7KAO: Protein transport protein SEC61

Name: PDB 7KAO: Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class without Sec62
Published: 2021-02-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: protein transport

Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class without Sec62. Determined by electron microscopy at 4.0 Å resolution. Released 3 Feb 2021.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 6
Atoms: 10,502
Mol. weight: 191.81 kDa
Released: 3 Feb 2021

Explore 7KAO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KAO contains 69 α-helices and 35 β-strands across 6 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 A: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	1
α-helix	21-23	3
α-helix	29-45	17
β-strand	50	1	2
α-helix	64-69	6
β-strand	76	1	2
α-helix	83-97	15
α-helix	108-136	29
α-helix	148-170	23
α-helix	171-175	5
α-helix	181-195	15
β-strand	202-204	3	3
β-strand	209-211	3	3
α-helix	214-224	11
α-helix	228-237	10
α-helix	244-261	18
β-strand	264-270	7	4
β-strand	279-284	6	4
α-helix	290-313	24
α-helix	318-323	6
β-strand	325-327	3	5
β-strand	337-339	3	5
α-helix	342-345	4
α-helix	348-349	2
α-helix	352-357	6
α-helix	359-383	25
α-helix	388-398	11
β-strand	401-402	2	4
α-helix	410-414	5
α-helix	418-439	22
α-helix	445-465	21

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	52	1	1
α-helix	54-81	28

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	27-38	12
β-strand	40	1	4
α-helix	44-79	36

Chain D: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	6
α-helix	14-35	22
α-helix	59-66	8
α-helix	69-77	9
α-helix	94-112	19
β-strand	205-207	3	3
β-strand	211	1	6
α-helix	213-216	4
α-helix	220-229	10
α-helix	230-234	5
α-helix	235-247	13
β-strand	249	1	7
β-strand	255	1	7
α-helix	256-267	12
α-helix	274-275	2
α-helix	277-284	8
α-helix	288-293	6
α-helix	299-310	12
α-helix	319-342	24
α-helix	346-361	16
α-helix	379-385	7
α-helix	392-396	5
α-helix	400-407	8
α-helix	412-422	11
β-strand	427	1	8
β-strand	430-436	7	9
β-strand	450-455	6	9
β-strand	458	1	8
α-helix	464-466	3
α-helix	467-469	3
α-helix	477-478	2
α-helix	481-484	4
α-helix	491-493	3
α-helix	495	1
β-strand	496	1	10
α-helix	497	1
β-strand	499	1	11
β-strand	510	1	11
β-strand	513-519	7	12
β-strand	525	1	12
α-helix	528-529	2
β-strand	530-532	3	12
β-strand	534	1	10
α-helix	538-540	3
α-helix	555-557	3
β-strand	570-574	5	9
α-helix	578-580	3
β-strand	584-594	11	12
β-strand	602-610	9	12

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	72-85	14
α-helix	89-123	35
α-helix	129-155	27
α-helix	161-181	21
α-helix	183-194	12
β-strand	198	1	13
α-helix	200-202	3
β-strand	204	1	13

Chain F: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	14
β-strand	13-14	2	14
α-helix	22-40	19
α-helix	49-51	3
α-helix	53-70	18
α-helix	75-90	16
α-helix	98-119	22
α-helix	123-134	12
α-helix	140-152	13
α-helix	156-167	12
α-helix	176-191	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein transport protein SEC61	A	protein	480	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32915 (AlphaFold model)
Protein transport protein SSS1	C	protein	80	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P35179 (AlphaFold model)
Protein transport protein SBH1	B	protein	82	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P52870 (AlphaFold model)
Protein translocation protein SEC63	D	protein	662	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14906 (AlphaFold model)
Translocation protein SEC66	E	protein	206	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33754
Translocation protein SEC72	F	protein	193	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P39742

Sequence of entity 1 (A), FASTA

>7KAO_1 Protein transport protein SEC61 (chains A)
MSSNRVLDLFKPFESFLPEVIAPERKVPYNQKLIWTGVSLLIFLILGQIPLYGIVSSETS
DPLYWLRAMLASNRGTLLELGVSPIITSSLIFQFLQGTQLLQIRPESKQDRELFQIAQKV
CAIILILGQALVVVMTGNYGAPSDLGLPICLLLIFQLMFASLIVMLLDELLSKGYGLGSG
ISLFIATNIAEQIFWRAFAPTTVNSGRGKEFEGAVIAFFHLLAVRKDKKRALVEAFYRTN
LPNMFQVLMTVAIFLFVLYLQGFRYELPIRSTKVRGQIGIYPIKLFYTSNTPIILQSALT
SNIFLISQILFQKYPTNPLIRLIGVWGIRPGTQGPQMALSGLAYYIQPLMSLSEALLDPI
KTIVYITFVLGSCAVFSKTWIEISGTSPRDIAKQFKDQGMVINGKRETSIYRELKKIIPT
AAAFGGATIGALSVGSDLLGTLGSGASILLATTTIYGYYEAAAKEGGFTKNLVPGFSDLM

Sequence of entity 2 (C), FASTA

>7KAO_2 Protein transport protein SSS1 (chains C)
MARASEKGEEKKQSNNQVEKLVEAPVEFVREGTQFLAKCKKPDLKEYTKIVKAVGIGFIA
VGIIGYAIKLIHIPIRYVIV

Sequence of entity 3 (B), FASTA

>7KAO_3 Protein transport protein SBH1 (chains B)
MSSPTPPGGQRTLQKRKQGSSQKVAASAPKKNTNSNNSILKIYSDEATGLRVDPLVVLFL
AVGFIFSVVALHVISKVAGKLF

Sequence of entity 4 (D), FASTA

>7KAO_4 Protein translocation protein SEC63 (chains D)
PTNYEYDEASETWPSFILTGLLMVVGPMTLLQIYQIFFGANAEDGNSGKSKEFNEEVFKN
LNEEYTSDEIKQFRRKFDKNSNKKSKIWSRRNIIIIVGWILVAILLQRINSNDAIKDAAT
KLFDPYEILGISTSASDRDIKSAYRKLSVKFHPDKLAKGLTPDEKSVMEETYVQITKAYE
SLTDELVRQNYLKYGHPDGPQSTSHGIALPRFLVDGSASPLLVVCYVALLGLILPYFVSR
WWARTQSYTKKGIHNVTASNFVSNLVNYKPSEIVTTDLILHWLSFAHEFKQFFPDLQPTD
FEKLLQDHINRRDSGKLNNAKFRIVAKCHSLLHGLLDIACGFRNLDIALGAINTFKCIVQ
AVPLTPNCQILQLPNVDKEHFITKTGDIHTLGKLFTLEDAKIGEVLGIKDQAKLNETLRV
ASHIPNLKIIKADFLVPGENQVTPSSTPYISLKVLVRSAKQPLIPTSLIPEENLTEPQDF
ESQRDPFAMMSKQPLVPYSFAPFFPTKRRGSWCCLVSSQKDGKILQTPIIIEKLSYKNLN
DDKDFFDKRIKMDLTKHEKFDINDWEIGTIKIPLGQPAPETVGDFFFRVIVKSTDYFTTD
LDITMNMKVRDSPAVEQVEVYSEEDDEYSTDDDETESDDESDASDYTDIDTDTEAEDDES
PE

Sequence of entity 5 (E), FASTA

>7KAO_5 Translocation protein SEC66 (chains E)
MSEFNETKFSNNGTFFETEEPIVETKSISVYTPLIYVFILVVSLVMFASSYRKKQAKKIS
EQPSIFDENDAHDLYFQIKEMSENEKIHEKVLKAALLNRGAESVRRSLKLKELAPQINLL
YKNGSIGEDYWKRFETEVKLIELEFKDTLQEAERLQPGWVQLFVMVCKEICFNQALSRRY
QSILKRKEVCIKEWELKINNDGRLVN

Sequence of entity 6 (F), FASTA

>7KAO_6 Translocation protein SEC72 (chains F)
MVTLEYNANSKLITASDAVVALSTETNIDQINVLTTSLIGETNPNFTPQPNEALSKMIKG
LFESGMKNLQQKKLNEALKNVSLAIEMAQRKRAPWEAFAIQLPELHFMLRSKIDLCLILG
KHLEALQDLDFLLGTGLIQPDVFVRKADCLLKLRQWEEARATCERGLALAPEDMKLRALL
IETARNLAEYNGE

Primary citation

Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Itskanov, S., Kuo, K.M., Gumbart, J.C. et al. Nat Struct Mol Biol (2021) 28:162-172. DOI 10.1038/s41594-020-00541-x · PubMed

Other PDB entries of the same protein (UniProt P32915 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KAH 3.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class without Sec62
7KAJ 3.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62,…
7KAI 3.2 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62,…
6N3Q 3.68 Å, Cryo-EM structure of the yeast Sec complex
7KB5 3.8 Å, Cryo-EM structure of the Sec complex from yeast, Sec63 FN3 and residues 210-216 mutated
7KAS 3.9 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class with…
7KAQ 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
7KAR 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec63 FN3 mutant, class without…
7KAU 4.0 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3…
6ND1 4.1 Å, CryoEM structure of the Sec Complex from yeast
7KAP 4.1 Å, Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class with…
7AFT 4.4 Å, Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon

Browse structure collections

About this viewer

MolViewer shows 7KAO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.