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- PDB-4dbg: Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative -

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Basic information

Entry
Database: PDB / ID: 4dbg
TitleCrystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative
Components
  • RING finger protein 31
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsLIGASE / Ubiquitin Fold / Ubiquitination
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / positive regulation of xenophagy / CD40 receptor complex / ubiquitin ligase activator activity / negative regulation of necroptotic process ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / positive regulation of xenophagy / CD40 receptor complex / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / protein sequestering activity / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Helix Hairpins - #1100 / : / : / : / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like ...Helix Hairpins - #1100 / : / : / : / : / : / : / : / : / 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 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Ubiquitin-associated (UBA) domain / 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 / Helix Hairpins / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ring finger / Helix non-globular / Zinc finger RING-type profile. / Zinc finger, RING-type / Special / Ubiquitin-like (UB roll) / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31 / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å
AuthorsYagi, H. / Hiromoto, T. / Mizushima, T. / Kurimoto, E. / Kato, K.
CitationJournal: Embo Rep. / Year: 2012
Title: A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex
Authors: Yagi, H. / Ishimoto, K. / Hiromoto, T. / Fujita, H. / Mizushima, T. / Uekusa, Y. / Yagi-Utsumi, M. / Kurimoto, E. / Noda, M. / Uchiyama, S. / Tokunaga, F. / Iwai, K. / Kato, K.
History
DepositionJan 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Structure summary
Revision 1.2May 16, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RanBP-type and C3HC4-type zinc finger-containing protein 1
B: RING finger protein 31


Theoretical massNumber of molelcules
Total (without water)30,2282
Polymers30,2282
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-12 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.973, 64.973, 161.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1 / HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X- ...HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X-associated protein 4 / RING finger protein 54 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 11972.618 Da / Num. of mol.: 1 / Fragment: Ub-like domain, residues 37-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBCK1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)
References: UniProt: Q9BYM8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein RING finger protein 31 / HOIL-1-interacting protein / HOIP / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 18255.342 Da / Num. of mol.: 1 / Fragment: Ub-associated domain, residues 480-636
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.17 %
Description: Bijvoet pairs were collected separately in the native data set. The averaged reflections were used for structure refinement.
Mosaicity: 1.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15%(w/v) PEG6000, 0.1M KCl, 0.1M HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.9791, 0.9794, 0.9642
Detector
TypeIDDetectorDateDetails
Bruker DIP-60401CCDFeb 16, 2009Horizontal focusing mirror
Bruker DIP-60402CCDJan 22, 2011HORIZONTAL FOCUSING MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2DOUBLE-CRYSTAL MONOCHROMATORMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97911
30.97941
40.96421
ReflectionRedundancy: 13.9 % / Av σ(I) over netI: 27.33 / Number: 99095 / Rmerge(I) obs: 0.137 / Χ2: 12.18 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 7141 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.675087.210.11546.6669.7
6.898.6710010.09821.80513.2
6.026.8910010.12519.33113.6
5.476.0210010.14317.99413.9
5.085.4799.410.13814.64514
4.785.0899.710.12112.14514
4.544.7810010.1099.76813.8
4.344.5410010.1078.60113.9
4.184.3410010.1228.06314.1
4.034.1899.510.1246.74414.2
3.914.0310010.1316.86914.3
3.793.9110010.1516.18714.3
3.693.7910010.1516.80514.2
3.63.6999.710.1896.9814.5
3.523.610010.2057.17614.3
3.453.5210010.2516.57214.3
3.383.4510010.2975.98514.6
3.313.3810010.32114.36614.2
3.263.3110010.36813.6814.3
3.23.2610010.39514.3314.5
ReflectionResolution: 2.7→300 Å / Num. obs: 20666 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.103 / Χ2: 2.308 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.85.70.33220721.4321100
2.8-2.915.80.26920411.551100
2.91-3.045.70.22720661.6551100
3.04-3.25.80.17720601.8231100
3.2-3.45.70.13720992.161100
3.4-3.665.70.11720132.6391100
3.66-4.035.60.09721163.031100
4.03-4.625.50.08320663.1391100
4.62-5.825.60.07720572.923199.9
5.82-3005.40.07120762.847199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.71→56.27 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.2361 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7971 / SU B: 27.035 / SU ML: 0.244 / SU R Cruickshank DPI: 0.4528 / SU Rfree: 0.2899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 539 4.8 %RANDOM
Rwork0.2182 ---
obs0.2199 10718 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 100.34 Å2 / Biso mean: 50.68 Å2 / Biso min: 26.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.96 Å21.98 Å20 Å2
2--3.96 Å20 Å2
3----5.93 Å2
Refinement stepCycle: LAST / Resolution: 2.71→56.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 0 32 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211864
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9532523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06323.63699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1415321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3271520
X-RAY DIFFRACTIONr_chiral_restr0.1110.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211443
X-RAY DIFFRACTIONr_mcbond_it0.5641.51130
X-RAY DIFFRACTIONr_mcangle_it1.16321808
X-RAY DIFFRACTIONr_scbond_it1.9313734
X-RAY DIFFRACTIONr_scangle_it3.4314.5715
LS refinement shellResolution: 2.709→2.779 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 34 -
Rwork0.26 723 -
all-757 -
obs-723 96.19 %
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)
15.101-2.0319-0.59988.743-2.49965.5157-0.19260.05550.22440.23210.1706-0.1702-0.2016-0.1860.0220.03020.0376-0.02940.1059-0.01520.041342.5568-15.3891-23.2611
21.5563-0.7144-1.02841.4072-0.02035.81020.13780.02340.10790.0982-0.0162-0.0511-0.3505-0.0675-0.12160.1355-0.03090.05510.12140.02970.250236.6691-18.26784.2382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 133
2X-RAY DIFFRACTION2B482 - 528
3X-RAY DIFFRACTION2B529 - 627

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