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- PDB-6gzy: HOIP-fragment5 complex -

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Basic information

Entry
Database: PDB / ID: 6gzy
TitleHOIP-fragment5 complex
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsLIGASE / Ubiquitin ligase / E3 / inhibitor complex
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
: / : / : / : / : / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-FHH / TRIETHYLENE GLYCOL / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJohansson, H. / Tsai, Y.C.I. / Fantom, K. / Chung, C.W. / Martino, L. / House, D. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
FC001142 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Fragment-Based Covalent Ligand Screening Enables Rapid Discovery of Inhibitors for the RBR E3 Ubiquitin Ligase HOIP.
Authors: Johansson, H. / Isabella Tsai, Y.C. / Fantom, K. / Chung, C.W. / Kumper, S. / Martino, L. / Thomas, D.A. / Eberl, H.C. / Muelbaier, M. / House, D. / Rittinger, K.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / software / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.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: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,39626
Polymers50,1992
Non-polymers2,19724
Water3,729207
1
A: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,32114
Polymers25,1001
Non-polymers1,22113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,07512
Polymers25,1001
Non-polymers97511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.202, 117.249, 37.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: 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: 25099.658 Da / Num. of mol.: 2
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, RING-type E3 ubiquitin transferase

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Non-polymers , 7 types, 231 molecules

#2: Chemical ChemComp-FHH / methyl 4-[(2-oxidanylidene-1,5,6,7-tetrahydrocyclopenta[b]pyridin-3-yl)carbonylamino]butanoate


Mass: 278.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N2O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris HCl pH 8.5, 28% w/v PEG 4000, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→117.25 Å / Num. obs: 22028 / % possible obs: 91.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.99 Å / Rmerge(I) obs: 1.174

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJO

4ljo


Resolution: 2.15→80.685 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.57
RfactorNum. reflection% reflection
Rfree0.246 1109 5.04 %
Rwork0.1985 --
obs0.2009 22017 78.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→80.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 111 207 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033366
X-RAY DIFFRACTIONf_angle_d0.594538
X-RAY DIFFRACTIONf_dihedral_angle_d15.4462032
X-RAY DIFFRACTIONf_chiral_restr0.041456
X-RAY DIFFRACTIONf_plane_restr0.003594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.24790.2715700.22591491X-RAY DIFFRACTION46
2.2479-2.36640.2406990.23011742X-RAY DIFFRACTION54
2.3664-2.51470.2977910.21342035X-RAY DIFFRACTION62
2.5147-2.70890.28191160.22962464X-RAY DIFFRACTION75
2.7089-2.98150.25791790.21413026X-RAY DIFFRACTION93
2.9815-3.41290.24181790.19763315X-RAY DIFFRACTION100
3.4129-4.29990.21121710.16113348X-RAY DIFFRACTION100
4.2999-80.74160.25192040.20733487X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 139.0814 Å / Origin y: 114.3752 Å / Origin z: 47.4549 Å
111213212223313233
T0.1262 Å2-0.0153 Å20.0374 Å2-0.1827 Å2-0.0418 Å2--0.1079 Å2
L0.3705 °2-0.6812 °20.4782 °2-2.8539 °2-1.3901 °2--1.4494 °2
S0.0352 Å °0.0286 Å °-0.0203 Å °-0.0491 Å °0.0015 Å °0.0633 Å °0.0523 Å °-0.0545 Å °-0.0513 Å °
Refinement TLS groupSelection details: all

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