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- PDB-2kkq: Solution NMR Structure of the Ig-like C2-type 2 Domain of Human M... -

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Basic information

Entry
Database: PDB / ID: 2kkq
TitleSolution NMR Structure of the Ig-like C2-type 2 Domain of Human Myotilin. Northeast Structural Genomics Target HR3158.
ComponentsMyotilin
KeywordsSTRUCTURAL PROTEIN / unknown function / Actin-binding / Cell membrane / Cytoplasm / Cytoskeleton / Disease mutation / Immunoglobulin domain / Limb-girdle muscular dystrophy / Membrane / Muscle protein / Polymorphism / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity / structural constituent of muscle / alpha-actinin binding / homophilic cell adhesion via plasma membrane adhesion molecules / muscle contraction / synapse organization / sarcolemma / Z disc ...axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity / structural constituent of muscle / alpha-actinin binding / homophilic cell adhesion via plasma membrane adhesion molecules / muscle contraction / synapse organization / sarcolemma / Z disc / actin cytoskeleton / actin binding / axon / neuronal cell body / plasma membrane
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Shastry, R. / Ciccosanti, C. / Hamilton, K. / Xiao, R. / Acton, T.B. / Swapna, G.V.T. / Nair, R. / Everett, J.K. / Rost, B. ...Rossi, P. / Shastry, R. / Ciccosanti, C. / Hamilton, K. / Xiao, R. / Acton, T.B. / Swapna, G.V.T. / Nair, R. / Everett, J.K. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the Ig-like C2-type 2 Domain of Human Myotilin. Northeast Structural Genomics Target HR3158.
Authors: Rossi, P. / Montelione, G.T.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myotilin


Theoretical massNumber of molelcules
Total (without water)13,3381
Polymers13,3381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Antibody Myotilin / Titin immunoglobulin domain protein / Myofibrillar titin-like Ig domains protein / 57 kDa cytoskeletal protein


Mass: 13338.207 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOT, TTID / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9UBF9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Ig-like C2-type 2 Domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HNCA
1313D HN(CA)CB
1413D HBHA(CO)NH
1513D (H)CCH-COSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HNCO
11013D HN(CA)CO
11112D 1H-15N HSQC
11212D 1H-13C HSQC
11322D 1H-13C HSQC hires
11422D 1H-15N het NOE
11521D 15N T1 series
11621D 15N T2 series
NMR detailsText: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG). CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. ...Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG). CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0. ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 90.16%, SIDECHAIN 76.91%, AROMATIC (SC) 100%, STEREOSPECIFIC VL METHYL ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 100%.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.87 mM [U-100% 13C; U-100% 15N] protein, 200 mM sodium chloride, 20 mM MES, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.68 mM [U-5% 13C] protein, 200 mM sodium chloride, 20 mM MES, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 5 mM Calcium Chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.87 mMprotein-1[U-100% 13C; U-100% 15N]1
200 mMsodium chloride-21
20 mMMES-31
50 uMDSS-41
10 mMDTT-51
0.02 %sodium azide-61
5 mMCalcium Chloride-71
0.68 mMprotein-8[U-5% 13C]2
200 mMsodium chloride-92
20 mMMES-102
50 uMDSS-112
10 mMDTT-122
0.02 %sodium azide-132
5 mMCalcium Chloride-142
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin2.1Bruker Biospincollection
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky2.113Goddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniadata analysis
MOLMOLKoradi, Billeter and Wuthrichstructure visualization
PSVS1.3Bhattacharya and Montelionestructure validation
PyMOLDeLano Scientificstructure visualization
PdbStat5.1Tejero, Montelionepdb processing
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). STRUCTURE BASED ON ...Details: 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). STRUCTURE BASED ON 2412 NOE, 230 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 8.1 DEG. 3 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 11-112 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - BETA STRANDS: 25-28, 31-38, 46-51, 54-55, 63-67, 72-80, 86-94, 97-108 RMSD(ANG): BACKBONE 0.4, ALL HEAVY ATOMS 0.7. RAMA. DISTRIBUTION: 94.7/5.1/0.2/0.0. PROCHECK (PSI-PHI): -0.39/-1.22 (RAW/Z), PROCHECK (ALL): -0.23/-1.36 (RAW/Z), MOLPROBITY CLASH: 14.45/-1.01 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.892, PRECISION: 0.934, F-MEASURE: 0.913, DP-SCORE: 0.76.
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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