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- PDB-6rqr: Extended NHERF1 PDZ2 domain in complex with the PDZ-binding motif... -

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Basic information

Entry
Database: PDB / ID: 6rqr
TitleExtended NHERF1 PDZ2 domain in complex with the PDZ-binding motif of CFTR
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1,Cystic fibrosis transmembrane conductance regulator
KeywordsPROTEIN BINDING / Complex / PDZ / PDZ-binding motif
Function / homology
Function and homology information


renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / maintenance of epithelial cell apical/basal polarity ...renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / maintenance of epithelial cell apical/basal polarity / import across plasma membrane / bile acid secretion / positive regulation of voltage-gated chloride channel activity / regulation of protein kinase activity / gamma-aminobutyric acid import / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / stereocilium tip / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / plasma membrane organization / transepithelial water transport / phospholipase C-activating dopamine receptor signaling pathway / RHO GTPases regulate CFTR trafficking / cilium organization / gland morphogenesis / channel activator activity / intracellular pH elevation / amelogenesis / ATPase-coupled inorganic anion transmembrane transporter activity / chloride channel inhibitor activity / establishment of Golgi localization / fibroblast migration / Golgi-associated vesicle membrane / intracellular phosphate ion homeostasis / multicellular organismal-level water homeostasis / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / cholesterol transport / negative regulation of fibroblast migration / type 3 metabotropic glutamate receptor binding / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / membrane hyperpolarization / auditory receptor cell stereocilium organization / vesicle docking involved in exocytosis / negative regulation of mitotic cell cycle / negative regulation of platelet-derived growth factor receptor signaling pathway / beta-2 adrenergic receptor binding / chloride transmembrane transporter activity / growth factor receptor binding / nuclear migration / sperm capacitation / cholesterol biosynthetic process / regulation of cell size / microvillus membrane / renal absorption / microvillus / chloride channel activity / RHOQ GTPase cycle / positive regulation of exocytosis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / 14-3-3 protein binding / endomembrane system / cellular response to forskolin / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / chloride transmembrane transport / response to endoplasmic reticulum stress / cellular response to cAMP / morphogenesis of an epithelium / cell periphery / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / protein localization to plasma membrane / filopodium / PDZ domain binding / ABC-family proteins mediated transport / establishment of localization in cell / sensory perception of sound / clathrin-coated endocytic vesicle membrane / brush border membrane / negative regulation of canonical Wnt signaling pathway / recycling endosome / beta-catenin binding / Chaperone Mediated Autophagy / negative regulation of ERK1 and ERK2 cascade / Aggrephagy / transmembrane transport / Wnt signaling pathway
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / PDZ domain ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / PDZ domain / Pdz3 Domain / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMartin, E.R. / Ford, R.C. / Robinson, R.C.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: In vivocrystals reveal critical features of the interaction between cystic fibrosis transmembrane conductance regulator (CFTR) and the PDZ2 domain of Na+/H+exchange cofactor NHERF1.
Authors: Martin, E.R. / Barbieri, A. / Ford, R.C. / Robinson, R.C.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Cystic fibrosis transmembrane conductance regulator
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Cystic fibrosis transmembrane conductance regulator


Theoretical massNumber of molelcules
Total (without water)32,2362
Polymers32,2362
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint3 kcal/mol
Surface area15240 Å2
Unit cell
Length a, b, c (Å)84.950, 85.039, 89.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-395-

HOH

31A-399-

HOH

41A-402-

HOH

51A-407-

HOH

61B-330-

HOH

71B-331-

HOH

81B-345-

HOH

91B-353-

HOH

101B-383-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 149 through 246 or resid 248 through 273))
21(chain B and (resid 149 through 246 or resid 248 through 273))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and (resid 149 through 246 or resid 248 through 273))AA149 - 24620 - 117
12GLNGLNLEULEU(chain A and (resid 149 through 246 or resid 248 through 273))AA248 - 273119 - 144
21PROPROPROPRO(chain B and (resid 149 through 246 or resid 248 through 273))BB149 - 24620 - 117
22GLNGLNLEULEU(chain B and (resid 149 through 246 or resid 248 through 273))BB248 - 273119 - 144

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Cystic fibrosis transmembrane conductance regulator / NHERF-1 / Ezrin-radixin-moesin-binding phosphoprotein 50 / EBP50 / Regulatory cofactor of Na(+)/H(+) ...NHERF-1 / Ezrin-radixin-moesin-binding phosphoprotein 50 / EBP50 / Regulatory cofactor of Na(+)/H(+) exchanger / Sodium-hydrogen exchanger regulatory factor 1 / Solute carrier family 9 isoform A3 regulatory factor 1 / CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 16118.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3R1, NHERF, NHERF1, CFTR, ABCC7 / Production host: Escherichia coli (E. coli)
References: UniProt: O14745, UniProt: P13569, channel-conductance-controlling ATPase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 1.65 M ammonium sulphate, 100 mM tri-sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 16793 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.984 / Net I/σ(I): 4.3
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 1653 / CC1/2: 0.634

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q3H

4q3h


Resolution: 2.2→19.81 Å / Cross valid method: THROUGHOUT / σ(F): 3.95 / Phase error: 21.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.233 783 4.68 %
Rwork0.2059 15813 -
obs0.2112 16735 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.34 Å2 / Biso mean: 39.3265 Å2 / Biso min: 7.3 Å2
Refinement stepCycle: final / Resolution: 2.2→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 204 2132
Biso mean---32.92 -
Num. residues----250
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1177X-RAY DIFFRACTION10.795TORSIONAL
12B1177X-RAY DIFFRACTION10.795TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.340.32051240.28622566269094
2.34-2.520.32011220.2882597271995
2.52-2.770.34471140.26592627274196
2.77-3.170.25041330.22112636276995
3.17-3.980.20451400.17072655279595
3.99-19.810.2161470.16812732287995

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