7KY8

Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E1-ATP state

PDB DOI: https://doi.org/10.2210/pdb7KY8/pdb
EM Map EMD-23071: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae S288C
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2020-12-07 Released: 2021-01-06
Deposition Author(s): Bai, L., You, Q., Jain, B.K., Duan, H.D., Kovach, A., Graham, T.R., Li, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 235.21 kDa
Atom Count: 10,520
Modelled Residue Count: 1,274
Deposited Residue Count: 2,026
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipid-transporting ATPase DNF2	A	1,612	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: DNF2, YDR093W, YD8557.01 EC: 7.6.2.1 Membrane Entity: Yes
UniProt
Find proteins for Q12675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12675 Go to UniProtKB: Q12675
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12675
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkylphosphocholine resistance protein LEM3	B	414	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: LEM3, BRE3, ROS3, YNL323W, N0333 Membrane Entity: Yes
UniProt
Find proteins for P42838 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42838 Go to UniProtKB: P42838
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42838
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(3-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4	N/A	N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B]	G [auth A], H [auth A], I [auth A], J [auth A], N [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B]	O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]