7PEM | pdb_00007pem

Cryo-EM structure of phophorylated Drs2p-Cdc50p in a PS and ATP-bound E2P state

PDB DOI: https://doi.org/10.2210/pdb7PEM/pdb
EM Map EMD-13353: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2021-08-10 Released: 2022-08-24
Deposition Author(s): Timcenko, M., Wang, Y., Lyons, J.A., Nissen, P., Lindorff-Larsen, K.
Funding Organization(s): Lundbeckfonden

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Substrate Transport and Specificity in a Phospholipid Flippase

Wang, Y., Lyons, J.A., Timcenko, M., Kummerer, F., de Groot, B.L., Nissen, P., Gapsys, V., Lindorff-Larsen, K.

To be published.

Macromolecule Content

Total Structure Weight: 202.9 kDa
Atom Count: 11,620
Modeled Residue Count: 1,416
Deposited Residue Count: 1,746
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phospholipid-transporting ATPase DRS2	A	1,355	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: DRS2, YAL026C, FUN38 EC: 7.6.2.1 Membrane Entity: Yes
UniProt
Find proteins for P39524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39524 Go to UniProtKB: P39524
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39524
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 50	B [auth C]	391	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CDC50, YCR094W, YCR94W Membrane Entity: Yes
UniProt
Find proteins for P25656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25656 Go to UniProtKB: P25656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25656
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth C]	Go to GlyGen: P25656-1
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 [auth B], D	2		N-Glycosylation	Interactions Focus chain C [auth B] Focus chain D Interactions & Density Focus chain C [auth B] Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G31886NL GlyCosmos: G31886NL GlyGen: G31886NL

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2Y5 Query on 2Y5 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate C₄₇ H₈₄ O₁₆ P₂ ROKMWIUSHIHOGI-BWTMTLBLSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
Q3G (Subject of Investigation/LOI) Query on Q3G Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine C₄₀ H₇₈ N O₁₀ P WZFUPCSEUKNOBF-PQQNNWGCSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]