6LI9

Heteromeric amino acid transporter b0,+AT-rBAT complex bound with Arginine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM structure of the human heteromeric amino acid transporter b0,+AT-rBAT.

Yan, R.Li, Y.Shi, Y.Zhou, J.Lei, J.Huang, J.Zhou, Q.

(2020) Sci Adv 6: eaay6379-eaay6379

  • DOI: https://doi.org/10.1126/sciadv.aay6379
  • Primary Citation of Related Structures:  
    6LI9, 6LID

  • PubMed Abstract: 

    Heteromeric amino acid transporters (HATs) catalyze the transmembrane movement of amino acids, comprising two subunits, a heavy chain and a light chain, linked by a disulfide bridge. The b 0,+ AT (SLC7A9) is a representative light chain of HATs, forming heterodimer with rBAT, a heavy chain which mediates the membrane trafficking of b 0,+ AT. The b 0,+ AT-rBAT complex is an obligatory exchanger, which mediates the influx of cystine and cationic amino acids and the efflux of neutral amino acids in kidney and small intestine. Here, we report the cryo-EM structure of the human b 0,+ AT-rBAT complex alone and in complex with arginine substrate at resolution of 2.7 and 2.3 Å, respectively. The overall structure of b 0,+ AT-rBAT exists as a dimer of heterodimer consistent with the previous study. A ligand molecule is bound to the substrate binding pocket, near which an occluded pocket is identified, to which we found that it is important for substrate transport.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutral and basic amino acid transport protein rBAT
A, C
699Homo sapiensMutation(s): 0 
Gene Names: SLC3A1RBAT
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07837 (Homo sapiens)
Explore Q07837 
Go to UniProtKB:  Q07837
PHAROS:  Q07837
GTEx:  ENSG00000138079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07837
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
b(0,+)-type amino acid transporter 1
B, D
507Homo sapiensMutation(s): 0 
Gene Names: SLC7A9BAT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P82251 (Homo sapiens)
Explore P82251 
Go to UniProtKB:  P82251
PHAROS:  P82251
GTEx:  ENSG00000021488 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82251
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I
E, F, G, H, I, J, K, L, M, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
Q [auth B],
R [auth B],
U [auth D],
V [auth D]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
ARG (Subject of Investigation/LOI)
Query on ARG

Download Ideal Coordinates CCD File 
P [auth B],
T [auth D]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
CA
Query on CA

Download Ideal Coordinates CCD File 
O [auth A],
S [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0500402
Ministry of Science and Technology (MoST, China)China2016YFA0501100
Ministry of Science and Technology (MoST, China)China2015CB910101
National Natural Science Foundation of China (NSFC)China31621092
National Natural Science Foundation of China (NSFC)China31630017
National Natural Science Foundation of China (NSFC)China81861138009
National Natural Science Foundation of China (NSFC)China31971123

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-07-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary