8QSL | pdb_00008qsl

Cryo-EM structure of human SLC15A4 dimer in outward open state in LMNG

PDB DOI: https://doi.org/10.2210/pdb8QSL/pdb
EM Map EMD-18635: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2023-10-10 Released: 2023-10-25
Deposition Author(s): Rehan, S., Matsuoka, R., Jazayeri, A., Duerr, K.L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8QSL

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of human SLC15A4 dimer in outward open state in LMNG

Rehan, S., Matsuoka, R., Jazayeri, A., Duerr, K.L.

To be published.

Macromolecule Content

Total Structure Weight: 131.79 kDa
Atom Count: 8,506
Modeled Residue Count: 1,046
Deposited Residue Count: 1,154
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 15 member 4	A, B [auth C]	577	Homo sapiens	Mutation(s): 2 Gene Names: SLC15A4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N697 (Homo sapiens) Explore Q8N697 Go to UniProtKB: Q8N697
PHAROS: Q8N697 GTEx: ENSG00000139370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N697
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B [auth C]	Go to GlyGen: Q8N697-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGT Query on PGT Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain J [auth A] MOL2 format, chain R [auth C] MOL2 format, chain J [auth A] mmCIF format, chain R [auth C] mmCIF format, chain J [auth A]	J [auth A], R [auth C]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain J [auth A] Focus chain R [auth C] Interactions & Density Focus chain J [auth A] Focus chain R [auth C]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth A] H [auth A] C [auth A], D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], K [auth C], L [auth C], M [auth C], O [auth C], P [auth C], Q [auth C]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain F [auth A] MOL2 format, chain N [auth C] MOL2 format, chain F [auth A] mmCIF format, chain N [auth C] mmCIF format, chain F [auth A]	F [auth A], N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.