7EPZ | pdb_00007epz

Overall structure of Erastin-bound xCT-4F2hc complex

PDB DOI: https://doi.org/10.2210/pdb7EPZ/pdb
EM Map EMD-31251: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-04-28 Released: 2022-04-06
Deposition Author(s): Yan, R.H., Li, Y.N., Zhang, Y.Y., Chi, X.M., Zhou, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

The structure of erastin-bound xCT-4F2hc complex reveals molecular mechanisms underlying erastin-induced ferroptosis.

Yan, R., Xie, E., Li, Y., Li, J., Zhang, Y., Chi, X., Hu, X., Xu, L., Hou, T., Stockwell, B.R., Min, J., Zhou, Q., Wang, F.

(2022) Cell Res 32: 687-690

PubMed: 35352032 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00642-w
Primary Citation Related Structures:
7EPZ

Organizational Affiliation

Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.

Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China.

The First Affiliated Hospital, The Fourth Affiliated Hospital, School of Public Health, Institute of Translational Medicine, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.

The First Affiliated Hospital, The Second Affiliated Hospital, Basic Medical Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, China.

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

Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.

Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, China.

Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA.

Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. zhouqiang@westlake.edu.cn.

The First Affiliated Hospital, The Second Affiliated Hospital, Basic Medical Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, China. fwang@zju.edu.cn.

Macromolecule Content

Total Structure Weight: 131.42 kDa
Atom Count: 7,431
Modeled Residue Count: 921
Deposited Residue Count: 1,168
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4F2 cell-surface antigen heavy chain	A	647	Homo sapiens	Mutation(s): 0 Gene Names: SLC3A2, hCG_2016598 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08195 (Homo sapiens) Explore P08195 Go to UniProtKB: P08195
PHAROS: P08195 GTEx: ENSG00000168003
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08195
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: P08195-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystine/glutamate transporter	B	521	Homo sapiens	Mutation(s): 0 Gene Names: SLC7A11 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPY5 (Homo sapiens) Explore Q9UPY5 Go to UniProtKB: Q9UPY5
PHAROS: Q9UPY5 GTEx: ENSG00000151012
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UPY5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX8 (Subject of Investigation/LOI) Query on PX8 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	H [auth B], I [auth B]	1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE C₃₉ H₇₆ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-M		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]
J9O (Subject of Investigation/LOI) Query on J9O Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one C₃₀ H₃₁ Cl N₄ O₄ BKQFRNYHFIQEKN-NRFANRHFSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.6

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971123
National Natural Science Foundation of China (NSFC)	China	81920108015
National Natural Science Foundation of China (NSFC)	China	31930059

Revision History (Full details and data files)

Version 1.0: 2022-04-06
Type: Initial release
Version 1.1: 2022-04-13
Changes: Database references
Version 2.0: 2022-05-25
Type: Coordinate replacement
Reason: Model completeness
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
Version 2.1: 2022-07-13
Changes: Database references
Version 2.2: 2024-10-30
Changes: Data collection, Structure summary