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- PDB-6sc6: dAb3/HOIP-RBR apo structure -

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Basic information

Entry
Database: PDB / ID: 6sc6
TitledAb3/HOIP-RBR apo structure
Components
  • E3 ubiquitin-protein ligase RNF31
  • Single domain antibodySingle-domain antibody
KeywordsLIGASE / Human Single Domain Antibody / HOIP / RBR
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 / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / 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
E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTsai, Y.-C.I. / 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 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Single domain antibody
C: Single domain antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46818
Polymers69,3943
Non-polymers1,07415
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-114 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.948, 87.490, 241.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21(chain C and (resid 1 through 12 or (resid 13...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUSERSERchain BBB1 - 1191 - 119
21GLUGLUVALVAL(chain C and (resid 1 through 12 or (resid 13...CC1 - 121 - 12
22GLNGLNGLNGLN(chain C and (resid 1 through 12 or (resid 13...CC1313
23GLUGLUSERSER(chain C and (resid 1 through 12 or (resid 13...CC1 - 1201 - 120
24GLUGLUSERSER(chain C and (resid 1 through 12 or (resid 13...CC1 - 1201 - 120
25GLUGLUSERSER(chain C and (resid 1 through 12 or (resid 13...CC1 - 1201 - 120
26GLUGLUSERSER(chain C and (resid 1 through 12 or (resid 13...CC1 - 1201 - 120
27GLUGLUSERSER(chain C and (resid 1 through 12 or (resid 13...CC1 - 1201 - 120

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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 / 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 , 4 types, 184 molecules

#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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.33 %
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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→60.482 Å / Num. obs: 33752 / % possible obs: 98.95 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02856 / Rrim(I) all: 0.04039 / Net I/σ(I): 21.22
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.2609 / Num. unique obs: 3317 / CC1/2: 0.863 / Rrim(I) all: 0.04039

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJQ, 6SCA

4ljq

6sca
PDB Unreleased entry


Resolution: 2.25→60.482 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.95
RfactorNum. reflection% reflection
Rfree0.2462 1600 4.79 %
Rwork0.1993 --
obs0.2019 33398 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.74 Å2 / Biso mean: 52.3047 Å2 / Biso min: 22.11 Å2
Refinement stepCycle: final / Resolution: 2.25→60.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4724 0 35 169 4928
Biso mean--75.47 48.24 -
Num. residues----604
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B722X-RAY DIFFRACTION6.191TORSIONAL
12C722X-RAY DIFFRACTION6.191TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.32260.36281330.2931276596
2.3226-2.40570.32721440.2636281498
2.4057-2.5020.36241540.2613281898
2.502-2.61590.24731250.2439286399
2.6159-2.75380.31111540.2433287399
2.7538-2.92630.29761470.2435285399
2.9263-3.15220.31431410.23822914100
3.1522-3.46940.29111440.21412909100
3.4694-3.97140.23751330.18762938100
3.9714-5.00310.1621690.14632950100
5.0031-60.480.20741560.16653101100
Refinement TLS params.Method: refined / Origin x: -27.78 Å / Origin y: 63.6983 Å / Origin z: 40.7439 Å
111213212223313233
T0.2438 Å2-0.0661 Å2-0.0489 Å2-0.2722 Å20.0253 Å2--0.3425 Å2
L0.5767 °2-0.0079 °2-0.3327 °2-0.3499 °20.1505 °2--1.581 °2
S-0.0972 Å °0.1681 Å °0.1524 Å °-0.1083 Å °0.0588 Å °0.0737 Å °-0.1471 Å °-0.0216 Å °0.022 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA697 - 1070
2X-RAY DIFFRACTION1allB1 - 119
3X-RAY DIFFRACTION1allC1 - 120
4X-RAY DIFFRACTION1allD1 - 8
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allH1 - 188

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