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- PDB-6jbj: Cryo-EM structure of human lysosomal cobalamin exporter ABCD4 -

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Basic information

Entry
Database: PDB / ID: 6jbj
TitleCryo-EM structure of human lysosomal cobalamin exporter ABCD4
ComponentsATP-binding cassette sub-family D member 4
KeywordsMEMBRANE PROTEIN / Human ABCD4 / Lysosomal cobalamin exporter / ATP-bound / lysosome-open conformation
Function / homology
Function and homology information


Defective ABCD4 causes MAHCJ / ABC-type vitamin B12 transporter / Transport of RCbl within the body / ABC-type vitamin B12 transporter activity / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / cobalamin transport / peroxisome organization ...Defective ABCD4 causes MAHCJ / ABC-type vitamin B12 transporter / Transport of RCbl within the body / ABC-type vitamin B12 transporter activity / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / cobalamin transport / peroxisome organization / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cellular response to leukemia inhibitory factor / transmembrane transport / peroxisome / lysosomal membrane / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / identical protein binding / membrane
Similarity search - Function
ABC transporter transmembrane region 2 / : / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...ABC transporter transmembrane region 2 / : / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Lysosomal cobalamin transporter ABCD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu, D. / Feng, Z. / Hou, W.T. / Jiang, Y.L. / Wang, L. / Sun, L.F. / Zhou, C.Z. / Chen, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2015CB910103 China
Chinese Academy of SciencesXDB08020304 China
National Natural Science Foundation of China31621002 China
CitationJournal: Cell Res / Year: 2019
Title: Cryo-EM structure of human lysosomal cobalamin exporter ABCD4.
Authors: Da Xu / Zhang Feng / Wen-Tao Hou / Yong-Liang Jiang / Liang Wang / Linfeng Sun / Cong-Zhao Zhou / Yuxing Chen /
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: ATP-binding cassette sub-family D member 4
B: ATP-binding cassette sub-family D member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,2624
Polymers146,2472
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17990 Å2
ΔGint-88 kcal/mol
Surface area43910 Å2

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Components

#1: Protein ATP-binding cassette sub-family D member 4 / PMP70-related protein / P70R / Peroxisomal membrane protein 1-like / PXMP1-L / Peroxisomal membrane ...PMP70-related protein / P70R / Peroxisomal membrane protein 1-like / PXMP1-L / Peroxisomal membrane protein 69 / PMP69


Mass: 73123.719 Da / Num. of mol.: 2 / Mutation: E549Q
Source method: isolated from a genetically manipulated source
Details: ATP / Source: (gene. exp.) Homo sapiens (human) / Gene: ABCD4, PXMP1L / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: O14678
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: Human ABCD4 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276557 / Symmetry type: POINT
Atomic model buildingB value: 199 / Protocol: AB INITIO MODEL

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