[English] 日本語
Yorodumi
- PDB-9j4p: Regulatory domain and kinase domain of ALPK1 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j4p
TitleRegulatory domain and kinase domain of ALPK1 protein
Components(Alpha-protein kinase 1) x 2
KeywordsANTIVIRAL PROTEIN / Complex / Kinase / Immunity
Function / homology
Function and homology information


Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / photoreceptor connecting cilium / monosaccharide binding / cytoplasmic pattern recognition receptor signaling pathway / cilium assembly / Alpha-protein kinase 1 signaling pathway / response to bacterium / TAK1-dependent IKK and NF-kappa-B activation / spindle pole ...Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / photoreceptor connecting cilium / monosaccharide binding / cytoplasmic pattern recognition receptor signaling pathway / cilium assembly / Alpha-protein kinase 1 signaling pathway / response to bacterium / TAK1-dependent IKK and NF-kappa-B activation / spindle pole / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / cilium / ciliary basal body / 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
: / Alpha-protein kinase 1 / Alpha-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsXu, C. / Xu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Regulatory domain and kinase domain of ALPK1 protein
Authors: Xu, C. / Xu, T.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,3834
Polymers81,6982
Non-polymers6852
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-16 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.383, 93.383, 172.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

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


Mass: 49545.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALPK1, KIAA1527, LAK / Production host: Escherichia coli (E. coli)
References: UniProt: Q96QP1, non-specific serine/threonine protein kinase
#2: Protein Alpha-protein kinase 1


Mass: 32152.516 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alpk1, Kiaa1527 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CXB8, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-DY0 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 619.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N5O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 12% PEG3350 and 0.1 M CBTP, pH 8.2, 0.1% seed

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→46.82 Å / Num. obs: 35402 / % possible obs: 99 % / Redundancy: 2.3 % / Biso Wilson estimate: 31.03 Å2 / CC1/2: 1 / Net I/σ(I): 1.64
Reflection shellResolution: 2.25→2.31 Å / Num. unique obs: 1172 / CC1/2: 0.5

-
Processing

Software
NameVersionClassification
HKL-20002.7data reduction
PHASER1.3phasing
BUCCANEER0.1model building
PHENIX1.13refinement
HKL-20002.7data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→38.01 Å / SU ML: 0.2312 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1779 5.03 %
Rwork0.2062 33610 -
obs0.2077 35389 84.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.23 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5434 0 41 222 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795579
X-RAY DIFFRACTIONf_angle_d0.98297551
X-RAY DIFFRACTIONf_chiral_restr0.053862
X-RAY DIFFRACTIONf_plane_restr0.0083954
X-RAY DIFFRACTIONf_dihedral_angle_d18.70322068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.2868590.2911172X-RAY DIFFRACTION38.6
2.31-2.380.3002870.24561633X-RAY DIFFRACTION54.11
2.38-2.450.2905950.25151922X-RAY DIFFRACTION63.07
2.45-2.540.3003880.25072149X-RAY DIFFRACTION70.61
2.54-2.640.26541170.24862450X-RAY DIFFRACTION80.42
2.64-2.760.28481500.25252727X-RAY DIFFRACTION89.65
2.76-2.910.24661670.25162969X-RAY DIFFRACTION97.54
2.91-3.090.28451360.24033059X-RAY DIFFRACTION99.91
3.09-3.330.24761570.2283088X-RAY DIFFRACTION99.88
3.33-3.670.24221660.1983052X-RAY DIFFRACTION99.78
3.67-4.20.21971710.17653072X-RAY DIFFRACTION99.27
4.2-5.280.18761800.16253114X-RAY DIFFRACTION99.91
5.29-38.010.21192060.1823203X-RAY DIFFRACTION98.96
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)
10.6949056491990.298364656294-0.2628474244561.367379581040.06332141518470.5617216538020.0562908505438-0.2799130232260.06501494870630.1965143669070.0195356554332-0.0824692404118-0.06601013418530.1140234140630.2911652923380.1786000216320.07556355683620.006472595091920.3593138510180.02764126029750.18049603544136.962951946143.147331953652.9149912686
20.5840450554460.0175834493664-0.02439009795380.1626098483810.5530440456481.169688814610.074267023182-0.716901457453-0.3276690379310.08582318576470.169870436846-1.11370256503-0.2657987331650.0817831115148-0.5344490154340.266207496430.178275050104-0.2098426034370.4918498803960.412658397314-0.66537705820128.454597553128.283229176161.5574131916
30.2889387697280.220845292180.08124738766340.36043017179-0.2550751378230.220182469344-0.1392188607620.0508133973693-0.3505469513630.004330937209470.07470069784520.180637445616-0.0019039126481-0.1978186975120.6558453445620.185534058910.01257073294440.0283671243080.385669429808-0.03697881928230.3327722307856.1471883926623.22457796632.7200662384
40.470972173291-0.166654832256-0.1691104970440.544458701602-0.0987096927560.436371441343-0.09042443631190.02381782845190.17290217088-0.01306789238260.06141245518690.00291731382129-0.347125651842-0.0971979373220.07881101438120.2912984010180.08628487579390.01023683991110.3646688078530.011889615720.339915683212.085667512836.552029047940.6747983951
50.788242908206-0.0446890682194-0.2915433395160.565647200723-0.43364821420.802402318193-0.06993071943050.0353268638514-0.107829135677-0.01997770066990.06095873089610.06897728627060.155565552584-0.0274311846569-0.8565817344030.233875286172-0.00569857316459-0.004488570629630.3464909868590.04984755418590.30071010413720.53071870140.850247883530.5458516459
60.133373255173-0.02433882238710.08949016960350.207450457397-0.1264171779410.3150446837-0.0496081374976-0.1270455292130.385505489289-0.0250177420176-0.138363576029-0.057036262172-0.3068297840270.0323404955520.04451440542440.390327078957-0.0112771795356-0.06414668648240.2775359308690.001046096002980.53024033419317.302681002349.350420324936.2181784048
71.09336632822-0.0775288150871-0.02761902099571.04614419934-0.4262740719750.535927001997-0.1222257017760.3109724796710.315237812838-0.1774606456430.1151857695290.317391857985-0.0931759541942-0.0984393120327-0.09469580678830.318236653596-0.0912270770494-0.0779905692730.7435221081890.3105302339340.61635803474121.721861260451.312951921818.9834142549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 393 )BA1 - 3931 - 374
22chain 'B' and (resid 394 through 446 )BA394 - 446375 - 427
33chain 'A' and (resid 3 through 47 )AB3 - 471 - 45
44chain 'A' and (resid 48 through 113 )AB48 - 11346 - 103
55chain 'A' and (resid 114 through 162 )AB114 - 162104 - 152
66chain 'A' and (resid 163 through 192 )AB163 - 192153 - 170
77chain 'A' and (resid 193 through 277 )AB193 - 277171 - 255

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more