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- PDB-8zd3: Crystal structure of ALPK1-N+K in complex with CDP-heptose -

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Basic information

Entry
Database: PDB / ID: 8zd3
TitleCrystal structure of ALPK1-N+K in complex with CDP-heptose
Components(Alpha-protein kinase ...) x 2
KeywordsIMMUNE SYSTEM / complex / angonist / pattern recognition receptor
Function / homology
Function and homology information


monosaccharide binding / cytoplasmic pattern recognition receptor signaling pathway / cilium assembly / Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / spindle pole / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / ciliary basal body / cilium ...monosaccharide binding / cytoplasmic pattern recognition receptor signaling pathway / cilium assembly / Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / spindle pole / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / ciliary basal body / cilium / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / cytosol
Similarity search - Function
Alpha-protein kinase 1 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / CYTIDINE-5'-DIPHOSPHATE / Alpha-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShe, Y. / Ding, J.J. / Shao, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: crystal structure of Alpha-kinase 1 N+K in complex with CDP-hep
Authors: She, Y. / Ding, J. / Shao, F.
History
DepositionMay 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-protein kinase 1
B: Alpha-protein kinase 1
C: Alpha-protein kinase 1
D: Alpha-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,84310
Polymers168,4854
Non-polymers1,3586
Water4,234235
1
A: Alpha-protein kinase 1
B: Alpha-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9215
Polymers84,2432
Non-polymers6793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-25 kcal/mol
Surface area32230 Å2
MethodPISA
2
C: Alpha-protein kinase 1
D: Alpha-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9215
Polymers84,2432
Non-polymers6793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-21 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.787, 65.944, 108.679
Angle α, β, γ (deg.)89.619, 107.771, 111.122
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Alpha-protein kinase ... , 2 types, 4 molecules ACBD

#1: Protein Alpha-protein kinase 1 / Chromosome 4 kinase / Lymphocyte alpha-protein kinase


Mass: 50672.184 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALPK1, KIAA1527, LAK
Production host: Insect expression vector pBlueBacmsGCB1His (others)
References: UniProt: Q96QP1, non-specific serine/threonine protein kinase
#2: Protein Alpha-protein kinase 1 / Chromosome 4 kinase / Lymphocyte alpha-protein kinase


Mass: 33570.363 Da / Num. of mol.: 2 / Fragment: C-terminal domain kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALPK1, KIAA1527, LAK
Production host: Insect expression vector pBlueBacmsGCB1His (others)
References: UniProt: Q96QP1, non-specific serine/threonine protein kinase

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Sugars , 1 types, 2 molecules

#4: Sugar ChemComp-A1L1P / (2R,3S,4S,5S,6R)-6-[(1S)-1,2-bis(oxidanyl)ethyl]oxane-2,3,4,5-tetrol / L-glycero-beta-D-manno-heptopyranose


Type: D-saccharide, beta linking / Mass: 210.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O7 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 239 molecules

#3: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.19 % / Description: cube
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8% tacsimate ph 6.0, 14% PEG 3350 / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.3→30.55 Å / Num. obs: 124422 / % possible obs: 96.39 % / Redundancy: 1.8 % / Biso Wilson estimate: 38.95 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.99
Reflection shellResolution: 2.303→2.386 Å / Rmerge(I) obs: 0.354 / Num. unique obs: 9482

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30.55 Å / SU ML: 0.328 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.8389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 1998 3.04 %
Rwork0.2399 63624 -
obs0.2407 65622 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11105 0 2 235 11342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006211332
X-RAY DIFFRACTIONf_angle_d0.78215328
X-RAY DIFFRACTIONf_chiral_restr0.05041733
X-RAY DIFFRACTIONf_plane_restr0.00441931
X-RAY DIFFRACTIONf_dihedral_angle_d15.26874157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.33041440.29984603X-RAY DIFFRACTION96.92
2.36-2.420.31521440.28854601X-RAY DIFFRACTION97.25
2.42-2.50.34721440.2914559X-RAY DIFFRACTION97.82
2.5-2.580.30941420.30214519X-RAY DIFFRACTION96.36
2.58-2.670.38461400.31864418X-RAY DIFFRACTION93.61
2.67-2.780.3041390.3034424X-RAY DIFFRACTION93.47
2.78-2.90.30691450.27674621X-RAY DIFFRACTION97.99
2.9-3.050.31321450.27914618X-RAY DIFFRACTION98.37
3.05-3.250.33381450.2744598X-RAY DIFFRACTION97.65
3.25-3.50.29921400.26494469X-RAY DIFFRACTION94.16
3.5-3.850.25511390.23324468X-RAY DIFFRACTION94.87
3.85-4.40.21671400.20534467X-RAY DIFFRACTION94.81
4.4-5.540.2221460.19414655X-RAY DIFFRACTION99.07
5.54-30.550.21121450.18584604X-RAY DIFFRACTION97.76

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