6TA1

Fatty acid synthase of S. cerevisiae

PDB DOI: https://doi.org/10.2210/pdb6TA1/pdb
EM Map EMD-10420: EMDB EMDataResource

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2019-10-29 Released: 2019-11-06
Deposition Author(s): Vonck, J., D'Imprima, E., Joppe, M., Grininger, M.
Funding Organization(s): Volkswagen Foundation

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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

Literature

The resolution revolution in cryoEM requires high-quality sample preparation: a rapid pipeline to a high-resolution map of yeast fatty acid synthase.

Joppe, M., D'Imprima, E., Salustros, N., Paithankar, K.S., Vonck, J., Grininger, M., Kuhlbrandt, W.

(2020) IUCrJ 7: 220-227

PubMed: 32148850 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2052252519017366
Primary Citation of Related Structures:
6TA1

PubMed Abstract:
Single-particle electron cryo-microscopy (cryoEM) has undergone a 'resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To fully exploit the new opportunities in molecular microscopy, new procedures for the cloning, expression and purification of macromolecular complexes need to be explored. Macromolecular assemblies are often unstable, and invasive construct design or inadequate purification conditions and sample-preparation methods can result in disassembly or denaturation. The structure of the 2.6 MDa yeast fatty acid synthase (FAS) has been studied by electron microscopy since the 1960s. Here, a new, streamlined protocol for the rapid production of purified yeast FAS for structure determination by high-resolution cryoEM is reported. Together with a companion protocol for preparing cryoEM specimens on a hydrophilized graphene layer, the new protocol yielded a 3.1 Å resolution map of yeast FAS from 15 000 automatically picked particles within a day. The high map quality enabled a complete atomic model of an intact fungal FAS to be built.

Organizational Affiliation

Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 2,624.44 kDa
Atom Count: 178,050
Modelled Residue Count: 22,686
Deposited Residue Count: 23,628
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit alpha	A C [auth B] E [auth D] G [auth K] I [auth F] A, C [auth B], E [auth D], G [auth K], I [auth F], K [auth I]	1,887	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: FAS2, YPL231W, P1409 EC: 2.3.1.86 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 2.3.1.41 (PDB Primary Data)
UniProt
Find proteins for P19097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19097 Go to UniProtKB: P19097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19097
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit beta	B [auth G] D [auth C] F [auth E] H [auth L] J [auth H] B [auth G], D [auth C], F [auth E], H [auth L], J [auth H], L [auth J]	2,051	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: FAS1, YKL182W EC: 2.3.1.86 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.9 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt
Find proteins for P07149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07149 Go to UniProtKB: P07149
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07149
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth K] SDF format, chain U [auth F] SDF format, chain W [auth I] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth K] MOL2 format, chain U [auth F] MOL2 format, chain W [auth I]	M [auth A] O [auth B] Q [auth D] S [auth K] U [auth F] M [auth A], O [auth B], Q [auth D], S [auth K], U [auth F], W [auth I]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth D] Focus chain S [auth K] Focus chain U [auth F] Focus chain W [auth I] Interactions & Density Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth D] Focus chain S [auth K] Focus chain U [auth F] Focus chain W [auth I]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain N [auth G] SDF format, chain P [auth C] SDF format, chain R [auth E] SDF format, chain T [auth L] SDF format, chain V [auth H] SDF format, chain X [auth J] MOL2 format, chain N [auth G] MOL2 format, chain P [auth C] MOL2 format, chain R [auth E] MOL2 format, chain T [auth L] MOL2 format, chain V [auth H] MOL2 format, chain X [auth J]	N [auth G] P [auth C] R [auth E] T [auth L] V [auth H] N [auth G], P [auth C], R [auth E], T [auth L], V [auth H], X [auth J]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain N [auth G] Focus chain P [auth C] Focus chain R [auth E] Focus chain T [auth L] Focus chain V [auth H] Focus chain X [auth J] Interactions & Density Focus chain N [auth G] Focus chain P [auth C] Focus chain R [auth E] Focus chain T [auth L] Focus chain V [auth H] Focus chain X [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A C [auth B] E [auth D] G [auth K] I [auth F] A, C [auth B], E [auth D], G [auth K], I [auth F], K [auth I]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER