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- PDB-2lu7: Solution NMR Structure of Ig like domain (1277-1357) of Obscurin-... -

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Basic information

Entry
Database: PDB / ID: 2lu7
TitleSolution NMR Structure of Ig like domain (1277-1357) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578D
ComponentsObscurin-like protein 1
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


3M complex / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / regulation of mitotic nuclear division / Golgi organization / intercalated disc / cytoskeleton organization ...3M complex / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / regulation of mitotic nuclear division / Golgi organization / intercalated disc / cytoskeleton organization / microtubule cytoskeleton organization / Z disc / Neddylation / centrosome / perinuclear region of cytoplasm / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Obscurin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPulavarti, S. / Eletsky, A. / Satyamoorthy, B. / Sukumaran, D.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. ...Pulavarti, S. / Eletsky, A. / Satyamoorthy, B. / Sukumaran, D.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Ig like domain (1277-1357) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578D (CASP Target)
Authors: Pulavarti, S. / Eletsky, A. / Satyamoorthy, B. / Sukumaran, D.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Obscurin-like protein 1


Theoretical massNumber of molelcules
Total (without water)9,1131
Polymers9,1131
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Obscurin-like protein 1


Mass: 9113.153 Da / Num. of mol.: 1 / Fragment: Ig-like domain 11 residues 1277-1357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0657, OBSL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: O75147

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D 1H-13C HSQC (CT-28 ms) aliphatic
1912D 1H-13C HSQC aromatic
11012D 1H-13C HSQC (CT-16 ms) aromatic
11112D 1H-13C HSQC (CT-27 ms) aliphatic
11213D C(CO)NH-TOCSY
11313D H(CCO)NH-TOCSY
11413D (H)CCH-TOCSY
11513D-(H)CCH-COSY-ali
11613D (H)CCH-COSY-aro
11722D 1H-13C HSQC (CT-56 ms) aliphatic
11813D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.56 mM [U-100% 13C; U-100% 15N] HR8578D.005, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5, 90% H2O/10% D2O90% H2O/10% D2O
20.52 mM [U-5% 13C; U-100% 15N] HR8578D.006, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.56 mMHR8578D.005-1[U-100% 13C; U-100% 15N]1
100 mMNaCl-21
5 mMDTT-31
0.02 %NaN3-41
10 mMTris-HCl pH 7.5-51
0.52 mMHR8578D.006-6[U-5% 13C; U-100% 15N]2
100 mMNaCl-72
5 mMDTT-82
0.02 %NaN3-92
10 mMTris-HCl pH 7.5-102
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readsolution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.8.4Keller and Wuthrichchemical shift assignment
VnmrJVariandata collection
CSI(CSI) Wishart and Sykessecondary structure analysis
PROSA6.4Guntertprocessing
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSENSUS PEAK ASSIGNMENTS GENERATED FROM ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY CYANA AND AUTOSTRUCTURE IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSENSUS PEAK ASSIGNMENTS GENERATED FROM THESE PARALLEL RUNS WERE SELECTED AND USED FOR FURTHER REFINEMENT WITH CYANA, THE RDC CONSTRAINTS WERE ADDED AT LATER STAGES. A TOTAL OF 20 CONFORMERS OUT OF 100 CONFORMERS WITH THE LOWEST TARGET FUNCTION WERE SELECTED FOR REFINEMENT WITH CNS USING CNS WATER BATH REFINEMENT.
NMR constraintsNOE constraints total: 1283 / NOE intraresidue total count: 171 / NOE long range total count: 612 / NOE medium range total count: 172 / Protein phi angle constraints total count: 32 / Protein psi angle constraints total count: 32
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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