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- PDB-7uy2: Structure of RNF31 in complex with FP06649, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uy2
TitleStructure of RNF31 in complex with FP06649, a Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase RNF31
  • Helicon FP06649
KeywordsLIGASE / Inhibitor / complex / stapled
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of NF-kappaB transcription factor activity / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : ...E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
AMINO GROUP / N,N'-(1,4-phenylene)diacetamide / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsAgarwal, S. / Thomson, T. / Wahl, S. / Walkup, W. / Olsen, T. / Verdine, G. / McGee, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: Helicon FP06649
D: Helicon FP06649
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0338
Polymers44,6164
Non-polymers4164
Water27015
1
A: E3 ubiquitin-protein ligase RNF31
C: Helicon FP06649
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5164
Polymers22,3082
Non-polymers2082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area10040 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase RNF31
D: Helicon FP06649
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5164
Polymers22,3082
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.420, 49.420, 267.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61

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Components

#1: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin- ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 20771.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Helicon FP06649


Mass: 1536.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Stapled peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 37.5% Precipitant Mix 4 (25% v/v ...Details: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.51→42.8 Å / Num. obs: 12531 / % possible obs: 99.79 % / Redundancy: 11.8 % / Biso Wilson estimate: 50.77 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.192 / Net I/σ(I): 10
Reflection shellResolution: 2.51→2.6 Å / Num. unique obs: 1268 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
PHASERphasing
XSCALEdata scaling
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DBG

4dbg


Resolution: 2.51→42.8 Å / SU ML: 0.2642 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.8684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 606 4.84 %RANDOM
Rwork0.2114 11922 --
obs0.2142 12528 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.82 Å2
Refinement stepCycle: LAST / Resolution: 2.51→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 30 15 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193070
X-RAY DIFFRACTIONf_angle_d0.54874165
X-RAY DIFFRACTIONf_chiral_restr0.0333466
X-RAY DIFFRACTIONf_plane_restr0.0038555
X-RAY DIFFRACTIONf_dihedral_angle_d3.5865424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.760.31871590.27092985X-RAY DIFFRACTION99.9
2.76-3.160.30421310.2532979X-RAY DIFFRACTION99.84
3.16-3.980.27591660.20872964X-RAY DIFFRACTION99.9
3.99-42.80.24331500.18872994X-RAY DIFFRACTION99.56
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)
15.692634042450.8827846808622.295643256634.10682195536-2.622043827523.41773514832-0.848904878622-0.7294343888961.24025083764-0.3099577203850.6435000508510.845709534235-1.13193369747-1.655255350810.3452118967350.683480491750.100417758048-0.2276376496670.539311840243-0.03306686461350.653352713844-30.5062492792-5.7282335142-32.9723618128
26.03029092270.65524676171-3.405154710413.26474786754-1.556468880229.275504203110.292120494540.5690802449790.1881868964720.803553137917-0.515959371950.0528166624175-1.84265567798-0.9952344778940.1747556781010.768626535444-0.0836952263126-0.03077906866340.5857283010160.02114754860.3196080512841.1551980603911.9479823414-0.719702398843
33.326389141150.05857799927183.329694470999.11735202166-0.2154867255913.469802205140.6580102357941.21430338495-1.58799610055-0.01813851952011.208329105550.9473760382161.327047186240.858236679142-1.512613085220.8463133503030.0697117925763-0.009519144182570.9476969652830.06211412401170.77155111297-11.9643059945-28.4430283995-26.093788126
45.62932010008-0.964518201679-1.261347735610.7001161344862.201815667427.0367149323-0.05729065536220.440999215919-0.4589025602790.193624183152-0.2771165552920.3582669178640.249899389618-0.853936039220.3010576003060.452913885273-0.0117164678112-0.05543384257380.430875383887-0.07991036315580.354278218825-23.3350178487-3.19723689463-5.64901086519
52.62978250983-0.8174079738680.5861344240452.747762384591.820805594722.711069610910.101703276241-0.0565197743994-0.4974630114510.3780482575370.003965518432320.2354031056390.158600690693-0.3184717647390.06450820400910.4168908524160.009775364714340.01535169632380.4342721653860.005073601788330.327183624676-16.0832054353-1.880071953835.36323470113
64.73482901604-0.6519959381270.5052639831263.94515567974-0.4026370709952.90912118608-0.164137875160.1195523949720.05688849507080.107697450176-0.173481368711-0.453529998951-0.3296420543180.7642961787220.2376084528040.381739960018-0.0478160169424-0.04374386440470.3161429522680.04287467987260.329165902184-1.514230150773.09631931482-0.00994150723517
74.90552780154-2.617816668-2.064881507626.03333594817-0.4253538958756.549630174590.6712515309840.809484218007-0.138534261672-0.323947963626-0.0318354265164-0.2268911602711.195806349890.675212236168-0.5695478673690.5643528085220.0300457413948-0.03714814565230.690731195678-0.08718918250760.5727377081312.39837094484-4.72097732108-11.667200105
84.46555196895-0.8846364888-0.1242674890052.816022258452.542643224075.09178168641-0.252207154585-0.419947812321-0.1876265766890.4459415401050.1104582580760.402858071092-0.159041032284-0.4397664216860.05778146867660.430112089750.045975978955-0.01696339179270.3225170847840.02755853141120.29605956848-16.26001812860.3501502477727.31171818953
95.92296351464-1.485843536090.9914826855719.515346449490.09935913794833.93162238144-0.313136662252-0.6386845425941.066600807972.2453888429-0.0318051338045-0.984330232887-0.371522792089-0.4887072651690.01639461770910.448437829236-0.02745625635840.04041911206740.569841601556-0.08008880960940.511870454751-28.3212846041-8.8739363864-10.9433171222
103.882638530890.9027455984941.249867561243.84075671660.7472282500092.581537944210.0739748991849-0.2068769136980.1478686650430.0684158211995-0.235784970338-0.0964753559960.11018684858-0.06975042632380.04675786468410.4220891127220.002423862231760.03867050137950.553320163708-0.03849374689470.339534671273-27.1547517717-11.2210885942-19.5898000146
118.66243250724-0.3367039102260.8791438134826.17135353601-0.08589409602477.65727842705-0.2239386412380.87601164471-0.232399637114-1.83865674389-0.184983459105-0.668237484940.0417109642941.31852041310.8220675509320.881827432357-0.1348814426670.08613721596880.463141534253-0.002383129058020.506078036899-15.0508861975-6.37197579451-34.0022053373
122.36658493613-0.959587845206-0.5532894225033.66124830939-1.361548472175.88207005041-0.07582156864650.32877720357-0.309732348602-0.8670010483190.332875121114-0.2972667239650.643072795669-0.605978624441-0.2657333734650.554451381681-0.1202386373790.07851089813640.373559485369-0.08454486279610.418382115445-16.7372744308-18.3944174255-28.172812617
138.95995840883-3.406900044561.054412373825.038260821692.63608141495.20416271691-0.5801060622671.90837706762-0.2119385402130.6542611961420.423914865108-1.073582821351.710241873530.8428333875740.1218962185470.6276473869470.04307558387730.03186777383250.9512434763190.02763684569950.666370420556-8.91551252294-27.4828302667-11.5122965482
146.33103260482-0.500121173651-1.74238000365.49775460209-1.331079326035.26185236449-0.0341229309133-0.0649947112842-0.906646704698-1.3189809717-0.0843740935106-1.07756278790.6848006515861.073587496470.1487031065290.692160145922-0.05453294763950.18874030190.656432603833-0.1243049820530.842233617493-3.27010976264-23.1937424283-27.3498936424
151.73677341096-0.525193569448-0.995357426011.13258379899-0.4966114214723.539014315740.003847297263550.0007839771330260.197833698074-0.03089980808420.208153750366-0.6232064626860.2597266513721.1516262221-0.2911552787610.458847817035-0.06886683289290.1327650004590.533257378937-0.09947264648370.748704452559-8.19511988139-14.053841119-24.9897788393
163.3916055647-0.89631668757-1.691684536650.2849462337790.5279185008340.9019493842710.241899682805-0.710779162584-0.315793179764-0.4577446858910.429099071887-0.428214514033-0.560459505360.990935951047-0.3385214519610.515651424546-0.03850075738-0.02289487359191.02102885398-0.1212185008280.6997109817480.435333278591-16.4838503316-17.9843184441
172.75979690609-1.92153870933-1.42288334011.578032551181.198211127030.929808746335-0.519975675174-0.1129502754880.04763139235650.5530991845470.491093672524-0.5561569621690.5338847171790.835778921816-0.1432217717940.5880301500760.0543398468115-0.1282711685311.18312438571-0.1004773992610.72535991394-4.90109408758-17.888185901-7.03355878508
184.146056408260.46230817283-1.841289172064.669583669711.708980239853.858001016410.0664578375648-0.228566018928-0.1612246982160.1785008108320.1847260838370.2613137314270.416764364478-0.0527853119436-0.09519313582940.28750854685-0.002634080795470.04150455171320.2985374050610.01280631079890.278683558519-22.1634087456-14.0888176651-21.7553409382
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 166 through 177 )BB166 - 177163 - 174
22chain 'C' and (resid 4 through 17 )CC4 - 171 - 14
33chain 'D' and (resid 4 through 17 )DF4 - 171 - 14
44chain 'A' and (resid 3 through 23 )AA3 - 231 - 21
55chain 'A' and (resid 24 through 64 )AA24 - 6422 - 62
66chain 'A' and (resid 65 through 122 )AA65 - 12263 - 120
77chain 'A' and (resid 123 through 142 )AA123 - 142121 - 140
88chain 'A' and (resid 143 through 177 )AA143 - 177141 - 175
99chain 'B' and (resid 4 through 23 )BB4 - 231 - 20
1010chain 'B' and (resid 24 through 52 )BB24 - 5221 - 49
1111chain 'B' and (resid 53 through 64 )BB53 - 6450 - 61
1212chain 'B' and (resid 65 through 86 )BB65 - 8662 - 83
1313chain 'B' and (resid 87 through 96 )BB87 - 9684 - 93
1414chain 'B' and (resid 97 through 106 )BB97 - 10694 - 103
1515chain 'B' and (resid 107 through 122 )BB107 - 122104 - 119
1616chain 'B' and (resid 123 through 133 )BB123 - 133120 - 130
1717chain 'B' and (resid 134 through 142 )BB134 - 142131 - 139
1818chain 'B' and (resid 143 through 165 )BB143 - 165140 - 162

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