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- PDB-6kc6: HOIP-HOIPIN8 complex -

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Basic information

Entry
Database: PDB / ID: 6kc6
TitleHOIP-HOIPIN8 complex
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsLIGASE / UBIQUITIN / E3 / INHIBITOR COMPLEX
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor 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-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-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-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger 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 signature. / Zinc finger, RanBP2-type superfamily / 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
Chem-D60 / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.123 Å
AuthorsSato, Y. / Fukai, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H06575 Japan
Japan Society for the Promotion of Science18H02619 Japan
Japan Society for the Promotion of Science18H05501 Japan
Japan Society for the Promotion of Science18K06967 Japan
19H05296 Japan
CitationJournal: Commun Biol / Year: 2020
Title: Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses.
Authors: Oikawa, D. / Sato, Y. / Ohtake, F. / Komakura, K. / Hanada, K. / Sugawara, K. / Terawaki, S. / Mizukami, Y. / Phuong, H.T. / Iio, K. / Obika, S. / Fukushi, M. / Irie, T. / Tsuruta, D. / ...Authors: Oikawa, D. / Sato, Y. / Ohtake, F. / Komakura, K. / Hanada, K. / Sugawara, K. / Terawaki, S. / Mizukami, Y. / Phuong, H.T. / Iio, K. / Obika, S. / Fukushi, M. / Irie, T. / Tsuruta, D. / Sakamoto, S. / Tanaka, K. / Saeki, Y. / Fukai, S. / Tokunaga, F.
History
DepositionJun 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
E: E3 ubiquitin-protein ligase RNF31
G: E3 ubiquitin-protein ligase RNF31
I: E3 ubiquitin-protein ligase RNF31
K: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,64255
Polymers152,2146
Non-polymers5,42849
Water4,846269
1
A: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,35811
Polymers25,3691
Non-polymers98910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-27 kcal/mol
Surface area12440 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,37910
Polymers25,3691
Non-polymers1,0109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area12530 Å2
MethodPISA
3
E: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2879
Polymers25,3691
Non-polymers9188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area12570 Å2
MethodPISA
4
G: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1958
Polymers25,3691
Non-polymers8267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area12340 Å2
MethodPISA
5
I: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1388
Polymers25,3691
Non-polymers7697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-18 kcal/mol
Surface area12400 Å2
MethodPISA
6
K: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2879
Polymers25,3691
Non-polymers9188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.586, 88.793, 104.438
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11K-1240-

HOH

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Components

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Protein , 1 types, 6 molecules ACEGIK

#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: 25369.004 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 318 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-D60 / 2-[3-[2,6-bis(fluoranyl)-4-(1~{H}-pyrazol-4-yl)phenyl]-3-oxidanylidene-propyl]-4-(1-methylpyrazol-4-yl)benzoic acid


Mass: 436.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H18F2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200 mM KCl, 20% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 76335 / % possible obs: 99.3 % / Redundancy: 7.04 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.45
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.783 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 12178 / CC1/2: 0.585 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJQ

4ljq


Resolution: 2.123→46.59 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.6
RfactorNum. reflection% reflection
Rfree0.2665 3807 5 %
Rwork0.2112 --
obs0.2139 76185 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.123→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9385 0 285 269 9939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019891
X-RAY DIFFRACTIONf_angle_d1.18313392
X-RAY DIFFRACTIONf_dihedral_angle_d16.23800
X-RAY DIFFRACTIONf_chiral_restr0.0421346
X-RAY DIFFRACTIONf_plane_restr0.0061777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.123-2.14990.39251370.38212597X-RAY DIFFRACTION97
2.1499-2.17820.36651390.34462640X-RAY DIFFRACTION98
2.1782-2.2080.35941390.32012646X-RAY DIFFRACTION99
2.208-2.23950.36451410.30672677X-RAY DIFFRACTION99
2.2395-2.2730.33591400.2942657X-RAY DIFFRACTION98
2.273-2.30850.38861410.27572681X-RAY DIFFRACTION99
2.3085-2.34630.33141360.26682614X-RAY DIFFRACTION98
2.3463-2.38680.33091410.27122680X-RAY DIFFRACTION99
2.3868-2.43020.31341410.25642680X-RAY DIFFRACTION99
2.4302-2.47690.32431380.24862632X-RAY DIFFRACTION99
2.4769-2.52750.31251400.2462696X-RAY DIFFRACTION99
2.5275-2.58240.32691410.24632670X-RAY DIFFRACTION99
2.5824-2.64250.28761400.25082658X-RAY DIFFRACTION99
2.6425-2.70860.34031410.24912674X-RAY DIFFRACTION99
2.7086-2.78180.33331420.23262683X-RAY DIFFRACTION99
2.7818-2.86370.29871410.22642677X-RAY DIFFRACTION99
2.8637-2.95610.28141420.21532700X-RAY DIFFRACTION100
2.9561-3.06170.26751410.21442683X-RAY DIFFRACTION100
3.0617-3.18430.2851420.22662691X-RAY DIFFRACTION100
3.1843-3.32920.27211410.22232684X-RAY DIFFRACTION100
3.3292-3.50460.26991440.21442734X-RAY DIFFRACTION100
3.5046-3.72410.30181400.20412675X-RAY DIFFRACTION100
3.7241-4.01150.24521440.18762731X-RAY DIFFRACTION100
4.0115-4.41490.23711420.18312708X-RAY DIFFRACTION100
4.4149-5.05310.21271440.17782716X-RAY DIFFRACTION100
5.0531-6.36380.2131440.18962737X-RAY DIFFRACTION100
6.3638-46.6010.22131450.17452757X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -42.9052 Å / Origin y: -21.7768 Å / Origin z: 25.3462 Å
111213212223313233
T0.3421 Å2-0.0044 Å2-0.0213 Å2-0.3683 Å20.0264 Å2--0.4052 Å2
L0.0411 °2-0.1293 °2-0.1648 °2-0.3177 °20.0675 °2--0.076 °2
S0.009 Å °-0.0276 Å °-0.032 Å °-0.0001 Å °0.0262 Å °0.0045 Å °0.0097 Å °0.0011 Å °-0.0235 Å °
Refinement TLS groupSelection details: all

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