SASDFZ7: Full-length myotilin with N-terminally fused thioredoxin tag

Basic information

• Entry: Database: SASBDB / ID: SASDFZ7

Sample

Full-length myotilin with N-terminally fused thioredoxin tag

• his-trx-myotilin (protein), trx-MYOT, Homo sapiens

Function / homology

Function:

axon guidance receptor activity / structural constituent of muscle / homophilic cell adhesion via plasma membrane adhesion molecules / alpha-actinin binding / muscle contraction / synapse organization / sarcolemma / Z disc / actin cytoskeleton / actin binding / axon / neuronal cell body / plasma membrane

Domain/homology:

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 / Immunoglobulin-like fold

Component:

Myotilin

• Biological species: Homo sapiens (human)

Contact author

• Melissa Graewert (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #3206: ; Type: dummy / Software: (dammif (r10552)) / Radius of dummy atoms: 2.90 A; Comment: The Ensemble Resolution is calculated to be 56 +- 4 Angstrom from 20 independent runs.; Chi-square value: 0.980 / P-value: 0.405151
• Model #3200: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.012 / P-value: 0.901331
• Model #3201: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.012 / P-value: 0.901331
• Model #3202: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.012 / P-value: 0.901331
• Model #3203: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.012 / P-value: 0.901331
• Model #3204: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.012 / P-value: 0.901331
• Model #3205: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.012 / P-value: 0.901331

Sample

• Sample: Name: Full-length myotilin with N-terminally fused thioredoxin tag; Specimen concentration: 7.3 mg/ml
• Buffer: Name: 20 mM Tris, 400 mM NaCl, 250 mM arginine, 5% v/v glycerol; pH: 7.5

Entity #1747

Name: trx-MYOT / Type: protein / Description: his-trx-myotilin / Formula weight: 69.732 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q9UBF9
Sequence:

MKSDKIIHLT DDSFDTDVLK ADGAILVDFW AEWCGPCKMI APILDEIADE YQGKLTVAKL NIDQNPGTAP KYGIRGIPTL LLFKNGEVAA TKVGALSKGQ LKEFLDANLA GSGSGHMHHH HHHSSGLEVL FQGPFNYERP KHFIQSQNPC GSRLQPPGPE TSSFSSQTKQ SSIIIQPRQC TEQRFSASST LSSHITMSSS AFPASPQQHA GSNPGQRVTT TYNQSPASFL SSILPSQPDY NSSKIPSAMD SNYQQSSAGQ PINAKPSQTA NAKPIPRTPD HEIQGSKEAL IQDLERKLKC KDTLLHNGNQ RLTYEEKMAR RLLGPQNAAA VFQAQDDSGA QDSQQHNSEH ARLQVPTSQV RSRSTSRGDV NDQDAIQEKF YPPRFIQVPE NMSIDEGRFC RMDFKVSGLP APDVSWYLNG RTVQSDDLHK MIVSEKGLHS LIFEVVRASD AGAYACVAKN RAGEATFTVQ LDVLAKEHKR APMFIYKPQS KKVLEGDSVK LECQISAIPP PKLFWKRNNE MVQFNTDRIS LYQDNTGRVT LLIKDVNKKD AGWYTVSAVN EAGVTTCNTR LDVTARPNQT LPAPKQLRVR PTFSKYLALN GKGLNVKQAF NPEGEFQRLA AQSGLYESEE L

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Full-length myotilin with N-terminally fused thioredoxin tag
Measurement date: Jun 11, 2016 / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 3000 / Unit: 1/A /

	Min	Max
Q	0.0101	0.3295

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 535 /

	Min	Max
Q	0.112259	1.56725
P(R) point	1	535
R	0	16.71

Result

Type of curve: sec
Comments: To better account for the flexibility of Trx-MYOT, the ensemble optimization method (EOM) was employed. For this a large pool of 10 000 independent models with random conformations was generated by connecting the available high resolution structures of individual domains with randomized linkers represented by chains of dummy residues. The pdb codes used are 2KDG.pdb for myotilin Ig1, 2KKQ.pdb for myotillin Ig2 and 1T7P.pdb for the Trx tag. With a genetic algorithm-based selection, representative models were picked resulting in the best fit to the data with χ2 = 1.0. Overall, the EOM-selected models tend to be more compact than those in the random pool, whereby the most extended models are not selected. The volume fractions of the selected and deposited models (starting from top to bottom) were 10%, 10%, 40%, 20%, 10% and 10% respectively.

	Experimental	Porod
MW	70 kDa	82 kDa
Volume	-	131 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	1850	1833.64	9.78
Radius of gyration, Rg	5.335 nm	5.1 nm	0.06

	Min	Max
D	-	16.71
Guinier point	5	55