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- PDB-4ljp: Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex -

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Basic information

Entry
Database: PDB / ID: 4ljp
TitleStructure of an active ligase (HOIP-H889A)/ubiquitin transfer complex
Components
  • E3 ubiquitin-protein ligase RNF31
  • Polyubiquitin-C
KeywordsLIGASE / E3 ligase-ubiquitin complex / HOIP / RNF31 / ubiquitin / RBR ligase / E3 ligase / RING domain / IBR domain / Zinc Finger
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...protein linear polyubiquitination / LUBAC complex / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / linear polyubiquitin binding / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis
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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
: / Ubiquitin-ribosomal protein eL40 fusion protein / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsRana, R.R. / Stieglitz, B. / Koliopoulos, M.G. / Morris-Davies, A.C. / Christodoulou, E. / Howell, S. / Brown, N.R. / Rittinger, K.
CitationJournal: Nature / Year: 2013
Title: Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP.
Authors: Stieglitz, B. / Rana, R.R. / Koliopoulos, M.G. / Morris-Davies, A.C. / Schaeffer, V. / Christodoulou, E. / Howell, S. / Brown, N.R. / Dikic, I. / Rittinger, K.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Dec 10, 2014Group: Other
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.location / _software.name / _software.type / _software.version
Revision 1.6Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: E3 ubiquitin-protein ligase RNF31
B: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8716
Polymers33,6092
Non-polymers2624
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-3 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.000, 46.000, 133.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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: 25032.590 Da / Num. of mol.: 1
Fragment: E3 ligase HOIP catalytic core (unp residues 853-1072)
Mutation: H889A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Plasmid: pET-49b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: unp residues 77-152 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1B9K1, UniProt: P63048*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M amino acids, 0.1 M imidazole, MES, 30 % P550 MME_P20K , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.15→38.17 Å / Num. all: 87792 / Num. obs: 17108 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 32.703 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.1 Å38.17 Å
Translation6.1 Å38.17 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
CCP4refinement
PHASER2.5.2phasing
CCP4data reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LJO

4ljo


Resolution: 2.15→38.17 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 0.91 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 865 5.06 %
Rwork0.1757 --
obs0.1778 17070 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.9131 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 4 120 2416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082340
X-RAY DIFFRACTIONf_angle_d1.1153163
X-RAY DIFFRACTIONf_dihedral_angle_d16.864900
X-RAY DIFFRACTIONf_chiral_restr0.071340
X-RAY DIFFRACTIONf_plane_restr0.006421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21330.29651320.26662697X-RAY DIFFRACTION98
2.2133-2.28470.33171220.26662682X-RAY DIFFRACTION97
2.2847-2.36640.26131510.2412570X-RAY DIFFRACTION98
2.3664-2.46110.28691710.23182664X-RAY DIFFRACTION99
2.4611-2.57310.349840.21732800X-RAY DIFFRACTION98
2.5731-2.70870.30561430.22712639X-RAY DIFFRACTION98
2.7087-2.87840.31411580.21372576X-RAY DIFFRACTION95
2.8784-3.10050.25451510.2112539X-RAY DIFFRACTION97
3.1005-3.41230.26791300.18742623X-RAY DIFFRACTION97
3.4123-3.90570.16311420.1552654X-RAY DIFFRACTION96
3.9057-4.91910.15451520.12642575X-RAY DIFFRACTION96
4.9191-38.17680.16071520.1252670X-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)
13.2813-4.3493-1.6668.47692.856.2392-0.2512-0.11260.18070.54930.0696-0.041-0.11560.11930.19050.40820.10750.06260.31210.03250.2815-15.154446.80817.3213
27.4308-1.2919-0.70632.89780.77024.608-0.02980.59630.2553-0.2045-0.0370.5624-0.3459-0.6010.0750.32590.0895-0.03590.31290.03610.2879-17.987950.17850.8215
33.23050.5525-0.8913.2007-0.02763.7752-0.2732-0.3719-0.72530.3886-0.0928-0.20670.86630.66260.29490.55780.25560.06570.39880.0480.3673-5.815333.139611.7477
43.27610.5522-2.61053.1328-2.10835.46210.12910.63580.4333-0.55080.17450.016-0.9803-0.5737-0.27430.49720.06140.05470.49530.05050.3222-3.266951.5709-12.092
59.2478-0.0773-5.53852.33660.03533.31060.2661-0.9347-0.1150.81620.0901-0.0179-1.4921.22250.02080.5467-0.0210.0010.4919-0.05590.3128-3.760754.32047.929
69.47670.59030.44814.34870.0321.9897-0.18670.2015-0.2740.43270.0141-0.33530.22380.03380.16240.3760.1185-0.01940.3618-0.02580.2904-16.942434.0321-3.7097
77.7815.8802-1.64995.0357-2.12136.5382-0.27220.30320.44050.18580.01390.2479-0.5391-0.74050.17360.30550.1824-0.07590.4438-0.09580.3493-23.829342.6363-6.1267
86.10563.3154-2.15683.6808-4.28486.5816-0.35971.36970.1221-0.57510.30590.41260.2213-0.564-0.10190.2324-0.0051-0.0310.6422-0.07780.372-21.801538.6168-15.6378
96.4128-5.8453-0.27118.12590.04666.9809-0.13621.1194-0.5332-0.47240.00571.05510.6014-1.1130.26270.2915-0.10790.0220.7216-0.07910.5503-31.401532.7316-10.5229
103.7796-3.82254.88617.0845-3.48416.973-0.2526-1.34280.18010.67560.06110.4520.0863-1.19940.2220.3890.02080.06370.6032-0.06870.3188-29.856833.2329-0.4311
115.0387-0.3963-5.47761.26140.02246.0837-0.66981.153-1.1425-0.25850.0013-0.04210.8181-0.53960.57830.32510.0112-0.01870.5347-0.10920.2157-20.400131.4395-10.8243
127.4947-4.658-5.27815.36685.89676.8911-0.0325-0.24930.0901-0.3676-0.15690.5199-0.37951.07190.41190.2962-0.1336-0.02210.5281-0.1450.2892-22.499337.5597-26.7189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 857 through 895 )
2X-RAY DIFFRACTION2chain 'A' and (resid 896 through 938 )
3X-RAY DIFFRACTION3chain 'A' and (resid 939 through 1012 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1013 through 1060 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1061 through 1071 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 16 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 34 )
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 54 )
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 65 )
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 76 )

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