.420.32841170.26632425X-RAY DIFFRACTION99.88
2.42-2.660.27431290.24462443X-RAY DIFFRACTION100
2.66-3.040.2331340.23132456X-RAY DIFFRACTION100
3.04-3.830.22491510.21052446X-RAY DIFFRACTION100
3.83-48.390.20541360.18732607X-RAY DIFFRACTION99.89
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)
11.33399173279-0.469334555236-0.1781208569764.22082766783-0.8908346506311.40551586279-0.3142293090430.003029763744440.208420457222-0.08292674492830.116787342307-0.230073482364-0.273076284044-0.03911691320140.206648044430.483143535323-0.0617441798406-0.08610705250050.442317113363-0.04296149023590.4543066125172.01598058832.92005147428-13.6239571394
21.48633517274-0.4028279576080.2531616288942.365894064270.4525758812171.65887744353-0.0449212235078-0.1862850885470.1958378501520.01138409083360.00526688495917-0.115456312942-0.3789434735110.2277751086570.02482993861610.431510456592-0.0682888002627-0.05344821107420.4703185857620.03571986014270.4684619387510.6499683093-3.99937037757-15.238306058
31.93390245475-0.141888689140.6753542830051.412290706170.03926585725481.378669741080.1253078431580.1417791501470.183929982638-0.0920979759656-0.133711767024-0.213247810729-0.1408303491380.348077875392-0.01751108230260.372163230557-0.06556720712080.01124832468310.3653158093840.01702241295480.35251487507911.9537082804-7.7092879546-23.9951273096
41.39980272838-1.47925696574-0.3554366635261.758836125170.8139381799562.193742123370.02390959173880.3782159842870.0963771844991-0.326483812853-0.0247523564410.0458553878621-0.129607761310.0451862259611-0.06524147020020.483609728539-0.0985981446198-0.01961678882740.4574780071240.01769860299930.3899285247877.06891496377-8.86171762322-28.7479137534
54.823707378410.104835752345-1.305144762641.25858435868-0.4137032632393.78251034410.636221978671.0019775988-0.251107778267-0.84672456196-0.139247612710.2945734344720.02463845488880.208388441031-0.4124003110750.8887662586940.0105380674832-0.05701578724510.716523495257-0.04983613774550.4991728013912.6653898258-19.8716007969-38.3967909676
61.754456033480.1321476267640.3810418347072.828042612381.92335389023.131876489380.0884947982656-0.494662842508-0.513407738502-0.4937509962420.205790351495-0.2899854245080.3212244073780.491120886017-0.1304690545740.570920313210.0702143571303-0.01281795807570.582278504916-0.02452511589010.55088363107921.2694205196-22.9935399717-27.021039208
75.73607982244-0.277045502412.339569210.421101079846-0.5829764286241.421767181770.181968906902-0.03296299806140.5226158105490.481957695938-0.4610644725240.7730897191571.01914381898-0.5643779197280.2027665484520.461787579403-0.128012145320.05925512427530.504910562561-0.06697437216920.4463824578219.49044253888-12.20335785761.93628339429
80.704070494336-0.0558947170596-0.9434880405461.04062095426-0.8857711790572.308462330440.0101755767742-0.3945164223930.2171767068240.3675804078260.2073080597560.2786083223530.8842691691240.29160297946-0.06340108659570.433465323787-0.0479099084231-0.005658217868870.5046446020680.0196458048390.4192099185868.76980684714-16.9535513514-3.50023644226
95.68580057701-0.2091673347731.20674076823.02254157254-1.238371206764.276392619690.27044959091-0.130030617048-0.1681831496580.424730260956-0.292472847582-0.516212674140.5305809412190.920452492456-0.1251191017580.4474157358660.0146875745495-0.0193330315690.4456287180170.0343512122730.41997832918518.839784001-17.9575005417-0.65571662332
105.18963079541-0.325038609222-1.313679078570.567260605276-0.08590047858083.876515876090.173974433710.1298861353470.3948696094150.1735612505380.01294235650730.185458809394-0.271321588395-0.0425903734108-0.3784647371960.324551255158-0.01181150684620.01293539156170.331449862922-0.005050572062380.48995136823716.2336067691-8.3312987386-3.91466620653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 147 )
7X-RAY DIFFRACTION7chain 'C' and (resid -1 through 7 )
8X-RAY DIFFRACTION8chain 'C' and (resid 8 through 17 )
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 44 )
10X-RAY DIFFRACTION10chain 'C' and (resid 45 through 72 )

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