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- PDB-6sc5: dAb3/HOIP-RBR-Ligand2 -

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Basic information

Entry
Database: PDB / ID: 6sc5
TitledAb3/HOIP-RBR-Ligand2
Components
  • E3 ubiquitin-protein ligase RNF31
  • Single domain antibody
KeywordsLIGASE / Human Single Domain Antibody / HOIP / RBR / Inhibitor
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 / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion ...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 / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / 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 / IBR domain, a half RING-finger domain / PUB domain / PUB-like domain superfamily / PUB domain / IBR 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-L6B / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTsai, Y.-C.I. / Johansson, H. / House, D. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell Chem Biol / Year: 2020
Title: Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases.
Authors: Tsai, Y.I. / Johansson, H. / Dixon, D. / Martin, S. / Chung, C.W. / Clarkson, J. / House, D. / Rittinger, K.
History
DepositionJul 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3May 1, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: Single domain antibody
C: Single domain antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,62717
Polymers69,3943
Non-polymers1,23314
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-94 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.578, 86.661, 240.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-2152-

HOH

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Components

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Protein / Antibody , 2 types, 3 molecules ABC

#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: 43246.379 Da / Num. of mol.: 1
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, RBR-type E3 ubiquitin transferase
#2: Antibody Single domain antibody


Mass: 13073.577 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 119 molecules

#3: Chemical ChemComp-L6B / methyl 4-[(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-quinolin-3-yl)carbonylamino]but-3-enoate


Mass: 290.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, sodium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.1→63.26 Å / Num. obs: 40506 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 48.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02479 / Rrim(I) all: 0.03506 / Net I/σ(I): 13.75
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.2638 / Num. unique obs: 4001 / CC1/2: 0.859 / Rrim(I) all: 0.3731

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Processing

Software
NameVersionClassification
REFMAC1.15.2_3472refinement
PHENIX1.15.2_3472refinement
DIALS1.15.2_3472data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: dAb3/HOIP-RBR apo structure

Resolution: 2.1→63.26 Å / SU ML: 0.2849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 1988 4.91 %
Rwork0.2191 38493 -
obs0.2207 40481 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→63.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 50 105 4786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194787
X-RAY DIFFRACTIONf_angle_d0.45916492
X-RAY DIFFRACTIONf_chiral_restr0.0391681
X-RAY DIFFRACTIONf_plane_restr0.0043839
X-RAY DIFFRACTIONf_dihedral_angle_d7.8932822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.36011360.28912717X-RAY DIFFRACTION99.86
2.15-2.210.3191510.29112701X-RAY DIFFRACTION99.86
2.21-2.280.321350.28772719X-RAY DIFFRACTION99.83
2.28-2.350.32671510.28162696X-RAY DIFFRACTION100
2.35-2.430.32451400.28032729X-RAY DIFFRACTION99.97
2.43-2.530.31711410.28132732X-RAY DIFFRACTION99.93
2.53-2.650.31521230.26042721X-RAY DIFFRACTION99.96
2.65-2.790.33551330.26852736X-RAY DIFFRACTION99.93
2.79-2.960.31071480.26752712X-RAY DIFFRACTION100
2.96-3.190.29531390.26452765X-RAY DIFFRACTION100
3.19-3.510.27421400.23072760X-RAY DIFFRACTION100
3.51-4.020.25171310.19462794X-RAY DIFFRACTION100
4.02-5.060.17541660.16772785X-RAY DIFFRACTION100
5.06-63.260.21611540.18782926X-RAY DIFFRACTION99.87

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