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- EMDB-65482: A membrane protein with ligands -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65482
TitleA membrane protein with ligands
Map data
Sample
  • Complex: A membrane protein with ligands
    • Protein or peptide: Long-chain fatty acid transport protein 2
  • Ligand: MAGNESIUM ION
  • Ligand: [[(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
  • Ligand: OLEIC ACID
KeywordsA membrane protein with ligands / PROTEIN TRANSPORT
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
Long-chain fatty acid transport protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsShi JH / Li A / Ma D
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303700 China
CitationJournal: To Be Published
Title: A membrane protein with ligands
Authors: Shi JH / Li A / Ma D
History
DepositionJul 22, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65482.png

Downloads & links

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Map

FileDownload / File: emd_65482.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 480 pix.
= 273.6 Å		0.57 Å/pix.
x 480 pix.
= 273.6 Å		0.57 Å/pix.
x 480 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.5325914 - 0.822704
Average (Standard dev.)0.00031485874 (±0.012400173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65482_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65482_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A membrane protein with ligands

EntireName: A membrane protein with ligands
Components
  • Complex: A membrane protein with ligands
    • Protein or peptide: Long-chain fatty acid transport protein 2
  • Ligand: MAGNESIUM ION
  • Ligand: [[(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
  • Ligand: OLEIC ACID

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Supramolecule #1: A membrane protein with ligands

SupramoleculeName: A membrane protein with ligands / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Long-chain fatty acid transport protein 2

MacromoleculeName: Long-chain fatty acid transport protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: arachidonate-CoA ligase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.405172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLSAIYTVLA GLLFLPLLVN LCCPYFFQDI GYFLKVAAVG RRVRSYGKRR PARTILRAFL EKARQTPHKP FLLFRDETLT YAQVDRRSN QVARALHDHL GLRQGDCVAL LMGNEPAYVW LWLGLVKLGC AMACLNYNIR AKSLLHCFQC CGAKVLLVSP E LQAAVEEI ...String:
MLSAIYTVLA GLLFLPLLVN LCCPYFFQDI GYFLKVAAVG RRVRSYGKRR PARTILRAFL EKARQTPHKP FLLFRDETLT YAQVDRRSN QVARALHDHL GLRQGDCVAL LMGNEPAYVW LWLGLVKLGC AMACLNYNIR AKSLLHCFQC CGAKVLLVSP E LQAAVEEI LPSLKKDDVS IYYVSRTSNT DGIDSFLDKV DEVSTEPIPE SWRSEVTFST PALYIYTSGT TGLPKAAMIT HQ RIWYGTG LTFVSGLKAD DVIYITLPFY HSAALLIGIH GCIVAGATLA LRTKFSASQF WDDCRKYNVT VIQYIGELLR YLC NSPQKP NDRDHKVRLA LGNGLRGDVW RQFVKRFGDI CIYEFYAATE GNIGFMNYAR KVGAVGRVNY LQKKIITYDL IKYD VEKDE PVRDENGYCV RVPKGEVGLL VCKITQLTPF NGYAGAKAQT EKKKLRDVFK KGDLYFNSGD LLMVDHENFI YFHDR VGDT FRWKGENVAT TEVADTVGLV DFVQEVNVYG VHVPDHEGRI GMASIKMKEN HEFDGKKLFQ HIADYLPSYA RPRFLR IQD TIEITGTFKH RKMTLVEEGF NPAVIKDALY FLDDTAKMYV PMTEDIYNAI SAKTLKL

UniProtKB: Long-chain fatty acid transport protein 2

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: [[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidany...

MacromoleculeName: [[(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
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1E1S
Molecular weightTheoretical: 611.667 Da

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Macromolecule #4: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 143446
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: AF2 predicted

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