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- PDB-6a3z: Zinc finger domain from the HRD1 Protein -

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Basic information

Entry
Database: PDB / ID: 6a3z
TitleZinc finger domain from the HRD1 Protein
ComponentsE3 ubiquitin-protein ligase synoviolin
KeywordsMETAL BINDING PROTEIN / HRD1
Function / homology
Function and homology information


Hrd1p ubiquitin ligase complex / endoplasmic reticulum mannose trimming / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / immature B cell differentiation / XBP1(S) activates chaperone genes / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol / ubiquitin-specific protease binding / smooth endoplasmic reticulum ...Hrd1p ubiquitin ligase complex / endoplasmic reticulum mannose trimming / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / immature B cell differentiation / XBP1(S) activates chaperone genes / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol / ubiquitin-specific protease binding / smooth endoplasmic reticulum / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ER Quality Control Compartment (ERQC) / endomembrane system / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / unfolded protein binding / protein-folding chaperone binding / ATPase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding / nucleoplasm / membrane
Similarity search - Function
: / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase synoviolin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K.
CitationJournal: To Be Published
Title: The structure of the zinc finger from the HRD1 protein
Authors: Miyamoto, K.
History
DepositionJun 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.2May 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase synoviolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6513
Polymers6,5211
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cystein modification
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4360 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase synoviolin / RING-type E3 ubiquitin transferase synoviolin / Synovial apoptosis inhibitor 1


Mass: 6520.612 Da / Num. of mol.: 1 / Fragment: Zinc finger domain / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q86TM6, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM U 13C; 15N hrd1, 90% H2O/10% D2O / Label: 15N 13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: hrd1 / Isotopic labeling: U 13C; 15N
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Discovery Studio2.1Accelrys Software Inc.structure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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