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- PDB-8u3g: Structure of NAAG-bound Sialin -

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Basic information

Entry
Database: PDB / ID: 8u3g
TitleStructure of NAAG-bound Sialin
ComponentsSialin
KeywordsMEMBRANE PROTEIN / Transporter
Function / homology
Function and homology information


sialic acid:proton symporter activity / sialic acid transport / D-glucuronate transmembrane transporter activity / Defective SLC17A5 causes Salla disease (SD) and ISSD / Organic anion transporters / sialic acid transmembrane transporter activity / carbohydrate:proton symporter activity / Sialic acid metabolism / monoatomic anion transport / amino acid transport ...sialic acid:proton symporter activity / sialic acid transport / D-glucuronate transmembrane transporter activity / Defective SLC17A5 causes Salla disease (SD) and ISSD / Organic anion transporters / sialic acid transmembrane transporter activity / carbohydrate:proton symporter activity / Sialic acid metabolism / monoatomic anion transport / amino acid transport / monoatomic ion transport / response to bacterium / synaptic vesicle membrane / basolateral plasma membrane / lysosome / lysosomal membrane / membrane / plasma membrane / cytosol
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
ACETYL GROUP / ASPARTIC ACID / GLUTAMIC ACID / Sialin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsSchmiege, P. / Li, X.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)135343 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)110229 United States
Welch FoundationI-1957 United States
CitationJournal: To Be Published
Title: Structure of NAAG-bound Sialin
Authors: Schmiege, P. / Li, X.
History
DepositionSep 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0054
Polymers55,6811
Non-polymers3243
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 Sialin


Mass: 55681.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC17A5 / Production host: Homo sapiens (human) / References: UniProt: Q9NRA2
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Structure of NAAG-bound Sialin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
13PHENIX1.20.1-4487model refinement
14ISOLDE1.6.0model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272923 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045237
ELECTRON MICROSCOPYf_angle_d0.6087126
ELECTRON MICROSCOPYf_dihedral_angle_d13.4612988
ELECTRON MICROSCOPYf_chiral_restr0.044799
ELECTRON MICROSCOPYf_plane_restr0.004880

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