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- PDB-6ezi: PDZK1 domain 4 in complex with C-terminal peptide of human PepT2. -

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Basic information

Entry
Database: PDB / ID: 6ezi
TitlePDZK1 domain 4 in complex with C-terminal peptide of human PepT2.
Components
  • Na(+)/H(+) exchange regulatory cofactor NHE-RF3
  • Solute carrier family 15 member 2
KeywordsPROTEIN BINDING / PDZK1 Human peptide transporter Na(+)-H(+) exchange regulatory cofactor NHE-RF3 Protein complex binding
Function / homology
Function and homology information


positive regulation of cation transmembrane transport / carnitine transport / positive regulation of ion transmembrane transporter activity / peptidoglycan transport / dipeptide transport / Proton/oligopeptide cotransporters / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / scavenger receptor binding ...positive regulation of cation transmembrane transport / carnitine transport / positive regulation of ion transmembrane transporter activity / peptidoglycan transport / dipeptide transport / Proton/oligopeptide cotransporters / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / scavenger receptor binding / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / xenobiotic detoxification by transmembrane export across the plasma membrane / positive regulation of protein localization to membrane / xenobiotic transport / microvillus membrane / renal absorption / brush border / transport across blood-brain barrier / positive regulation of protein targeting to membrane / monoatomic ion transport / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / brush border membrane / protein transport / apical plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / extracellular exosome / plasma membrane
Similarity search - Function
Oligopeptide transporter / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / PDZ domain / Alpha/beta knot methyltransferases / PDZ domain / Pdz3 Domain ...Oligopeptide transporter / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / PDZ domain / Alpha/beta knot methyltransferases / PDZ domain / Pdz3 Domain / MFS transporter superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Solute carrier family 15 member 2 / Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50332103817 Å
AuthorsLoew, C. / Flayhan, A. / Pieprzyk, J.
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.
History
DepositionNov 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-RF3
B: Solute carrier family 15 member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9513
Polymers10,8592
Non-polymers921
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-5 kcal/mol
Surface area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.400, 54.400, 150.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF3 / NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi ...NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / PDZ domain-containing protein 1 / Sodium-hydrogen exchanger regulatory factor 3


Mass: 9653.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDZK1, CAP70, NHERF3, PDZD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5T2W1
#2: Protein/peptide Solute carrier family 15 member 2 / Kidney H(+)/peptide cotransporter / Oligopeptide transporter / kidney isoform / Peptide transporter 2


Mass: 1205.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16348
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Trisodium citrate pH 6.45 20% PEG 4000 20 %(v/v) isopropanol

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.07166 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07166 Å / Relative weight: 1
ReflectionResolution: 1.5→47.12 Å / Num. obs: 21856 / % possible obs: 99.7 % / Redundancy: 35 % / Biso Wilson estimate: 18.8597757139 Å2 / Rmerge(I) obs: 0.06612 / Rrim(I) all: 0.06711 / Net I/σ(I): 33.85
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 34.8 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3421 / CC1/2: 0.776 / Rrim(I) all: 0.9771 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Coot1.10.1_2155model building
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2Z

4r2z


Resolution: 1.50332103817→47.1117819659 Å / SU ML: 0.217232632749 / Cross valid method: FREE R-VALUE / σ(F): 1.36321607249 / Phase error: 25.1660957435
RfactorNum. reflection% reflectionSelection details
Rfree0.214201883363 1093 5.00137274641 %5%
Rwork0.193827423621 ---
obs0.194841046699 21854 99.708002555 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.6794828473 Å2
Refinement stepCycle: LAST / Resolution: 1.50332103817→47.1117819659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 6 124 820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00700564800598809
X-RAY DIFFRACTIONf_angle_d0.8359815742081100
X-RAY DIFFRACTIONf_chiral_restr0.0588887482759127
X-RAY DIFFRACTIONf_plane_restr0.00504508991792146
X-RAY DIFFRACTIONf_dihedral_angle_d14.9040965594314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5033-1.57170.4157355081091310.3806827514212499X-RAY DIFFRACTION98.7978963186
1.5717-1.65460.3473710478971340.3335239337882542X-RAY DIFFRACTION100
1.6546-1.75830.3255349466441340.2908441510562540X-RAY DIFFRACTION99.9252615845
1.7583-1.8940.2589359859671340.2401354762282547X-RAY DIFFRACTION99.8138495905
1.894-2.08470.2343627457811350.1935947868292569X-RAY DIFFRACTION99.5948434622
2.0847-2.38630.2172273689021360.1726824101772581X-RAY DIFFRACTION99.8897058824
2.3863-3.00640.196460394151390.1846198154522648X-RAY DIFFRACTION99.7851772288
3.0064-47.13490.1676314483751500.1565621267852835X-RAY DIFFRACTION99.8995983936
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.384263472-1.023670295041.922080936048.366256923943.736823596443.546203810360.2910058155760.3714813648680.03136865893520.132317736851-0.410171053865-0.26229380727-0.285078360246-0.003533054472160.05209253962910.223252011175-0.0398861201901-0.007838385235550.1191055679880.008190586245570.22835618705518.27120264837.455989044480.2120414887
22.670109521740.4527354956590.8390516940472.274634177820.4754865970712.72287190618-0.1984309335720.231274957650.376978936332-0.085440358452-0.0576859864364-0.0735599247933-0.9542067139090.176264388120.274747540070.478318308947-0.0544930662121-0.03018000747280.200754797035-0.01259651534170.25514281478618.188081515315.428206665477.7726075767
32.90555915669-1.451871198850.9916159880247.570393565421.239967197024.469445067410.108272906601-0.1508158287670.2171959739-0.236828143165-0.2138726291630.297088486311-0.660330488775-0.8538378173640.06786291640590.2813112451880.0901257050295-0.005353541757330.253835756215-0.02132980905420.2286467937987.3814318329511.311047653873.5245059663
46.72173991622-3.597185689271.08065359473.147903730631.757179778714.653516698060.05015051564580.07209409011130.07434515526540.09698800333830.04035322625340.0831635591723-0.4362273570340.0179156592636-0.1346716781370.238232037949-0.063040599183-0.004285858236310.0994903717453-0.0184149904020.18597069792414.43869442546.8350382236678.1073325961
52.94754000248-1.155759807460.4778863391164.84615371117-5.72561272637.06013091195-0.114266729719-0.03110522803291.054256952310.191416871618-0.0440515817007-0.0895919202619-2.282466511670.3817399807880.08755386037380.8800350415970.0343895368058-0.0595667999040.316901134688-0.0493438878960.52021735877511.709557243822.295320257480.8669161435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 372 through 390 )
2X-RAY DIFFRACTION2chain 'A' and (resid 391 through 426 )
3X-RAY DIFFRACTION3chain 'A' and (resid 427 through 444 )
4X-RAY DIFFRACTION4chain 'A' and (resid 445 through 457 )
5X-RAY DIFFRACTION5chain 'B' and (resid 764 through 771 )

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