6HD5: Ribosome-NatA complex

Cryo-EM structure of the ribosome-NatA complex. Determined by electron microscopy at 4.8 Å resolution. Released 19 Dec 2018.

Method: Electron microscopy
Resolution: 4.8 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 3
Atoms: 9,707
Mol. weight: 146.44 kDa
Released: 19 Dec 2018

Explore 6HD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HD5 contains 61 α-helices and 17 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain t: 50 helices, 0 β-strands

Element	Residues	Length
α-helix	19-32	14
α-helix	37-49	13
α-helix	54-67	14
α-helix	71-82	12
α-helix	91-103	13
α-helix	108-121	14
α-helix	126-138	13
α-helix	142-154	13
α-helix	159-172	14
α-helix	175-188	14
α-helix	196-214	19
α-helix	220-233	14
α-helix	241-254	14
α-helix	257-270	14
α-helix	275-285	11
α-helix	291-302	12
α-helix	310-313	4
α-helix	314-317	4
α-helix	322-339	18
α-helix	344-347	4
α-helix	349-354	6
α-helix	360-371	12
α-helix	380-396	17
α-helix	401-413	13
α-helix	418-430	13
α-helix	434-445	12
α-helix	453-463	11
α-helix	469-475	7
α-helix	488-493	6
α-helix	498-524	27
α-helix	532-535	4
α-helix	538-558	21
α-helix	561-570	10
α-helix	575-581	7
α-helix	585-597	13
α-helix	598-600	3
α-helix	602-626	25
α-helix	647-668	22
α-helix	691-695	5
α-helix	696-700	5
α-helix	701-705	5
α-helix	714-722	9
α-helix	728-740	13
α-helix	746-758	13
α-helix	767-780	14
α-helix	797-804	8
α-helix	811-818	8
α-helix	828-837	10
α-helix	843-848	6
α-helix	849-853	5

Chain u: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
α-helix	10-12	3
α-helix	13-21	9
α-helix	30-38	9
β-strand	45-48	4	1
β-strand	85-87	3	2
β-strand	90-91	2	2
β-strand	92-100	9	1
β-strand	113-120	8	1
α-helix	130-144	15
β-strand	149-154	6	1
α-helix	159-162	4
α-helix	163-168	6
β-strand	173-177	5	1
β-strand	187-193	7	1
α-helix	202-204	3

Chain v: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	3
α-helix	16-22	7
α-helix	34-37	4
β-strand	58-66	9	3
β-strand	70-78	9	3
β-strand	91-98	8	3
α-helix	107-121	15
β-strand	127-132	6	3
α-helix	137-146	10
β-strand	148-149	2	3
β-strand	154-159	6	3
β-strand	165-173	9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-terminal acetyltransferase A complex subunit NAT1	t	protein	854	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P12945 (AlphaFold model)
N-terminal acetyltransferase A complex catalytic subunit ARD1	u	protein	238	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P07347 (AlphaFold model)
N-alpha-acetyltransferase NAT5	v	protein	176	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q08689 (AlphaFold model)

Sequence of entity 1 (t), FASTA

>6HD5_1 N-terminal acetyltransferase A complex subunit NAT1 (chains t)
MSRKRSTKPKPAAKIALKKENDQFLEALKLYEGKQYKKSLKLLDAILKKDGSHVDSLALK
GLDLYSVGEKDDAASYVANAIRKIEGASASPICCHVLGIYMRNTKEYKESIKWFTAALNN
GSTNKQIYRDLATLQSQIGDFKNALVSRKKYWEAFLGYRANWTSLAVAQDVNGERQQAIN
TLSQFEKLAEGKISDSEKYEHSECLMYKNDIMYKAASDNQDKLQNVLKHLNDIEPCVFDK
FGLLERKATIYMKLGQLKDASIVYRTLIKRNPDNFKYYKLLEVSLGIQGDNKLKKALYGK
LEQFYPRCEPPKFIPLTFLQDKEELSKKLREYVLPQLERGVPATFSNVKPLYQRRKSKVS
PLLEKIVLDYLSGLDPTQDPIPFIWTNYYLSQHFLFLKDFPKAQEYIDAALDHTPTLVEF
YILKARILKHLGLMDTAAGILEEGRQLDLQDRFINCKTVKYFLRANNIDKAVEVASLFTK
NDDSVNGIKDLHLVEASWFIVEQAEAYYRLYLDRKKKLDDLASLKKEVESDKSEQIANDI
KENQWLVRKYKGLALKRFNAIPKFYKQFEDDQLDFHSYCMRKGTPRAYLEMLEWGKALYT
KPMYVRAMKEASKLYFQMHDDRLKRKSDSLDENSDEIQNNGQNSSSQKKKAKKEAAAMNK
RKETEAKSVAAYPSDQDNDVFGEKLIETSTPMEDFATEFYNNYSMQVREDERDYILDFEF
NYRIGKLALCFASLNKFAKRFGTTSGLFGSMAIVLLHATRNDTPFDPILKKVVTKSLEKE
YSENFPLNEISNNSFDWLNFYQEKFGKNDINGLLFLYRYRDDVPIGSSNLKEMIISSLSP
LEPHSQNEILQYYL

Sequence of entity 2 (u), FASTA

>6HD5_2 N-terminal acetyltransferase A complex catalytic subunit ARD1 (chains u)
MPINIRRATINDIICMQNANLHNLPENYMMKYYMYHILSWPEASFVATTTTLDCEDSDEQ
DENDKLELTLDGTNDGRTIKLDPTYLAPGEKLVGYVLVKMNDDPDQQNEPPNGHITSLSV
MRTYRRMGIAENLMRQALFALREVHQAEYVSLHVRQSNRAALHLYRDTLAFEVLSIEKSY
YQDGEDAYAMKKVLKLEELQISNFTHRRLKENEEKLEDDLESDLLEDIIKQGVNDIIV

Sequence of entity 3 (v), FASTA

>6HD5_3 N-alpha-acetyltransferase NAT5 (chains v)
MGRDICTLDNVYANNLGMLTKLAHVTVPNLYQDAFFSALFAEDSLVAKNKKPSSKKDVHF
TQMAYYSEIPVGGLVAKLVPKKQNELSLKGIQIEFLGVLPNYRHKSIGSKLLKFAEDKCS
ECHQHNVFVYLPAVDDLTKQWFIAHGFEQVGETVNNFIKGVNGDEQDAILLKKHIS

Primary citation

Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Knorr, A.G., Schmidt, C., Tesina, P. et al. Nat Struct Mol Biol (2019) 26:35-39. DOI 10.1038/s41594-018-0165-y · PubMed

Other PDB entries of the same protein (UniProt P12945 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4XNH 2.1 Å, Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a…
4HNY 2.25 Å, Apo N-terminal acetyltransferase complex A
4HNX 2.34 Å, The NatA Acetyltransferase Complex Bound To ppGpp
6O07 2.7 Å, Structure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex
4HNW 2.8 Å, The NatA Acetyltransferase Complex Bound To Inositol Hexakisphosphate
4XPD 2.81 Å, Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a…
6HD7 3.4 Å, Cryo-EM structure of the ribosome-NatA complex
4Y49 3.95 Å, Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a…

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