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- PDB-9iic: Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain -

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Basic information

Entry
Database: PDB / ID: 9iic
TitleCrystal structure of HOIP RING2-LDD in complex with STK4 KD domain
Components
  • E3 ubiquitin-protein ligase RNF31
  • Serine/threonine-protein kinase 4 37kDa subunit
KeywordsLIGASE / HOIP / STK4 / E3 ligase / Phosphorylation
Function / homology
Function and homology information


positive regulation of hepatocyte apoptotic process / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / protein linear polyubiquitination / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / LUBAC complex / linear polyubiquitin binding / positive regulation of hippo signaling ...positive regulation of hepatocyte apoptotic process / regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / protein linear polyubiquitination / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / LUBAC complex / linear polyubiquitin binding / positive regulation of hippo signaling / RBR-type E3 ubiquitin transferase / positive regulation of substrate-dependent cell migration, cell attachment to substrate / CD40 signaling pathway / endocardium development / positive regulation of xenophagy / negative regulation of organ growth / CD40 receptor complex / hippo signaling / negative regulation of necroptotic process / Signaling by Hippo / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / organ growth / K63-linked polyubiquitin modification-dependent protein binding / branching involved in blood vessel morphogenesis / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / keratinocyte differentiation / positive regulation of peptidyl-serine phosphorylation / protein serine/threonine kinase activator activity / central nervous system development / epithelial cell proliferation / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / protein tetramerization / Regulation of TNFR1 signaling / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cytoplasmic side of plasma membrane / protein import into nucleus / protein polyubiquitination / negative regulation of epithelial cell proliferation / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell receptor signaling pathway / peptidyl-serine phosphorylation / positive regulation of protein phosphorylation / protein autophosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of canonical NF-kappaB signal transduction / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / intracellular signal transduction / defense response to bacterium / nuclear body / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / magnesium ion binding / signal transduction / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : ...Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / 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 / p53-like tetramerisation domain superfamily / 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 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase 4 / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsWang, Y.R. / Zhou, X.D. / Pan, L.F.
Funding support China, 5items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2022YFC2303102 China
National Natural Science Foundation of China (NSFC)32071219 China
National Natural Science Foundation of China (NSFC)92253301 China
National Natural Science Foundation of China (NSFC)21822705 China
National Natural Science Foundation of China (NSFC)32071297 China
CitationJournal: To Be Published
Title: Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain
Authors: Wang, Y.R. / Zhou, X.D. / Pan, L.F.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine/threonine-protein kinase 4 37kDa subunit
C: E3 ubiquitin-protein ligase RNF31
A: Serine/threonine-protein kinase 4 37kDa subunit
D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,96414
Polymers117,2574
Non-polymers70710
Water1086
1
B: Serine/threonine-protein kinase 4 37kDa subunit
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9827
Polymers58,6282
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase 4 37kDa subunit
D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9827
Polymers58,6282
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.989, 96.363, 115.773
Angle α, β, γ (deg.)90.00, 118.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein kinase 4 37kDa subunit / MST1/N


Mass: 34386.531 Da / Num. of mol.: 2 / Fragment: KD domain / Mutation: K59R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK4, KRS2, MST1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13043
#2: 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: 24241.730 Da / Num. of mol.: 2 / Fragment: RING2-LDD
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate tribasic (pH 7.0), 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.78→75.57 Å / Num. obs: 32995 / % possible obs: 97.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 74.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 2.78→2.83 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1682 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→68.87 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1640 5 %
Rwork0.237 --
obs0.2392 32802 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→68.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7984 0 20 6 8010
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint function
X-RAY DIFFRACTIONf_bond_d0.0038175Z= 0.194
X-RAY DIFFRACTIONf_angle_d0.67311057Z= 0.368
X-RAY DIFFRACTIONf_dihedral_angle_d13.5943104
X-RAY DIFFRACTIONf_chiral_restr0.0451194
X-RAY DIFFRACTIONf_plane_restr0.0051447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.860.41881260.40272597X-RAY DIFFRACTION97
2.86-2.950.37921480.36192635X-RAY DIFFRACTION99
2.95-3.060.39121290.33722638X-RAY DIFFRACTION98
3.06-3.180.36931330.34672600X-RAY DIFFRACTION98
3.18-3.330.3371300.32532663X-RAY DIFFRACTION98
3.33-3.50.38311260.31012631X-RAY DIFFRACTION99
3.5-3.720.33721060.2852105X-RAY DIFFRACTION79
3.72-4.010.29441550.23212672X-RAY DIFFRACTION100
4.01-4.410.27311450.22122663X-RAY DIFFRACTION100
4.41-5.050.2411610.20072622X-RAY DIFFRACTION99
5.05-6.360.27771510.22972635X-RAY DIFFRACTION98
6.36-68.870.20251300.16332701X-RAY DIFFRACTION98
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)
12.05651.2265-1.32867.06060.42331.05870.2335-0.346-1.35870.80950.2490.75320.40410.0001-0.11950.7877-0.00260.00021.31990.19041.1927-0.4895-73.458551.7687
23.83092.0113-1.64339.64870.12574.4107-0.33930.3158-0.447-0.86170.25190.7116-0.0475-0.9136-0.09180.57390.1683-0.03340.79940.17960.6364-2.4887-57.402438.0521
33.40250.47130.34832.8171-0.15735.52460.02960.1150.0317-0.1098-0.02650.2972-0.8274-0.7607-0.01410.70540.29630.08120.75390.05180.414-11.8161-37.419432.2344
46.7488-2.9605-2.94112.61025.7228.3236-0.8628-0.96470.36961.1470.88630.3186-1.0863-1.37450.08481.48010.4649-0.03621.24970.09150.5784-19.4572-31.98454.4503
55.35810.34681.2199-0.0030.09120.2695-0.08540.02791.28240.05390.47771.4601-0.6324-1.4051-0.35592.12171.1965-0.13962.00690.00941.0547-28.1115-20.9254-2.3598
67.3502-1.60460.8426.05371.01613.0295-0.33690.74050.4849-0.38450.33180.6259-1.0863-1.17420.05121.24150.2455-0.07631.34410.18150.5569-21.9877-33.5659-13.2758
79.0213-4.8658-2.99291.9797-0.40378.3943-0.2741-0.758-2.09521.86050.8685-0.74552.8042-1.50690.08211.4625-0.3501-0.08991.55080.1170.9888-16.0908-53.6632.4903
82.01552.25-8.4355.54451.12147.63190.0572-0.6573-0.29821.13381.62522.0314-0.3043-1.1732-0.50911.24020.11440.17822.53070.59571.0574-28.138-41.573511.8865
94.9919-1.28171.20383.11880.9739.5918-0.18490.50380.0166-1.40290.09460.1745-0.8644-2.0169-0.02351.2390.0364-0.06931.2285-0.00910.3845-20.9952-36.6692-14.0467
104.74232.24534.77651.68191.40575.841-1.9409-0.6121-0.1636-1.1493-0.45240.2083-0.119-0.34052.15683.02020.371-0.26991.8250.36351.4901-29.248-19.7962-32.62
115.86320.2343-3.6893.3997-0.36892.39780.14381.6950.2668-0.5893-0.1760.2297-2.13130.6525-0.00572.07860.52660.05511.59380.27730.8379-16.9591-23.8279-20.8795
128.07360.77781.39325.432-2.73892.719-0.0054-1.52740.07770.88090.5331-0.2396-1.44450.2147-0.25381.36640.1115-0.03071.4589-0.27171-58.7765-2.5451.9154
132.51940.16431.43172.6652-0.78639.34730.25720.75120.7123-0.50910.0359-0.57390.81760.2171-0.44480.92340.16440.10581.1506-0.26391.1263-51.1368-17.733836.9267
145.2278-2.8833-1.80253.61662.0483.89660.18460.06850.4345-0.09250.0497-0.17980.56750.0007-0.24770.80980.1151-0.09240.8059-0.1030.4473-53.8047-26.43334.5854
158.30651.0761-0.09842.2390.42297.58950.6001-0.2162-0.03580.0024-0.12630.09541.2389-0.1708-0.46911.06240.1035-0.17470.5142-0.0880.493-54.7803-38.362631.3746
162.1083-0.04681.07233.39551.42015.92020.49640.4313-0.4532-0.4559-0.0433-0.03871.77960.3792-0.49561.72970.3126-0.39740.8351-0.18470.7187-51.8035-46.72219.396
173.8590.60681.45723.10041.47436.19540.7966-0.0094-0.60360.3719-0.0705-1.2081.22910.4569-0.72411.14510.4106-0.17320.8172-0.15960.5985-41.7035-38.512437.3935
184.57-1.48312.76275.2074-3.27993.07760.63960.5733-0.70790.7144-0.2067-0.31541.88881.9546-0.41952.00010.651-0.48131.5201-0.28650.8277-48.5876-46.5818-2.367
195.7283-0.1985-1.54351.1207-0.96291.2848-1.3750.1014-0.1696-0.09350.8706-1.41140.50710.50230.30242.35081.0074-0.35192.7617-0.79591.5492-37.19-59.0206-16.198
208.54850.51772.71822.2361-1.1046.6011-0.1851.07690.3693-0.2389-0.0445-0.1790.31631.33170.10081.12110.2304-0.22791.2214-0.03180.6432-52.2993-35.3439-11.2329
212.32760.97731.78123.27610.30575.76760.37641.8242-0.5618-1.08720.1646-0.76321.61271.4864-0.20772.01110.4689-0.33051.8403-0.35990.9614-52.5216-49.0331-27.707
223.5245-0.6405-2.36343.58540.87373.91210.23371.08250.0377-0.84340.4678-0.19772.8410.3728-0.39482.71520.492-0.56372.2851-0.44921.1786-55.3175-54.0491-29.4975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 10 through 35 )
2X-RAY DIFFRACTION2chain 'B' and (resid 36 through 103 )
3X-RAY DIFFRACTION3chain 'B' and (resid 104 through 311 )
4X-RAY DIFFRACTION4chain 'C' and (resid 857 through 895 )
5X-RAY DIFFRACTION5chain 'C' and (resid 896 through 913 )
6X-RAY DIFFRACTION6chain 'C' and (resid 914 through 958 )
7X-RAY DIFFRACTION7chain 'C' and (resid 959 through 971 )
8X-RAY DIFFRACTION8chain 'C' and (resid 972 through 985 )
9X-RAY DIFFRACTION9chain 'C' and (resid 986 through 1034 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1035 through 1045 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1046 through 1071 )
12X-RAY DIFFRACTION12chain 'A' and (resid 11 through 29 )
13X-RAY DIFFRACTION13chain 'A' and (resid 30 through 66 )
14X-RAY DIFFRACTION14chain 'A' and (resid 67 through 122 )
15X-RAY DIFFRACTION15chain 'A' and (resid 123 through 191 )
16X-RAY DIFFRACTION16chain 'A' and (resid 192 through 271 )
17X-RAY DIFFRACTION17chain 'A' and (resid 272 through 308 )
18X-RAY DIFFRACTION18chain 'D' and (resid 857 through 903 )
19X-RAY DIFFRACTION19chain 'D' and (resid 904 through 923 )
20X-RAY DIFFRACTION20chain 'D' and (resid 924 through 1012 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1013 through 1034 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1035 through 1071 )

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