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- PDB-1b4r: PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1 -

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Basic information

Entry
Database: PDB / ID: 1b4r
TitlePKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1
ComponentsPROTEIN (PKD1_HUMAN)
KeywordsMEMBRANE PROTEIN / PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1 / POLYCYSTIN (PRECURSOR)
Function / homology
Function and homology information


metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / polycystin complex / mesonephric tubule development / mesonephric duct development / lung epithelium development / metanephric ascending thin limb development / lymph vessel morphogenesis / mitocytosis / metanephric proximal tubule development ...metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / polycystin complex / mesonephric tubule development / mesonephric duct development / lung epithelium development / metanephric ascending thin limb development / lymph vessel morphogenesis / mitocytosis / metanephric proximal tubule development / calcium-independent cell-matrix adhesion / Wnt receptor activity / migrasome / VxPx cargo-targeting to cilium / genitalia development / detection of mechanical stimulus / placenta blood vessel development / response to fluid shear stress / Golgi-associated vesicle membrane / cation channel complex / metanephric collecting duct development / digestive tract development / cartilage development / neural tube development / motile cilium / ciliary membrane / cartilage condensation / protein heterotetramerization / branching morphogenesis of an epithelial tube / skin development / spinal cord development / establishment of cell polarity / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of G1/S transition of mitotic cell cycle / cell surface receptor signaling pathway via JAK-STAT / anatomical structure morphogenesis / lateral plasma membrane / embryonic placenta development / regulation of cell adhesion / transcription regulator inhibitor activity / regulation of proteasomal protein catabolic process / calcium channel complex / regulation of mitotic spindle organization / protein export from nucleus / liver development / cell-matrix adhesion / kidney development / calcium ion transmembrane transport / calcium channel activity / Wnt signaling pathway / calcium ion transport / peptidyl-serine phosphorylation / heart development / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / basolateral plasma membrane / in utero embryonic development / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / cilium / protein domain specific binding / Golgi membrane / protein kinase binding / cell surface / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. ...Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / PKD domain / Polycystin domain / Polycystin domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Polycystic kidney disease (PKD) domain profile. / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / PKD domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SA
AuthorsBycroft, M.
CitationJournal: EMBO J. / Year: 1999
Title: The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.
Authors: Bycroft, M. / Bateman, A. / Clarke, J. / Hamill, S.J. / Sandford, R. / Thomas, R.L. / Chothia, C.
History
DepositionDec 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PKD1_HUMAN)


Theoretical massNumber of molelcules
Total (without water)7,9641
Polymers7,9641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein PROTEIN (PKD1_HUMAN)


Mass: 7963.906 Da / Num. of mol.: 1 / Fragment: PKD DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98161

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 500 / Manufacturer: Bruker / Model: AMX 500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XPLORstructure solution
RefinementMethod: SA / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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