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- PDB-9tka: Structure of human CLN8 in the presence of oleate -

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Basic information

Entry
Database: PDB / ID: 9tka
TitleStructure of human CLN8 in the presence of oleate
ComponentsProtein CLN8
KeywordsMEMBRANE PROTEIN / Bis(monoacylglycero)phosphate / Batten disease / Glycerophosphoglycerol / Lysophosphatidylglycerol / Acyltransferase / Neurodegeneration
Function / homology
Function and homology information


ceramide metabolic process / ceramide binding / ceramide biosynthetic process / lipid transport / lipid biosynthetic process / lipid homeostasis / endoplasmic reticulum-Golgi intermediate compartment / phospholipid metabolic process / cholesterol metabolic process / negative regulation of proteolysis ...ceramide metabolic process / ceramide binding / ceramide biosynthetic process / lipid transport / lipid biosynthetic process / lipid homeostasis / endoplasmic reticulum-Golgi intermediate compartment / phospholipid metabolic process / cholesterol metabolic process / negative regulation of proteolysis / endoplasmic reticulum-Golgi intermediate compartment membrane / protein catabolic process / nervous system development / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
: / TRAM/LAG1/CLN8 homology domain / TLC domain / TLC domain profile. / TRAM, LAG1 and CLN8 homology domains.
Similarity search - Domain/homology
COENZYME A / OLEIC ACID / Protein CLN8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLacabanne, D. / Sheokand, P.K. / Ruprecht, J.J. / Petkevicius, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00028 United Kingdom
Wellcome TrustSBF00101078 United Kingdom
CitationJournal: To Be Published
Title: Stereospecific GPG acylation by CLN8 drives BMP biosynthesis and underpins Batten disease
Authors: Sheokand, P.K. / Lacabanne, D. / James, A.M. / Ruprecht, J.J. / van der Kleij, J. / Muller-Niva, J. / Salo, M.H. / Juneja, N. / Jenkins, J. / Shun Yu, C. / Pratt, M.A. / King, M.S. / Weimer, ...Authors: Sheokand, P.K. / Lacabanne, D. / James, A.M. / Ruprecht, J.J. / van der Kleij, J. / Muller-Niva, J. / Salo, M.H. / Juneja, N. / Jenkins, J. / Shun Yu, C. / Pratt, M.A. / King, M.S. / Weimer, J.M. / Koulman, A. / Hinttala, R. / Santorelli, F.M. / Murphy, M.P. / Kunji, E.R.S. / Petkevicus, K.
History
DepositionDec 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein CLN8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5833
Polymers33,5331
Non-polymers1,0502
Water19811
1
B: Protein CLN8
hetero molecules

B: Protein CLN8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1666
Polymers67,0662
Non-polymers2,1004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)262.44, 262.44

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Components

#1: Protein Protein CLN8


Mass: 33532.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLN8, C8orf61 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9UBY8
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CLN8 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 51.05 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1Warpparticle selection
2EPUimage acquisition
4WarpCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247856 / Symmetry type: POINT
RefinementResolution: 2.7→262.44 Å / Num. reflection obs: 1923431 / Average fsc free: 0.7261 / Average fsc work: 0.7489
Displacement parametersBiso mean: 83.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.002321710.0118
ELECTRON MICROSCOPYs_angle_nonh_deg0.960229661.7837
ELECTRON MICROSCOPYs_dihedral_angle_1_deg5.50852485
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.9144115
ELECTRON MICROSCOPYs_dihedral_angle_3_deg11.842432110
ELECTRON MICROSCOPYs_dihedral_angle_6_deg13.98349010
ELECTRON MICROSCOPYs_chiral_restr0.07363280.1324
ELECTRON MICROSCOPYs_planes0.003416760.02
ELECTRON MICROSCOPYs_nbd0.17929580.2
ELECTRON MICROSCOPYs_nbtor0.269413580.2
ELECTRON MICROSCOPYs_hbond_nbd0.0841460.2
ELECTRON MICROSCOPYs_symmetry_nbd0.234290.2
ELECTRON MICROSCOPYs_symmetry_hbond_nbd0.013410.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc freeFsc work
2.7-2.719ELECTRON MICROSCOPY415630.36060.3477
2.72-2.748ELECTRON MICROSCOPY579450.38750.3864
2.748-2.777ELECTRON MICROSCOPY561610.40860.435
2.777-2.807ELECTRON MICROSCOPY553630.42450.4758
2.807-2.837ELECTRON MICROSCOPY542730.44370.5071
2.837-2.868ELECTRON MICROSCOPY531730.46160.5305
2.868-2.9ELECTRON MICROSCOPY518850.47890.5554
2.9-2.932ELECTRON MICROSCOPY512950.50340.5779
2.932-2.965ELECTRON MICROSCOPY498450.53220.6027
2.965-2.999ELECTRON MICROSCOPY486370.57430.6322
2.999-3.034ELECTRON MICROSCOPY472390.61770.6639
3.034-3.069ELECTRON MICROSCOPY465690.65140.6861
3.07-3.106ELECTRON MICROSCOPY457690.67320.6991
3.106-3.143ELECTRON MICROSCOPY440670.68980.7086
3.143-3.181ELECTRON MICROSCOPY432730.70610.7177
3.181-3.22ELECTRON MICROSCOPY423330.72170.7316
3.22-3.26ELECTRON MICROSCOPY415930.73650.7477
3.26-3.301ELECTRON MICROSCOPY400150.75560.7673
3.301-3.343ELECTRON MICROSCOPY391890.77120.7883
3.343-3.386ELECTRON MICROSCOPY378610.78460.804
3.386-3.43ELECTRON MICROSCOPY374550.79360.8135
3.431-3.476ELECTRON MICROSCOPY363730.8040.8238
3.476-3.522ELECTRON MICROSCOPY350130.81680.8322
3.523-3.57ELECTRON MICROSCOPY348490.82980.8456
3.571-3.62ELECTRON MICROSCOPY333430.84220.8577
3.62-3.67ELECTRON MICROSCOPY328650.85140.8709
3.671-3.722ELECTRON MICROSCOPY312850.86120.8806
3.723-3.775ELECTRON MICROSCOPY306030.87140.8888
3.776-3.831ELECTRON MICROSCOPY303130.87810.8929
3.831-3.888ELECTRON MICROSCOPY287410.88250.8949
3.888-3.946ELECTRON MICROSCOPY284550.88580.9
3.947-4.006ELECTRON MICROSCOPY271570.89050.9049
4.007-4.068ELECTRON MICROSCOPY270450.8950.9105
4.069-4.133ELECTRON MICROSCOPY257770.89470.9084
4.134-4.199ELECTRON MICROSCOPY244350.8960.9079
4.199-4.266ELECTRON MICROSCOPY242770.89610.9069
4.267-4.337ELECTRON MICROSCOPY233170.89950.9102
4.338-4.41ELECTRON MICROSCOPY228510.90070.9117
4.411-4.485ELECTRON MICROSCOPY217450.90050.9115
4.486-4.564ELECTRON MICROSCOPY210330.90280.9113
4.564-4.644ELECTRON MICROSCOPY207130.90770.9158
4.645-4.728ELECTRON MICROSCOPY196470.91180.9195
4.729-4.815ELECTRON MICROSCOPY188410.91380.9209
4.816-4.904ELECTRON MICROSCOPY182170.91330.9192
4.906-4.998ELECTRON MICROSCOPY177270.9160.9204
4.999-5.095ELECTRON MICROSCOPY171250.91850.9222
5.097-5.195ELECTRON MICROSCOPY161250.91730.9214
5.197-5.301ELECTRON MICROSCOPY158710.91140.9174
5.302-5.41ELECTRON MICROSCOPY152250.89990.9068
5.411-5.524ELECTRON MICROSCOPY145330.88340.8894
5.525-5.643ELECTRON MICROSCOPY137530.86740.8735
5.644-5.765ELECTRON MICROSCOPY130590.86160.8657
5.768-5.896ELECTRON MICROSCOPY129730.86040.8622
5.899-6.032ELECTRON MICROSCOPY120210.86260.8641
6.034-6.172ELECTRON MICROSCOPY117310.86060.8608
6.175-6.322ELECTRON MICROSCOPY109810.85820.8571
6.324-6.479ELECTRON MICROSCOPY107250.85360.8515
6.48-6.642ELECTRON MICROSCOPY101170.85120.8472
6.645-6.815ELECTRON MICROSCOPY93750.85860.8545
6.817-6.994ELECTRON MICROSCOPY91330.87740.8738
6.999-7.188ELECTRON MICROSCOPY85770.8970.8953
7.191-7.39ELECTRON MICROSCOPY82270.90410.9042
7.393-7.601ELECTRON MICROSCOPY75970.90210.9028
7.608-7.831ELECTRON MICROSCOPY73770.89670.896
7.835-8.072ELECTRON MICROSCOPY69010.89220.8884
8.076-8.328ELECTRON MICROSCOPY63030.89220.8889
8.332-8.601ELECTRON MICROSCOPY60730.89090.8894
8.606-8.887ELECTRON MICROSCOPY56130.89580.8959
8.898-9.204ELECTRON MICROSCOPY52750.90930.9094
9.21-9.539ELECTRON MICROSCOPY49810.91750.9175
9.545-9.891ELECTRON MICROSCOPY45330.92420.9242
9.905-10.286ELECTRON MICROSCOPY43030.92310.9225
10.294-10.705ELECTRON MICROSCOPY40170.92730.9265
10.714-11.16ELECTRON MICROSCOPY35650.93850.9376
11.17-11.655ELECTRON MICROSCOPY33010.950.9495
11.667-12.183ELECTRON MICROSCOPY29910.95630.9557
12.21-12.791ELECTRON MICROSCOPY28570.95550.9545
12.806-13.445ELECTRON MICROSCOPY25170.95460.953
13.481-14.15ELECTRON MICROSCOPY21790.95430.9521
14.191-14.978ELECTRON MICROSCOPY20850.95180.9496
15.003-15.884ELECTRON MICROSCOPY18610.95430.9526
15.913-16.905ELECTRON MICROSCOPY16690.96120.9601
17.011-18.067ELECTRON MICROSCOPY13110.96660.966
18.11-19.347ELECTRON MICROSCOPY12490.96510.9653
19.453-20.945ELECTRON MICROSCOPY10890.95670.9581
21.08-22.756ELECTRON MICROSCOPY9070.93840.9405
22.842-24.688ELECTRON MICROSCOPY7290.9340.9361
25.023-27.511ELECTRON MICROSCOPY6250.96220.9633
27.664-30.716ELECTRON MICROSCOPY5710.96940.9701
30.929-34.761ELECTRON MICROSCOPY3810.96190.9624
35.07-40.022ELECTRON MICROSCOPY3010.95840.9585
40.495-46.393ELECTRON MICROSCOPY2250.96730.9671
47.915-57.269ELECTRON MICROSCOPY1750.98530.985
58.683-72.788ELECTRON MICROSCOPY1050.99660.9965
75.76-92.787ELECTRON MICROSCOPY490.99920.9992
107.141-262.44ELECTRON MICROSCOPY400.97440.9744

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