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- PDB-7uyj: Structure of RNF31 in complex with FP06652, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uyj
TitleStructure of RNF31 in complex with FP06652, a Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase RNF31
  • Helicon FP06652
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 / : / 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: 2.32 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 FP06652
D: Helicon FP06652
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7568
Polymers45,3394
Non-polymers4164
Water46826
1
A: E3 ubiquitin-protein ligase RNF31
C: Helicon FP06652
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8784
Polymers22,6702
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-11 kcal/mol
Surface area10180 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase RNF31
D: Helicon FP06652
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8784
Polymers22,6702
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-12 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.370, 95.370, 93.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z

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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 FP06652


Mass: 1898.186 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: obtained synthetically / Formula: C10H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Amino Acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine),0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) ...Details: 0.1 M Amino Acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine),0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 30.0% Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

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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: 2.32→61.8 Å / Num. obs: 21131 / % possible obs: 99.84 % / Redundancy: 11.5 % / Biso Wilson estimate: 50.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.7
Reflection shellResolution: 2.32→2.4 Å / Num. unique obs: 2105 / CC1/2: 0.576

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Processing

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

4dbg


Resolution: 2.32→61.8 Å / SU ML: 0.4124 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.3817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 1054 4.99 %
Rwork0.2176 20074 -
obs0.2203 21128 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.08 Å2
Refinement stepCycle: LAST / Resolution: 2.32→61.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 30 26 3072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283100
X-RAY DIFFRACTIONf_angle_d0.63294207
X-RAY DIFFRACTIONf_chiral_restr0.035462
X-RAY DIFFRACTIONf_plane_restr0.0058563
X-RAY DIFFRACTIONf_dihedral_angle_d4.8632426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.430.39091250.31042505X-RAY DIFFRACTION99.96
2.43-2.550.35871200.29142494X-RAY DIFFRACTION99.89
2.55-2.710.35891480.28692483X-RAY DIFFRACTION99.92
2.71-2.920.30671520.25342450X-RAY DIFFRACTION99.77
2.92-3.220.26671340.25822503X-RAY DIFFRACTION99.89
3.22-3.680.29091350.22792505X-RAY DIFFRACTION99.7
3.68-4.640.2341150.18422535X-RAY DIFFRACTION99.77
4.64-61.80.24191250.18442599X-RAY DIFFRACTION99.85
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)
19.244858578035.805278934376.436879672273.829654605434.46919759596.08033167922-0.699853759930.1755622602240.47475483108-0.2624411480910.1936309465521.134865431090.062354420713-0.4374274950030.4723744409780.380650529828-0.09912544235790.05953990493310.708802176118-0.07262465984150.56396956103313.0651159877-19.06333413737.76946357129
26.504513282341.77056686434-0.3784309723912.520317410360.1782254000032.56150481756-0.1504170128990.273399352499-0.2553986502990.1007728498680.1011273251290.05544800563530.1981418375520.1985265880880.1218310950080.329094544878-0.009732894925350.005868227174040.503234252423-0.05575738699120.28543730389429.6712348373-20.06615301029.29483672309
37.439550982453.126156173152.614295039044.42383865619-1.57389330033.97419183334-0.5224900424681.89263885399-0.129935528523-0.8744909675970.420196846375-0.3826289013310.3886477001260.171995968523-0.09982014740180.370951477551-0.06078760893460.09506197039390.762243328655-0.05967289817490.38516244074744.0704649397-16.6130013913.80656243362
47.249957211020.740440208819-2.144093314684.92111942841-2.302017596337.25784153225-0.5566710299140.874238401412-0.220655990012-0.7882382674290.5007304263860.1902018443270.489384473135-0.3356361952670.01775288450960.341547124028-0.08939366890830.002433153463170.632879118525-0.1129118494140.33130537025629.5396034071-19.42221512474.630306978
57.36086022616-6.25558469741-2.861325735159.464839958273.670517075731.48622674121-0.580046042351-0.6861810104550.09270941986120.1213630270270.3089573006060.279943701151-0.115898895859-0.8741913760070.2493663913260.5388756794660.2207038629550.06660587935130.609536086599-0.02143049531330.69273113528216.65792629812.290682665932.7062178801
69.30530766258-5.25441990973-2.394869731953.543672201382.78189573834.084419084210.7005042100291.07321419352-1.32341123751-0.329004601633-0.8153946190171.157643810370.501775520197-0.7868669061020.3851167145330.4829308533650.02964858572310.04413238816520.639272318893-0.08034159033380.75337179829118.69113859262.4165700560126.4020816814
79.83820831269-5.9713318834-1.484619856618.139526447232.846003301833.471280944850.3687639772321.670603839471.42914524204-1.61297201063-0.2067879953920.374796533957-1.01859196746-0.481057376314-0.1768957888740.9829892966620.3498586848650.1848051486180.8137101595670.251375008660.75041303514722.040874110117.686361695922.880758854
85.18973712906-0.339397726209-0.0628175642094.741040925660.02790868700896.331013768070.2638186627771.068349832860.468417934127-0.4934551684120.3438001172840.162813138136-0.641273036847-0.368260114354-0.2374777253450.4094145880970.1416361528430.09065452401280.5766403252660.0855757200710.49011073452233.5672873188.4866714026317.5613049305
96.049284971561.25744581092-0.8608555179035.30935431122-1.993866357594.92249079169-0.405509428565-0.412241233907-0.5852204307120.524834735044-0.185849282672-0.521032307490.201537803519-0.116067837496-0.09057208745320.5090021016970.0564814006431-0.007336123505320.584581338468-0.04510568085910.54242228866243.73702627682.6466713019234.6060146781
104.65674655702-1.51006794482-3.167049248923.575893431941.503949486858.286327765460.4820894344080.2939561856230.729250929738-0.4894259915-0.171613856947-0.200514096193-1.261931813380.01990202071-0.4396949518650.41982456997-0.02042536191410.08408968005550.3187619393910.00662331024610.45351585591941.5925605910.098520980922.640223198
114.10320220542-1.13849134499-0.7252930651363.698237567991.379329094737.621392480190.141434030829-0.5333020800510.460314600440.3692564105390.1799848269470.0251784979283-0.7609157786270.121419708323-0.2374707561980.5506998148890.04692348541850.09349080835460.3140917339790.02079603782020.49613959389534.54574813110.506442725830.4672352483
122.63339753521-1.56011154712-0.04185938659271.04609587639-0.03699888744120.1222676115890.5351624425741.57249761298-0.5382391073180.339515709965-0.4824831053831.22941576207-0.813670588477-1.405415664670.1006325534230.9528744534940.1447110904350.006285309971611.60903585382-0.1781649742521.1624334562716.3786576658.5189227796411.74170362
135.43063338874-4.612314605615.900314256694.01653262764-5.37435222689.67521299993-0.01503915310160.2502542786060.102309064301-0.1248949420110.7211118307160.9794251425440.109670713915-0.433355427637-0.1205920413920.316578016328-0.04837298644140.03599469676610.4501571605240.0002700842999910.4540313560440.3743193283-9.2670526341413.0749502447
143.5527686941-0.8465179544542.483645829666.700749028122.419986473099.6204062515-0.203142282115-0.075315508763-0.2541199511890.4754360422410.393618590894-0.01400374417430.6406407330870.4746355455850.05971699858610.2695542548720.07598888725930.04472487890940.567361307697-0.03463526528850.57113224981640.246065835-3.6827666775325.2436619043
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 23 )AA3 - 231 - 21
22chain 'A' and (resid 24 through 96 )AA24 - 9622 - 94
33chain 'A' and (resid 97 through 114 )AA97 - 11495 - 112
44chain 'A' and (resid 115 through 177 )AA115 - 177113 - 175
55chain 'B' and (resid 3 through 23 )BB3 - 231 - 21
66chain 'B' and (resid 24 through 38 )BB24 - 3822 - 36
77chain 'B' and (resid 39 through 52 )BB39 - 5237 - 50
88chain 'B' and (resid 53 through 87 )BB53 - 8751 - 85
99chain 'B' and (resid 88 through 102 )BB88 - 10286 - 100
1010chain 'B' and (resid 103 through 122 )BB103 - 122101 - 120
1111chain 'B' and (resid 123 through 164 )BB123 - 164121 - 162
1212chain 'B' and (resid 165 through 171 )BB165 - 171163 - 169
1313chain 'C' and (resid 1 through 17 )CC1 - 171 - 17
1414chain 'D' and (resid 1 through 17 )DF1 - 171 - 17

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