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- PDB-7uyk: Structure of RNF31 in complex with FP06655, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uyk
TitleStructure of RNF31 in complex with FP06655, a Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase RNF31
  • Helicon FP06655
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: 2.7 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
D: Helicon FP06655
C: Helicon FP06655
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4608
Polymers41,0444
Non-polymers4164
Water18010
1
A: E3 ubiquitin-protein ligase RNF31
C: Helicon FP06655
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7304
Polymers20,5222
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RNF31
D: Helicon FP06655
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7304
Polymers20,5222
Non-polymers2082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.730, 70.140, 89.220
Angle α, β, γ (deg.)90.000, 134.180, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 489 through 626)
d_2ens_1chain "B"
d_1ens_2(chain "C" and (resid 1 through 17 or resid 18))
d_2ens_2(chain "D" and (resid 1 through 17 or resid 18))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUASPA3 - 140
d_21ens_1LEUASPB1 - 138
d_11ens_2ASPSERF1 - 17
d_21ens_2ASPSERC1 - 17

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.0253722981634, -0.00353915438078, 0.999671806581), (-0.00139910577871, -0.999992879482, -0.00350478089721), (0.99967709236, -0.00130972225548, -0.0253770691509)-31.2552819403, -47.5392687437, 31.9035837233
2given(0.0304575205755, 0.00162348892664, 0.99953474363), (-0.00117978002998, -0.99999792594, 0.00166019114847), (0.999535365837, -0.00122979643587, -0.030455542045)-30.8976187854, -47.5589385718, 31.9369184775

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Components

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


Mass: 18687.729 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, RBR-type E3 ubiquitin transferase
#2: Protein/peptide Helicon FP06655


Mass: 1834.125 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
#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.: 10 / 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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 10% w/v glycerol, 20% w/v ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.7→44.61 Å / Num. obs: 15585 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 68.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.79 Å / Rmerge(I) obs: 0.81 / Num. unique obs: 1551 / CC1/2: 0.519

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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: 2.7→44.61 Å / SU ML: 0.3031 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 685 4.4 %
Rwork0.198 14894 -
obs0.2001 15579 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 30 10 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322533
X-RAY DIFFRACTIONf_angle_d0.70133415
X-RAY DIFFRACTIONf_chiral_restr0.0381355
X-RAY DIFFRACTIONf_plane_restr0.0053461
X-RAY DIFFRACTIONf_dihedral_angle_d18.455949
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.62677199736
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.339871135209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.31771520.27952943X-RAY DIFFRACTION99.71
2.91-3.20.3251080.25882963X-RAY DIFFRACTION99.64
3.2-3.660.28631540.21452965X-RAY DIFFRACTION99.62
3.66-4.620.21061200.18042995X-RAY DIFFRACTION99.55
4.62-44.610.22091510.17593028X-RAY DIFFRACTION99.13
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)
19.86970800875-4.176355745252.61174208212.065117399-1.200932501994.67879179874-0.232310046089-1.18200407058-0.0795109688470.5531931433380.568344712261.20606374526-0.218351492204-0.530330908971-0.4592352963480.745786296976-0.08421305217420.1763197564130.771909570050.007680007808630.854480467861-43.8528505764-25.754211260710.9757586751
28.55286156909-1.11644268393-0.1554707892223.9961491238-0.8781496513363.226040144760.096804883399-0.575316683046-0.154506163870.26674522011-0.089934547828-0.2903827571230.236029817340.3176708143230.04710355917880.481269321773-0.0730492712406-0.0003736737880330.4416096886940.00393252886950.441540843463-20.5266735438-34.69250022536.4054062297
37.804756544824.926972813280.6464231471913.985981000130.1060280510160.2178885066810.565716555411-1.114321337060.07836664338770.516452989301-0.22440742296-0.599876739031-0.151984782850.271247347403-0.3878805876330.635669801561-0.0663714669337-0.01376723193241.09647971425-0.09281053815230.7580787556431.52764019866-25.778101902410.9628938441
45.71088598565-2.862707707255.217433242075.861166691041.412678106168.40791350731-0.7297587902290.944647088896-1.33878505065-0.4913039661620.612256077676-0.07549496140160.6290318831521.901435175190.221606637361.05170394842-0.03834973275080.5549897273511.091645640610.03950972107611.07471597365-19.3045582756-27.7870716555-11.7736527269
58.629721364441.436696731980.6654538400559.811567713443.188308654552.01798750026-0.07822012539091.634810958441.15381740011-1.312166643430.398185960769-0.317953884016-1.054843116820.630743933052-0.3566548366130.8225844070220.04038529794640.2334309560320.7724276577910.1227903620920.647700455069-21.7596533411-16.7321746162-11.9699391835
64.589257817950.5451782886121.714542754433.411697310611.026650733249.944134552480.00932853071246-0.107153066661-0.186177617991-0.06121452441530.0323829440502-0.6076864340910.3769581959030.971823605402-0.1364411436280.4853723032980.05916366225290.04276233639750.4224429541830.09155874313420.470994584215-21.8173121929-16.10209950126.06632312917
79.704433394271.508909961522.187570265229.30402368517-1.457616070697.045255986080.127489064998-0.6009409351160.2635163052120.548882679137-0.1478037264490.00189577713878-0.1541179510590.09193536843240.03127120497270.420179669193-0.00974550622750.006887200799960.4662172387190.03077715901240.37627783422-30.5688651351-14.010083558.92789374207
85.503241218240.6650067464741.556472243355.29425282839-1.911556977372.02113533354-0.196282378409-0.5990191066840.3366000040530.78990355776-0.218398245750.0998688016368-1.21472520114-0.5288220733820.3271522201250.644664764563-0.0433464451481-0.01231025677690.51504861715-0.01782271936950.520355204872-26.1052565366-8.0035910238919.2540748582
98.447326662890.446032761488-0.5231984806046.88381426015-0.6147888760262.022652669990.233357265902-1.54531342970.07988044197761.00102520797-0.145935579282-0.2851677039320.450672793650.515930935839-0.06367604194490.641684094455-0.0449641540605-0.05838326931720.9369944786250.08359110625880.457558475534-20.7064569833-16.814683811926.5650893009
107.97242462974-3.489667933096.364335183292.08644709982-7.4941588142.07668910636-0.007370187766720.666986876637-0.112321349655-0.717628148732-0.709358871055-0.68668089771.424295255421.135772009031.136841563140.9704089765010.2090941438720.0307770917861.098489054450.0118576348330.851477725975-19.8310687133-25.053070709437.6304832793
112.013583494179.74025492803-2.013895962272.05329149509-1.03151495467.15106399818-0.04957021726670.8791775086641.06346307039-0.02408914795740.2547817190660.4544172670050.1688982049120.430709309124-0.1396624552020.4804334855580.1050950989080.05014610848230.4411907295820.1824717635560.757852349339-26.1581529831-12.4768195648-2.69231050786
128.32796578461-2.54889697132.235238218562.0609261594-7.128094145149.380515005890.166198664402-0.684163604989-0.212278287716-0.2862465868230.1582156427810.4352822299571.34937230371-1.20194924337-0.3391272725370.701065934815-0.1717123489290.03227840372710.459226489098-0.05080124785090.470923861591-34.4651025992-35.03403853325.86378271235
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 487 through 520 )AA487 - 5201 - 34
22chain 'A' and (resid 521 through 586 )AA521 - 58635 - 100
33chain 'A' and (resid 587 through 626 )AA587 - 626101 - 140
44chain 'B' and (resid 489 through 501 )BB489 - 5011 - 13
55chain 'B' and (resid 502 through 520 )BB502 - 52014 - 32
66chain 'B' and (resid 521 through 550 )BB521 - 55033 - 62
77chain 'B' and (resid 551 through 564 )BB551 - 56463 - 76
88chain 'B' and (resid 565 through 586 )BB565 - 58677 - 98
99chain 'B' and (resid 587 through 604 )BB587 - 60499 - 116
1010chain 'B' and (resid 605 through 626 )BB605 - 626117 - 138
1111chain 'D' and (resid 1 through 17 )DC1 - 171 - 17
1212chain 'C' and (resid 1 through 17 )CF1 - 171 - 17

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