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- PDB-7ddx: Crystal structure of KANK1 S1179F mutant in complex wtih eIF4A1 -

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Basic information

Entry
Database: PDB / ID: 7ddx
TitleCrystal structure of KANK1 S1179F mutant in complex wtih eIF4A1
Components
  • Eukaryotic initiation factor 4A-I
  • KN motif and ankyrin repeat domains 1
KeywordsPROTEIN BINDING / nephrotic syndrome / kidney ankyrin repeat-containing protein / eukaryotic initiation factor / complex
Function / homology
Function and homology information


negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / podocyte cell migration / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / podocyte cell migration / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of substrate adhesion-dependent cell spreading / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / negative regulation of actin filament polymerization / regulation of establishment of cell polarity / negative regulation of Rho protein signal transduction / positive regulation of wound healing / translational initiation / translation initiation factor activity / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration / beta-catenin binding / ruffle membrane / double-stranded RNA binding / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cell population proliferation / RNA helicase activity / cytoskeleton / RNA helicase / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / Kank N-terminal motif / KN motif / ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain ...: / Kank N-terminal motif / KN motif / ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Helicase conserved C-terminal domain / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
KN motif and ankyrin repeat domains 1 / Eukaryotic initiation factor 4A-I
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPan, W. / Xu, Y. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770791 China
National Natural Science Foundation of China (NSFC)31971131 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Nephrotic-syndrome-associated mutation of KANK2 induces pathologic binding competition with physiological interactor KIF21A.
Authors: Xu, Y. / Guo, C. / Pan, W. / Zhao, C. / Ding, Y. / Xie, X. / Wei, Z. / Sun, Y. / Yu, C.
History
DepositionOct 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KN motif and ankyrin repeat domains 1
B: Eukaryotic initiation factor 4A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1488
Polymers54,5752
Non-polymers5726
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.628, 137.628, 57.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1505-

HOH

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Components

#1: Protein KN motif and ankyrin repeat domains 1


Mass: 27765.633 Da / Num. of mol.: 1 / Mutation: S1179F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kank1 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9Q238
#2: Protein Eukaryotic initiation factor 4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1


Mass: 26809.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4a1, Ddx2a, Eif4a / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60843, RNA helicase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 2.5M ammonium sulfate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21919 / % possible obs: 100 % / Redundancy: 10.7 % / Net I/σ(I): 21.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1716 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YAZ

5yaz


Resolution: 2.5→32.7 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.216 1091 4.99 %
Rwork0.191 --
obs0.192 21862 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 82.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 31 13 3518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023558
X-RAY DIFFRACTIONf_angle_d0.5724825
X-RAY DIFFRACTIONf_dihedral_angle_d11.3421284
X-RAY DIFFRACTIONf_chiral_restr0.023562
X-RAY DIFFRACTIONf_plane_restr0.003621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61380.3231320.29192547X-RAY DIFFRACTION99
2.6138-2.75160.31941330.25952578X-RAY DIFFRACTION100
2.7516-2.92390.24471380.23242561X-RAY DIFFRACTION100
2.9239-3.14940.25761300.22712596X-RAY DIFFRACTION100
3.1494-3.46610.26311360.2032581X-RAY DIFFRACTION100
3.4661-3.96690.21421400.18842597X-RAY DIFFRACTION100
3.9669-4.9950.21381430.15742628X-RAY DIFFRACTION100
4.995-32.69640.15181390.1682683X-RAY DIFFRACTION99
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)
18.0238-2.67310.15567.0762-1.12357.070.01560.6941-0.7987-0.2873-0.10040.91040.096-1.16820.15540.3852-0.0303-0.00340.7617-0.09270.5853-22.276-68.839-13.0567
24.90550.0220.09211.765-0.06671.0493-0.06340.51130.0487-0.13810.00420.18590.0467-0.13170.03060.372-0.01060.05710.6159-0.02140.4521-9.1902-64.0233-10.7935
36.32111.2107-1.32341.3859-0.05270.87460.0625-0.27060.1470.0599-0.14610.011-0.06750.0930.07410.3998-0.0340.0430.56180.02140.340921.8963-61.6248-8.3919
43.61641.1704-0.71420.7928-0.73190.9920.1526-0.84631.11260.5354-0.6931.5907-0.7182-1.03640.26850.79880.11780.08411.4896-0.73951.5441-6.4447-35.11118.8464
52.24381.5487-0.28432.1751.4572.62020.1357-0.67440.13780.4096-0.61410.58260.1327-0.2970.42240.4943-0.10640.13030.8338-0.21150.66513.6034-51.18319.7517
64.32051.09950.37583.18560.4243.0384-0.224-0.67580.76430.1721-0.26750.7198-0.3376-0.40550.50570.5468-0.0148-0.08330.759-0.25240.804412.3816-37.837414.292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1089 THROUGH 1107 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1108 THROUGH 1206 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1207 THROUGH 1334 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 25 THROUGH 93 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 94 THROUGH 167 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 168 THROUGH 236 )

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