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- PDB-2kdb: Solution Structure of human ubiquitin-like domain of Herpud2_9_85... -

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Basic information

Entry
Database: PDB / ID: 2kdb
TitleSolution Structure of human ubiquitin-like domain of Herpud2_9_85, Northeast Structural Genomics Consortium (NESG) target HT53A
ComponentsHomocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein
KeywordsPROTEIN BINDING / ubl domain / Membrane / Transmembrane / Unfolded protein response / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP / unknown function / SGC
Function / homology
Function and homology information


endoplasmic reticulum unfolded protein response / spermatogenesis / membrane => GO:0016020
Similarity search - Function
Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 /2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Gutmanas, A. / Doherty, R. / Semesi, A. / Dhe-Paganon, S. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
Citation
Journal: To be Published
Title: Structure of human homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2 (Herpud2 or Herp)
Authors: Doherty, R. / Wu, B. / Fares, C. / Lemak, A. / Gutmanas, A. / Semesi, A. / Yee, A. / Arrowsmith, C.H. / Dhe-Paganon, S.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionJan 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein


Theoretical massNumber of molelcules
Total (without water)11,5701
Polymers11,5701
Non-polymers00
Water0
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 Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein


Mass: 11570.251 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain, residues 9-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERPUD2 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSE4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
2923D 1H-13C NOESY
11013D 1H-13C NOESY aromatic
31132D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] humna ubiquitin-like domain of Herp-1, 10 mM [U-100% 2H] TRIS-2, 300 mM sodium chloride-3, 0.01 % sodium azide-4, 10 mM benzamidine-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] humna ubiquitin-like domain of Herp-6, 10 mM [U-100% 2H] TRIS-7, 300 mM sodium chloride-8, 0.01 % sodium azide-9, 10 mM benzamidine-10, 100% D2O100% D2O
30.5 mM [U-7% 13C; U-100% 15N] humna ubiquitin-like domain of Herp-11, 10 mM [U-100% 2H] TRIS-12, 300 mM sodium chloride-13, 0.01 % sodium azide-14, 10 mM benzamidine-15, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhumna ubiquitin-like domain of Herp-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
0.01 %sodium azide-41
10 mMbenzamidine-51
0.5 mMhumna ubiquitin-like domain of Herp-6[U-100% 13C; U-100% 15N]2
10 mMTRIS-7[U-100% 2H]2
300 mMsodium chloride-82
0.01 %sodium azide-92
10 mMbenzamidine-102
0.5 mMhumna ubiquitin-like domain of Herp-11[U-7% 13C; U-100% 15N]3
10 mMTRIS-12[U-100% 2H]3
300 mMsodium chloride-133
0.01 %sodium azide-143
10 mMbenzamidine-153
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 7 ambient 298 K
2300 7 ambient 298 K
3300 7 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
MNRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
FAWN1Lemak and Arrowsmithbackbone assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / 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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