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- PDB-4juy: Crystal structure of the PUB domain of E3 ubiquitin ligase RNF31 -

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Basic information

Entry
Database: PDB / ID: 4juy
TitleCrystal structure of the PUB domain of E3 ubiquitin ligase RNF31
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsUNKNOWN FUNCTION / E3 Ubiquitin Ligase / PUB domain / RNF31 (HOIP) / Structural Genomics / Structural Genomics Consortium / SGC
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 / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsDong, A. / Hu, J. / Li, Y. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the PUB domain of E3 ubiquitin ligase RNF31
Authors: Hu, J. / Dong, A. / Li, Y. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)45,35112
Polymers45,3512
Non-polymers010
Water66737
1
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31

A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31

A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31

A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31


Theoretical massNumber of molelcules
Total (without water)181,40348
Polymers181,4038
Non-polymers040
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation51_554-x+1/2,y,-z-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
Buried area21120 Å2
ΔGint-41 kcal/mol
Surface area61260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.488, 256.488, 256.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
DetailsAUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN.

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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: 22675.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96EP0
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.88 Å3/Da / Density % sol: 68.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.8M K/Na tartrate tetrahydrate, 0.5% PEG MME 5000, 0.1 M BisTris, pH 8.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionRedundancy: 21.8 % / Number: 185947 / Rmerge(I) obs: 0.052 / Χ2: 1.05 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 8535 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.055098.610.020.81318.7
5.67.0510010.0341.2820.3
4.895.610010.0461.80821
4.454.8910010.0411.54121.5
4.134.4510010.0381.08721.9
3.884.1310010.0420.93721.8
3.693.8810010.0510.87122.1
3.533.6910010.0650.97522.1
3.393.5310010.0941.0422.3
3.283.3910010.1270.96622.6
3.173.2810010.185122.2
3.083.1710010.2510.97622.4
33.0810010.3720.9922.7
2.93310010.441.00422.5
2.862.9310010.5240.96722.4
2.82.8610010.6690.94222.5
2.742.810010.9490.92622.9
2.692.7410010.91322.1
2.642.6910010.96921.8
2.62.6410010.91220.5
ReflectionResolution: 2.4→50 Å / Num. all: 28765 / Num. obs: 28765 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 43.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 3 / Num. unique all: 1403 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.98 Å / D res low: 50 Å / FOM : 0.2 / Reflection: 5630
Phasing MAD set siteAtom type symbol: S / B iso: 60 / Fract x: 0.797 / Fract y: 0.301 / Fract z: 0.253 / Occupancy: 0.709
Phasing MAD shell
Resolution (Å)FOM Reflection
10.73-500.27295
6.77-10.730.38500
5.3-6.770.34618
4.49-5.30.3715
3.97-4.490.26793
3.59-3.970.17855
3.31-3.590.09920
3.08-3.310.02934

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Processing

Software
NameVersionClassificationNB
SOLVE2.13phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.41 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 16.373 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 932 3.2 %RANDOM
Rwork0.2363 ---
obs0.237 27821 99.87 %-
all-28765 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.48 Å2 / Biso mean: 70.9644 Å2 / Biso min: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 10 37 2946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192963
X-RAY DIFFRACTIONr_bond_other_d0.0010.022747
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9794035
X-RAY DIFFRACTIONr_angle_other_deg0.76936262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.195381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63323.262141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97415453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1081531
X-RAY DIFFRACTIONr_chiral_restr0.0640.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_mcbond_it1.0572.3831524
X-RAY DIFFRACTIONr_mcbond_other1.0562.3821523
X-RAY DIFFRACTIONr_mcangle_it1.7143.5731902
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 78 -
Rwork0.27 1993 -
all-2071 -
obs--100 %
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)
11.6383-0.0001-1.17551.9916-0.35294.5293-0.2468-0.3479-0.23390.14290.0153-0.0861.03180.1220.23150.6630.07950.09750.16680.05590.198463.7234-24.2158-46.4932
24.6503-1.9185-2.31736.26560.75471.4144-0.41530.19870.01250.97710.3430.85540.4396-0.41590.07230.5815-0.27360.16080.4043-0.03010.457937.0562-13.8839-56.7904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 198
2X-RAY DIFFRACTION2B11 - 198

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