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- PDB-9vzp: A membrane protein with ligands -

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Basic information

Entry
Database: PDB / ID: 9vzp
TitleA membrane protein with ligands
ComponentsLong-chain fatty acid transport protein 2
KeywordsPROTEIN TRANSPORT / A membrane protein with ligands
Function / homology
Function and homology information


arachidonate-CoA ligase / phytanate-CoA ligase / very long-chain fatty acid-CoA ligase activity / arachidonate-CoA ligase activity / phytanate-CoA ligase activity / pristanate-CoA ligase activity / cholate-CoA ligase / cholate-CoA ligase activity / Alpha-oxidation of phytanate / long-chain-fatty-acid-CoA ligase ...arachidonate-CoA ligase / phytanate-CoA ligase / very long-chain fatty acid-CoA ligase activity / arachidonate-CoA ligase activity / phytanate-CoA ligase activity / pristanate-CoA ligase activity / cholate-CoA ligase / cholate-CoA ligase activity / Alpha-oxidation of phytanate / long-chain-fatty-acid-CoA ligase / methyl-branched fatty acid metabolic process / long-chain fatty acid-CoA ligase activity / long-chain fatty acid import into cell / fatty acid alpha-oxidation / Beta-oxidation of very long chain fatty acids / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / fatty acid beta-oxidation using acyl-CoA oxidase / long-chain fatty acid metabolic process / fatty-acyl-CoA biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / Fatty acyl-CoA biosynthesis / bile acid metabolic process / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / specific granule membrane / Peroxisomal protein import / endoplasmic reticulum lumen / Neutrophil degranulation / endoplasmic reticulum membrane / enzyme binding / extracellular exosome / ATP binding / plasma membrane / cytosol
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
: / OLEIC ACID / Long-chain fatty acid transport protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsShi, J.H. / Li, A. / Ma, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303700 China
CitationJournal: To Be Published
Title: A membrane protein with ligands
Authors: Shi, J.H. / Li, A. / Ma, D.
History
DepositionJul 22, 2025Deposition site: PDBJ / Processing site: PDBC
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: 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: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Long-chain fatty acid transport protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3244
Polymers70,4051
Non-polymers9183
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Long-chain fatty acid transport protein 2 / Arachidonate--CoA ligase / Fatty acid transport protein 2 / FATP-2 / Fatty-acid-coenzyme A ligase / ...Arachidonate--CoA ligase / Fatty acid transport protein 2 / FATP-2 / Fatty-acid-coenzyme A ligase / very long-chain 1 / Long-chain-fatty-acid--CoA ligase / Phytanate--CoA ligase / Solute carrier family 27 member 2 / THCA-CoA ligase / Very long-chain acyl-CoA synthetase / VLACS / VLCS / Very long-chain-fatty-acid-CoA ligase


Mass: 70405.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC27A2, ACSVL1, FACVL1, FATP2, VLACS / Production host: Homo sapiens (human)
References: UniProt: O14975, arachidonate-CoA ligase, long-chain-fatty-acid-CoA ligase, phytanate-CoA ligase, cholate-CoA ligase, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1E1S / [[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (~{Z})-octadec-9-enoate


Mass: 611.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H46N5O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
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: A membrane protein with ligands / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: 1400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.17.1_3660model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143446 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065078
ELECTRON MICROSCOPYf_angle_d0.5876864
ELECTRON MICROSCOPYf_dihedral_angle_d12.669720
ELECTRON MICROSCOPYf_chiral_restr0.044752
ELECTRON MICROSCOPYf_plane_restr0.004880

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