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- PDB-3b0a: Crystal structure of the mouse HOIL1-L-NZF in complex with linear... -

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Basic information

Entry
Database: PDB / ID: 3b0a
TitleCrystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin
Components
  • Polyubiquitin-C
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / protein complex / SIGNALING PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway ...TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / tumor necrosis factor-mediated signaling pathway / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / protein kinase C binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis
Similarity search - Function
: / : / : / Zn-finger domain of Sec23/24 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. ...: / : / : / Zn-finger domain of Sec23/24 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / SH3 type barrels. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Authors: Sato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S.
History
DepositionJun 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
D: Polyubiquitin-C
E: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1207
Polymers48,8264
Non-polymers2943
Water5,747319
1
A: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6414
Polymers24,4132
Non-polymers2292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-9 kcal/mol
Surface area12120 Å2
MethodPISA
2
D: Polyubiquitin-C
E: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4783
Polymers24,4132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.650, 113.650, 75.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11E-191-

MET

21E-191-

MET

31A-307-

HOH

41B-89-

HOH

51B-310-

HOH

61E-178-

HOH

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Components

#1: Protein Polyubiquitin-C / Ubiquitin


Mass: 17135.654 Da / Num. of mol.: 2 / Fragment: linear di ubiquitin, UNP residues 1-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG48
#2: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1 / Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin- ...Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 7277.155 Da / Num. of mol.: 2 / Fragment: UNP residues 192-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbck1, Rbck, Ubce7ip3, Uip28 / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9WUB0
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.45M tri-ammonium citrate (pH 7.0), 3% 1,6-diaminohexane, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2826 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 43879 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 37.3
Reflection shellResolution: 1.9→1.92 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.85 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B08

3b08


Resolution: 1.9→45.438 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.48 / σ(F): 2.12 / Phase error: 23.17 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2271 4131 5.07 %
Rwork0.1801 --
obs0.1825 43879 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.179 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 130.24 Å2 / Biso mean: 39.4892 Å2 / Biso min: 17.16 Å2
Baniso -1Baniso -2Baniso -3
1-5.089 Å2-0 Å20 Å2
2--5.089 Å2-0 Å2
3----10.1779 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 13 319 3679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073426
X-RAY DIFFRACTIONf_angle_d1.0554617
X-RAY DIFFRACTIONf_dihedral_angle_d16.6641366
X-RAY DIFFRACTIONf_chiral_restr0.07515
X-RAY DIFFRACTIONf_plane_restr0.004608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.34471130.326231685
1.9216-1.94420.31661400.3129235488
1.9442-1.96790.30961370.2797240789
1.9679-1.99280.2771350.2666251890
1.9928-2.0190.27451260.25243492
2.019-2.04670.29471470.246255192
2.0467-2.07590.2938990.2497245691
2.0759-2.10690.2651380.2302258393
2.1069-2.13980.3121330.2272254093
2.1398-2.17490.2851540.2186252795
2.1749-2.21240.25171680.1999252994
2.2124-2.25260.2441300.2027245590
2.2526-2.2960.26851180.2104252892
2.296-2.34280.24761460.1886260394
2.3428-2.39380.22561540.1799255195
2.3938-2.44940.23721420.1856260496
2.4494-2.51070.27231210.1891265896
2.5107-2.57860.24151510.1819263297
2.5786-2.65440.27321540.1902263997
2.6544-2.74010.24691170.1903267897
2.7401-2.8380.22491220.1949268798
2.838-2.95160.25861540.1975267498
2.9516-3.08590.25671320.1952272499
3.0859-3.24860.21221430.1858271199
3.2486-3.45210.21841250.1734269699
3.4521-3.71850.2261470.1496270599
3.7185-4.09250.16621440.1394269699
4.0925-4.68410.17341580.1317270399
4.6841-5.89950.20651590.1411266999
5.8995-45.45060.17461240.161251892
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)
10.3784-0.1673-0.12542.57682.21153.5993-0.0328-0.1061-0.0987-0.0108-0.02010.15350.006-0.05940.05350.0885-0.0249-0.01580.2330.03310.2064-44.242240.3559-0.9373
23.304-0.58660.32294.16530.14911.84230.0997-0.2212-0.4257-0.1534-0.0077-0.04690.43140.0810.0210.1658-0.05190.00170.16050.01730.1628-29.318536.13550.0945
30.76490.57230.54811.86132.18994.428-0.04850.01480.1375-0.0753-0.10780.2222-0.2079-0.42680.17290.17570.0109-0.01010.33060.03860.2619-43.498659.8793-24.8177
43.32671.07430.02024.20370.68111.8815-0.11440.19320.1925-0.02750.0854-0.1678-0.38230.07960.0270.1921-0.0668-0.0170.20680.01140.1329-27.871162.9911-26.3774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 151
2X-RAY DIFFRACTION2chain BB191 - 247
3X-RAY DIFFRACTION3chain DD1 - 152
4X-RAY DIFFRACTION4chain EE187 - 249

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