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- PDB-7npo: Branched K48-K63-Ub3 -

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Basic information

Entry
Database: PDB / ID: 7npo
TitleBranched K48-K63-Ub3
Components(Polyubiquitin-B) x 2
KeywordsSIGNALING PROTEIN / Branched ubiquitin chains / heterotypic ubiquitin chains / K48-K63-Triubiquitin / K48-K63-Ub3
Function / homology
Function and homology information


Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLange, S.M. / Kwasna, D. / Kulathu, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains.
Authors: Lange, S.M. / McFarland, M.R. / Lamoliatte, F. / Carroll, T. / Krshnan, L. / Perez-Rafols, A. / Kwasna, D. / Shen, L. / Wallace, I. / Cole, I. / Armstrong, L.A. / Knebel, A. / Johnson, C. / ...Authors: Lange, S.M. / McFarland, M.R. / Lamoliatte, F. / Carroll, T. / Krshnan, L. / Perez-Rafols, A. / Kwasna, D. / Shen, L. / Wallace, I. / Cole, I. / Armstrong, L.A. / Knebel, A. / Johnson, C. / De Cesare, V. / Kulathu, Y.
History
DepositionFeb 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B
B: Polyubiquitin-B
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5504
Polymers25,4583
Non-polymers921
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Two ubiquitin K48R K63R molecules are linked with the C-terminal Gly residue to the K48 and K63 residues of a third ubiquitin with C-terminal truncation (1-72).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-2 kcal/mol
Surface area12320 Å2
Unit cell
Length a, b, c (Å)59.630, 77.570, 50.610
Angle α, β, γ (deg.)90.000, 123.975, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-101-

GOL

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Components

#1: Protein Polyubiquitin-B


Mass: 8192.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3QS39
#2: Protein Polyubiquitin-B


Mass: 8632.859 Da / Num. of mol.: 2 / Mutation: K48R K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3QS39
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.48 % / Description: Round plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 20 mM Tris pH 7.5, 50 mM NaCl, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v PEG 4000; 22 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.19→24.73 Å / Num. obs: 9868 / % possible obs: 99.58 % / Redundancy: 2 % / Biso Wilson estimate: 45.93 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 8.8
Reflection shellResolution: 2.19→2.268 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1910 / CC1/2: 0.843 / CC star: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
MxCuBEdata collection
pointlessdata scaling
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 2.19→24.73 Å / SU ML: 0.3248 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.0506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 459 4.65 %
Rwork0.224 9403 -
obs0.2269 9862 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.17 Å2
Refinement stepCycle: LAST / Resolution: 2.19→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 6 25 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251766
X-RAY DIFFRACTIONf_angle_d0.56632380
X-RAY DIFFRACTIONf_chiral_restr0.0432285
X-RAY DIFFRACTIONf_plane_restr0.0059308
X-RAY DIFFRACTIONf_dihedral_angle_d5.3267239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.510.36111400.32773121X-RAY DIFFRACTION99.36
2.51-3.160.37151320.29833149X-RAY DIFFRACTION99.91
3.16-24.730.2521870.18343133X-RAY DIFFRACTION99.61
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)
18.40763364256-8.70636489938-1.72593705589.201364284122.010923039293.649545882710.902073259126-0.540416751363-1.004355061112.53338994751-1.140712184350.444857242577-1.667952909750.1617924057030.5939332692211.111141389470.111686669528-0.05448672075350.7181384617490.1076391403471.3604100260525.5847037565-8.32174751234-5.94745313821
27.449748654591.780861705813.574630782968.909910964754.189189516548.06323020398-0.4836883912771.14297454704-0.943320018193-0.1130385247820.734824895897-1.170352182450.5368770371341.0587921968-0.2235966606550.3310342540070.0605017106637-0.005779850431150.3639855515510.0161651353090.46409161586424.19529192456.300097611235.18215646445
32.838147867940.6974240620062.882462961422.55495272922-0.2597732539163.34570915644-0.17475223791-1.64459812325-0.9445921670010.8153431090860.0150603906311-0.2392277266531.015141250750.8214216853550.2520947980690.4730108674270.1477300049360.04093895122820.7841156356830.1655936650410.54499270330722.98599748954.5426091012813.9783129726
42.150607791210.753050369112-0.02556111725968.34489711234.21489340872.242334357750.0624533238832-0.878640592511.305738416531.66650228141-0.4972828045480.6205607757380.5019663409380.5775652373980.1731003747070.34597926536-0.103874327589-0.03006459915260.7094738560470.09286421530110.51439294296722.939893033812.316554206316.8618466572
54.14179633456-0.8032769129111.327181354819.72643873372.33440666.95507617342-0.392043170599-0.6505993339060.04322662829190.6643162553830.2399670882260.639478931054-0.0094228699770.4412124210760.1519714006780.221753520585-0.0419476665247-0.02631133290070.4327934159720.09989188698040.49657976182213.287106909712.68369931518.70087013146
65.57550718642-0.6605268070013.774085816778.839649398651.576185359433.455666011850.239669297837-0.390910715514-0.300093839558-0.328738194422-0.1564898151680.166481292692-0.02920502392140.0652901881892-0.1775489625250.250888390924-0.03242011096310.02932423047480.4447329410170.1164618139850.28998203414718.896331974310.58203191774.05141382467
73.59738020803-3.00797344498-2.738735987093.83634013044.555795987517.603193545760.1881646319990.5241129388160.777376501354-0.7634932775810.0296407115375-2.10124968887-1.785553495571.31558404612-0.6386015060171.01388306341-0.304794784245-0.3613653103010.6057250115250.3138636187650.91450183473424.403026074433.60853625414.52243805856
81.225549184510.1802574373521.165535564079.491613502531.633020285321.63381084646-0.2161983730160.166861480140.0081097349467-1.459749353371.18778344572-0.83380798574-1.346391375031.48578487805-0.976531693261.3466032742-0.1148605023220.2719503726681.063347229170.1270445661660.96764236232425.238965144640.306547021817.8221630322
94.31080990062-1.25386517061-2.296796580476.31649599075-0.2361357656494.90601797944-0.400965037813-0.1542183137271.19521124534-0.242872621545-0.4387241544080.163493040624-1.654904168310.1761886900160.7915182272450.906101089788-0.045194214168-0.3959133211110.4451111412220.018536999870.88725540133620.154050587230.786521122614.4411908417
103.186903387952.87858629572-2.243664300873.75083769616-2.415344032481.693248326840.4592130902020.0603352410367-1.009191500430.3885265873480.673080108987-0.7685434274991.52387897349-0.8076435646220.1953332839070.84193445574-1.18397001212-0.6541470829940.540003003856-0.0450298111210.94239662702133.699562894535.788979216411.2654394691
114.785636978184.622129387650.4685747994635.734093221332.749004814266.48722004604-0.578651841607-0.1791372873470.6885410245120.886577115024-0.509055346112-0.116063308443-1.93480621792-0.4776756565440.6514301805690.607723506521-0.0591690331622-0.3282325541190.4845810446520.03785228251430.84497669704616.487737020323.38071543039.65601023664
127.270972476092.42248718192-7.527775042975.14941630595-1.037769240419.200781698651.262118127830.7033210628520.237277766073-0.709224275264-0.7250305550510.122327475904-0.172730838242-0.152065603438-0.3153388922760.303085036102-0.0448394879782-0.04034979367520.4700720564230.06825684592870.3212160773537.4696243349-27.4431685335-10.6788810299
138.18855787924-0.663279173789-6.14597855724.44567094338-1.317646236486.92720739222-0.7774995856810.109039239003-0.547736742527-0.255932717066-0.2956550446380.3741245386320.803227713039-0.5214565252710.8163964233290.405234601787-0.0190159272928-0.06907571207180.7081317970710.01807291538550.42445592498931.9720696499-26.7496165831-11.6835549486
147.49531571489-2.93795077331.596703567454.833259411682.313255962168.091531676210.1985698848930.8768346322340.396304774897-0.626552051145-0.355830276614-0.533618454525-0.1967441501840.3637954926190.1728896866480.402675671224-0.0192640451417-0.0639211063210.6499529004050.1819366703790.4481078864539.5497508023-18.1584144675-15.3357693515
158.22252360608-3.791484974323.867818899017.56236217856-1.242610080392.19119584837-0.183678552359-0.4088925182211.099751566950.1322720458770.3917056332781.66739175132-1.2293074366-2.19203658818-0.04725225648930.5690193325870.128905185951-0.09477885126270.7707515327560.05683136798670.69462911330131.3389485992-14.274865927-9.44460502301
165.82077265492-1.636747191840.04694164274969.584000988130.7462585147187.230857319630.17927164785-0.1487180361471.459336203110.06058106149430.00907381872009-0.351085963913-0.6927146538380.3797144529520.1639647378120.29210407881-0.0408156281185-0.0781347711110.5401882125390.06972094844970.55802350965742.3525236741-16.332048587-3.63894037622
172.22300347227-0.2943433334220.6403803443174.34736068671.3416864622.361736756470.4378262215550.946947243419-0.0759726622471-0.385778268736-0.228500289394-2.319114978720.502740097211.405612725760.03791681547910.4883485279990.080882224556-0.04543226246820.6141598297780.04533689367140.46834637343346.9425586675-25.0738175548-6.40476673246
186.17053485052-2.65745172258-2.299093867697.635578130972.476357426624.68334670188-0.7038073926370.187675119053-0.271673620955-0.7463328793270.2104088348540.6988646690970.63005719398-1.00501353180.3000228455730.310529195504-0.0118497519271-0.05201019321550.568690077691-0.04573057714430.33051328157933.847077729-22.6927194655-5.51148697444
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 72 through 76 )CC72 - 7672 - 76
22chain 'A' and (resid 1 through 22 )AA1 - 221 - 22
33chain 'A' and (resid 23 through 34 )AA23 - 3423 - 34
44chain 'A' and (resid 35 through 44 )AA35 - 4435 - 44
55chain 'A' and (resid 45 through 56 )AA45 - 5645 - 56
66chain 'A' and (resid 57 through 72 )AA57 - 7257 - 72
77chain 'B' and (resid 1 through 16 )BB1 - 161 - 16
88chain 'B' and (resid 17 through 22 )BB17 - 2217 - 22
99chain 'B' and (resid 23 through 59 )BB23 - 5923 - 59
1010chain 'B' and (resid 60 through 65 )BB60 - 6560 - 65
1111chain 'B' and (resid 66 through 76 )BB66 - 7666 - 76
1212chain 'C' and (resid 1 through 7 )CC1 - 71 - 7
1313chain 'C' and (resid 8 through 16 )CC8 - 168 - 16
1414chain 'C' and (resid 17 through 34 )CC17 - 3417 - 34
1515chain 'C' and (resid 35 through 44 )CC35 - 4435 - 44
1616chain 'C' and (resid 45 through 56 )CC45 - 5645 - 56
1717chain 'C' and (resid 57 through 64 )CC57 - 6457 - 64
1818chain 'C' and (resid 65 through 71 )CC65 - 7165 - 71

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