6LCR | pdb_00006lcr

Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP state

PDB DOI: https://doi.org/10.2210/pdb6LCR/pdb
EM Map EMD-0873: EMDB EMDataResource

Classification: LIPID TRANSPORT
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2019-11-19 Released: 2020-04-29
Deposition Author(s): He, Y., Xu, J., Wu, X., Li, L.
Funding Organization(s): National Natural Science Foundation of China

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 2.1 of the entry. See complete history.

Literature

Structures of a P4-ATPase lipid flippase in lipid bilayers.

He, Y., Xu, J., Wu, X., Li, L.

(2020) Protein Cell 11: 458-463

PubMed: 32303992 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s13238-020-00712-y
Primary Citation Related Structures:
6LCP, 6LCR

Organizational Affiliation

State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.

Macromolecule Content

Total Structure Weight: 225.4 kDa
Atom Count: 11,561
Modeled Residue Count: 1,420
Deposited Residue Count: 1,962
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipid-transporting ATPase	A	1,555	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0012810 EC: 7.6.2.1 Membrane Entity: Yes
UniProt
Find proteins for G0S196 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S196 Go to UniProtKB: G0S196
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S196
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cdc50	B	407	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0052360 Membrane Entity: Yes
UniProt
Find proteins for G0SDN0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SDN0 Go to UniProtKB: G0SDN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SDN0
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B
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, E	2		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P5S Query on P5S 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)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ACP Query on ACP 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]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
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]

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
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31870835

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2020-06-10
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-13
Changes: Data collection, Database references, Structure summary