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- PDB-5h7s: Structural basis of the flanking zinc-finger motifs crucial for t... -

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Basic information

Entry
Database: PDB / ID: 5h7s
TitleStructural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain
Components
  • E3 ubiquitin-protein ligase LNX
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-like 1
KeywordsPROTEIN BINDING/LIGASE/TRANSFERASE / RING / ubiquitin / E3 ligase / zinc finger motif / PROTEIN BINDING-LIGASE-TRANSFERASE complex
Function / homology
Function and homology information


UBC13-MMS2 complex / synapse maturation / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / hypothalamus gonadotrophin-releasing hormone neuron development / DNA damage tolerance / female meiosis I / positive regulation of protein monoubiquitination ...UBC13-MMS2 complex / synapse maturation / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / hypothalamus gonadotrophin-releasing hormone neuron development / DNA damage tolerance / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development / positive regulation of double-strand break repair / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / antiviral innate immune response / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / positive regulation of DNA repair / Activated NOTCH1 Transmits Signal to the Nucleus / hippocampal mossy fiber to CA3 synapse / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / ubiquitin binding / Josephin domain DUBs / positive regulation of protein ubiquitination / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PDZ domain / Ring finger / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 N / E3 ubiquitin-protein ligase LNX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsNayak, D. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R154000625112 Singapore
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1.
Authors: Nayak, D. / Sivaraman, J.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 8, 2023Group: 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
E: Ubiquitin-like 1
D: E3 ubiquitin-protein ligase LNX
A: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin-like 1
B: E3 ubiquitin-protein ligase LNX
C: Ubiquitin-conjugating enzyme E2 N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,18014
Polymers80,6576
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-21 kcal/mol
Surface area32710 Å2
Unit cell
Length a, b, c (Å)122.372, 122.372, 135.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21B
12E
22F
13A
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLYGLYDB2 - 1252 - 125
21PROPROGLYGLYBE2 - 1252 - 125
12METMETGLYGLYEA1 - 761 - 76
22METMETGLYGLYFD1 - 761 - 76
13LEULEUASNASNAC4 - 1514 - 151
23LEULEUASNASNCF4 - 1514 - 151

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ubiquitin-like 1


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein E3 ubiquitin-protein ligase LNX / Ligand of Numb-protein X 1 / Numb-binding protein 1 / PDZ domain-containing RING finger protein 2 / ...Ligand of Numb-protein X 1 / Numb-binding protein 1 / PDZ domain-containing RING finger protein 2 / RING-type E3 ubiquitin transferase LNX


Mass: 14625.937 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 11-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNX1, LNX, PDZRN2, UNQ574/PRO1136 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TBB1, RING-type E3 ubiquitin transferase
#3: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17125.705 Da / Num. of mol.: 2 / Mutation: C87K, K92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.48→134.95 Å / Num. obs: 15353 / % possible obs: 99.8 % / Redundancy: 9.9 % / Net I/σ(I): 16.1
Reflection shellResolution: 3.48→3.81 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIN, 3HCT, 1UBQ

5din

3hct

1ubq


Resolution: 3.49→105.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 108.669 / SU ML: 0.63 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28649 1421 10 %RANDOM
Rwork0.24085 ---
obs0.24547 12753 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å2-0 Å2
2---0.23 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 3.49→105.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 8 0 5534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195668
X-RAY DIFFRACTIONr_bond_other_d0.0020.025326
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9837704
X-RAY DIFFRACTIONr_angle_other_deg0.9863.00312400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.95690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34124.688256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.527151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5041532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216152
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021048
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D75780.05
12B75780.05
21E43720.01
22F43720.01
31A94240.05
32C94240.05
LS refinement shellResolution: 3.486→3.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.632 61 -
Rwork0.641 535 -
obs--53.17 %
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)
14.35692.16360.8396.0355-0.10035.4240.2374-0.06260.04750.0781-0.03830.89910.3108-0.8713-0.19910.3143-0.0203-0.01150.29140.02090.157741.4-18.3618
211.5085-0.57421.23748.5018-2.85976.814-0.4070.19360.71290.29590.1033-0.6606-0.36140.43590.30380.60350.00920.050.6401-0.17520.528168.318-14.39133.483
36.39771.69492.4644.62723.1739.4384-0.23650.44380.0255-0.35940.24890.87060.25840.125-0.01250.4704-0.0147-0.01090.16210.17630.384955.448-16.238-23.898
47.6013-0.5402-0.46381.9862-0.71153.71250.2219-0.14420.2773-0.0613-0.0795-0.5624-0.29370.837-0.14230.4439-0.07220.0740.1926-0.05810.195366.168-9.2736.861
56.5685-3.85454.28072.6802-1.87143.87750.22870.23570.1078-0.2235-0.50190.07630.172-0.15020.27321.3254-0.2505-0.01921.49010.12440.961641.544-21.336-9.27
68.49231.09314.48893.4783-2.08979.40460.0567-0.9482-0.01930.50390.0858-0.20140.057-0.5292-0.14240.53160.15160.09350.2472-0.09370.22654.232-19.06848.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D2 - 125
2X-RAY DIFFRACTION1D201
3X-RAY DIFFRACTION1D202
4X-RAY DIFFRACTION1D204
5X-RAY DIFFRACTION2E1 - 76
6X-RAY DIFFRACTION3A4 - 151
7X-RAY DIFFRACTION4B2 - 125
8X-RAY DIFFRACTION4B201
9X-RAY DIFFRACTION4B202
10X-RAY DIFFRACTION4B204
11X-RAY DIFFRACTION5F1 - 76
12X-RAY DIFFRACTION6C4 - 151

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