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- PDB-2n9p: Solution structure of RNF126 N-terminal zinc finger domain in com... -

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Basic information

Entry
Database: PDB / ID: 2n9p
TitleSolution structure of RNF126 N-terminal zinc finger domain in complex with BAG6 Ubiquitin-like domain
Components
  • E3 ubiquitin-protein ligase RNF126
  • Large proline-rich protein BAG6
KeywordsLIGASE / E3 ligase / zinc finger
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / protein K27-linked ubiquitination / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / protein K27-linked ubiquitination / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / natural killer cell activation / endoplasmic reticulum stress-induced pre-emptive quality control / retrograde transport, endosome to Golgi / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / epidermal growth factor receptor binding / proteasome binding / ubiquitin-specific protease binding / negative regulation of epidermal growth factor receptor signaling pathway / protein monoubiquitination / protein K63-linked ubiquitination / regulation of embryonic development / positive regulation of double-strand break repair via homologous recombination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / protein K48-linked ubiquitination / ERAD pathway / Hsp70 protein binding / kidney development / molecular function activator activity / negative regulation of proteolysis / lung development / RING-type E3 ubiquitin transferase / regulation of protein stability / brain development / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ribosome binding / chromatin organization / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / cell differentiation / protein stabilization / protein ubiquitination / intracellular membrane-bounded organelle / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF126-like, zinc-ribbon / zinc-ribbon / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ring finger domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase RNF126-like, zinc-ribbon / zinc-ribbon / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ring finger domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Large proline-rich protein BAG6 / E3 ubiquitin-protein ligase RNF126
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model16
AuthorsMartinez-Lumbreras, S. / Krysztofinska, E.M. / Thapaliya, A. / Isaacson, R.L.
CitationJournal: Sci Rep / Year: 2016
Title: Structural and functional insights into the E3 ligase, RNF126.
Authors: Krysztofinska, E.M. / Martinez-Lumbreras, S. / Thapaliya, A. / Evans, N.J. / High, S. / Isaacson, R.L.
History
DepositionDec 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF126
C: Large proline-rich protein BAG6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0483
Polymers15,9822
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase RNF126 / RING finger protein 126


Mass: 4705.398 Da / Num. of mol.: 1 / Fragment: N-terminal zinc finger domain residues 1-40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF126 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9BV68, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / BAG6 / HLA-B- ...BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / BAG6 / HLA-B-associated transcript 3 / Protein G3 / Protein Scythe


Mass: 11276.791 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain, residues 17-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6, BAT3, G3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P46379
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CO
1713D 1H-15N NOESY
1823D 1H-13C NOESY
1923D 12C14N filtered 13C edited NOESY
11023D (H)CCH-TOCSY
11132D 1H-15N HSQC
11242D 1H-13C HSQC
11333D HN(CA)CB
11433D CBCA(CO)NH
11533D HNCO
11633D HN(CA)CO
11733D 1H-15N NOESY
11843D 1H-13C NOESY
11943D 12C14N filtered 13C edited NOESY
12043D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM [U-99% 13C; U-99% 15N] RNF126, 800 uM BAG6, 10 mM potassium phosphate, 100 mM sodium chloride, 250 uM TCEP, 10 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
2600 uM [U-99% 13C; U-99% 15N] RNF126, 800 uM BAG6, 10 mM potassium phosphate, 100 mM sodium chloride, 250 uM TCEP, 10 uM DSS, 100% D2O100% D2O
3600 uM protein_1, 400 uM [U-99% 13C; U-99% 15N] BAG6, 10 mM potassium phosphate, 100 mM sodium chloride, 250 uM TCEP, 10 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
4600 uM protein_1, 400 uM [U-99% 13C; U-99% 15N] BAG6, 10 mM potassium phosphate, 100 mM sodium chloride, 250 uM TCEP, 10 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMentity_1-1[U-99% 13C; U-99% 15N]1
800 uMentity_2-21
10 mMpotassium phosphate-31
100 mMsodium chloride-41
250 uMTCEP-51
10 uMDSS-61
600 uMentity_1-7[U-99% 13C; U-99% 15N]2
800 uMentity_2-82
10 mMpotassium phosphate-92
100 mMsodium chloride-102
250 uMTCEP-112
10 uMDSS-122
600 uMentity_1-133
400 uMentity_2-14[U-99% 13C; U-99% 15N]3
10 mMpotassium phosphate-153
100 mMsodium chloride-163
250 uMTCEP-173
10 uMDSS-183
600 uMentity_1-194
400 uMentity_2-20[U-99% 13C; U-99% 15N]4
10 mMpotassium phosphate-214
100 mMsodium chloride-224
250 uMTCEP-234
10 uMDSS-244
Sample conditionsIonic strength: 0.12 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
CcpNmr Analysis2.3CCPNchemical shift assignment
CcpNmr Analysis2.3CCPNpeak picking
CcpNmr Analysis2.3CCPNstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Refinement in water with default parametres
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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