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- PDB-9gs7: Cryo-EM structure of human SLC35B1-E33A variant with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 9gs7
TitleCryo-EM structure of human SLC35B1-E33A variant with AMP-PNP
Components
  • Fv-MBP
  • Solute carrier family 35 member B1
KeywordsTRANSPORT PROTEIN / ATP:ADP exchanger / AXER / AMP-PNP / membrane protein
Function / homology
Function and homology information


UDP-galactose transmembrane transporter activity / UDP-glucose transmembrane transporter activity / UDP-galactose transmembrane transport / ATP:ADP antiporter activity / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / nucleoplasm
Similarity search - Function
UAA transporter / UAA transporter family
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Solute carrier family 35 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsGulati, A. / Ahn, D. / Suades, A. / Drew, D.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structure and step-wise nucleotide translocation of the human ATP/ADP exchanger SLC35B1
Authors: Gulati, A. / Ahn, D. / Suades, A. / Chatzikyriakidou, Y. / Wolf, G. / Iwata, S. / Nomura, N. / Drew, D.
History
DepositionSep 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data 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
A: Solute carrier family 35 member B1
B: Fv-MBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7683
Polymers104,2622
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Solute carrier family 35 member B1 / ATP/ADP exchanger ER / AXER / Endoplasmic reticulum ATP/ADP translocase / UDP-galactose transporter- ...ATP/ADP exchanger ER / AXER / Endoplasmic reticulum ATP/ADP translocase / UDP-galactose transporter-related protein 1 / UGTrel1


Mass: 36566.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC35B1, UGTREL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P78383
#2: Antibody Fv-MBP


Mass: 67695.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Brevibacillus choshinensis (bacteria)
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationY

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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: Complex of human SLC35B1-E33A variant with Fv-MBP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223502 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 126.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214394
ELECTRON MICROSCOPYf_angle_d0.48835976
ELECTRON MICROSCOPYf_chiral_restr0.0376675
ELECTRON MICROSCOPYf_plane_restr0.0035735
ELECTRON MICROSCOPYf_dihedral_angle_d6.6524597

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