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- SASDD85: PDZK1 Domain 1-4 (Uncharacterized protein C1orf159) -

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Basic information

Entry
Database: SASBDB / ID: SASDD85
SamplePDZK1 Domain 1-4
  • Uncharacterized protein C1orf159 (protein), Homo sapiens
Function / homologyProtein of unknown function DUF4501 / Domain of unknown function (DUF4501) / membrane => GO:0016020 / Uncharacterized protein C1orf159
Function and homology information
Biological speciesHomo sapiens (human)
CitationJournal: Structure / Year: 2018
Title: Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.
Authors: Nelly R Hajizadeh / Joanna Pieprzyk / Petr Skopintsev / Ali Flayhan / Dmitri I Svergun / Christian Löw /
Abstract: The scaffolding protein PDZK1 has been associated with the regulation of membrane transporters. It contains four conserved PDZ domains, which typically recognize a 3-5-residue long motif at the C ...The scaffolding protein PDZK1 has been associated with the regulation of membrane transporters. It contains four conserved PDZ domains, which typically recognize a 3-5-residue long motif at the C terminus of the binding partner. The atomic structures of the individual domains are available but their spatial arrangement in the full-length context influencing the binding properties remained elusive. Here we report a systematic study of full-length PDZK1 and deletion constructs using small-angle X-ray scattering, complemented with biochemical and functional studies on PDZK1 binding to known membrane protein partners. A hybrid modeling approach utilizing multiple scattering datasets yielded a well-defined, extended, asymmetric L-shaped domain organization of PDZK1 in contrast to a flexible "beads-on-string" model predicted by bioinformatics analysis. The linker regions of PDZK1 appear to play a central role in the arrangement of the four domains underlying the importance of studying scaffolding proteins in their full-length context.
Contact author
  • Nelly Hajizadeh (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #1863
Type: dummy / Radius of dummy atoms: 1.90 A / Chi-square value: 0.83 / P-value: 0.371417
Search similar-shape structures of this assembly by Omokage search (details)
Model #1864
Type: dummy / Radius of dummy atoms: 2.50 A / Chi-square value: 1.200
Search similar-shape structures of this assembly by Omokage search (details)
Model #1885
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.15 / P-value: 0.000007
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: PDZK1 Domain 1-4 / Specimen concentration: 0.80-6.40
BufferName: 20mM Hepes 150 NaCl 0.5 mM TCEP / pH: 7.5
Entity #1004Type: protein / Description: Uncharacterized protein C1orf159 / Formula weight: 53.405 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q5T2W7
Sequence: MHHHHHHSSG VDLGTENLYF QSMMTSTFNP RECKLSKQEG QNYGFFLRIE KDTEGHLVRV VEKCSPAEKA GLQDGDRVLR INGVFVDKEE HMQVVDLVRK SGNSVTLLVL DGDSYEKAVK TRVDLKELGQ SQKEQGLSDN ILSPVMNGGV QTWTQPRLCY LVKEGGSYGF ...Sequence:
MHHHHHHSSG VDLGTENLYF QSMMTSTFNP RECKLSKQEG QNYGFFLRIE KDTEGHLVRV VEKCSPAEKA GLQDGDRVLR INGVFVDKEE HMQVVDLVRK SGNSVTLLVL DGDSYEKAVK TRVDLKELGQ SQKEQGLSDN ILSPVMNGGV QTWTQPRLCY LVKEGGSYGF SLKTVQGKKG VYMTDITPQG VAMRAGVLAD DHLIEVNGEN VEDASHEEVV EKVKKSGSRV MFLLVDKETD KRHVEQKIQF KRETASLKLL PHQPRIVEMK KGSNGYGFYL RAGSEQKGQI IKDIDSGSPA EEAGLKNNDL VVAVNGESVE TLDHDSVVEM IRKGGDQTSL LVVDKETDNM YRLAHFSPFL YYQSQELPNG SVKEAPAPTP TSLEVSSPPD TTEEVDHKPK LCRLAKGENG YGFHLNAIRG LPGSFIKEVQ KGGPADLAGL EDEDVIIEVN GVNVLDEPYE KVVDRIQSSG KNVTLLVCGK KAY

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Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 4 mm
DetectorName: Pilatus 2M
Scan
Title: PDZK1 Domain 1-4 / Measurement date: Oct 28, 2016 / Storage temperature: 11 °C / Cell temperature: 15 °C / Exposure time: 0.045 sec. / Number of frames: 30 / Unit: 1/nm /
MinMax
Q0.0279 3.7771
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 956 /
MinMax
Q0.0592187 2.05055
P(R) point1 956
R0 14.98
Result
Type of curve: merged
ExperimentalStandardPorod
MW50.2 kDa50.2 kDa75 kDa
Volume--120.03 nm3

P(R)GuinierGuinier error
Forward scattering, I00.0435 0.043 -
Radius of gyration, Rg4.056 nm3.94 nm0.02

MinMax
D-14.98
Guinier point16 147

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