8AGE: PDB entry 8AGE

Name: PDB 8AGE: Structure of yeast oligosaccharylransferase complex with acceptor peptide bound
Published: 2022-12-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of yeast oligosaccharylransferase complex with acceptor peptide bound. Determined by electron microscopy at 2.8 Å resolution. Released 7 Dec 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae
Chains: 9
Atoms: 17,534
Mol. weight: 299.48 kDa
Ligands: CPL, PTY, KZB, NAG
Released: 7 Dec 2022

Explore 8AGE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AGE contains 83 α-helices and 96 β-strands across 9 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: 37 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-32	25
α-helix	34-38	5
α-helix	47-60	14
α-helix	63-67	5
β-strand	70-71	2	1
β-strand	80-81	2	1
α-helix	89-103	15
α-helix	111-116	6
α-helix	118-137	20
α-helix	140-152	13
α-helix	154-157	4
α-helix	168-188	21
α-helix	191-207	17
α-helix	211-227	17
α-helix	233-250	18
α-helix	259-262	4
α-helix	264-266	3
α-helix	267-288	22
β-strand	348	1	2
α-helix	349-351	3
α-helix	357-362	6
α-helix	366-378	13
α-helix	383-401	19
α-helix	403-405	3
α-helix	406-428	23
α-helix	442-472	31
β-strand	481	1	3
β-strand	493	1	3
α-helix	496-505	10
β-strand	512-514	3	4
α-helix	517-519	3
α-helix	520-522	3
α-helix	523-527	5
β-strand	530-531	2	4
α-helix	540-549	10
α-helix	554-563	10
β-strand	568-572	5	4
α-helix	583-597	15
α-helix	604-607	4
α-helix	622-625	4
α-helix	628-633	6
α-helix	638-640	3
β-strand	646-648	3	5
β-strand	653-655	3	5
α-helix	661-663	3
β-strand	666-671	6	4
β-strand	677-682	6	4
α-helix	683-686	4
α-helix	692-699	8

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-31	28

Chain C: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	14-15	2	6
α-helix	25-48	24
α-helix	53-82	30

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	23-40	18
α-helix	42-68	27
α-helix	74-99	26
α-helix	107-128	22

Chain E: 8 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	31-41	11	7
β-strand	48-57	10	7
β-strand	65-70	6	8
α-helix	72-77	6
β-strand	78-85	8	7
β-strand	91	1	7
β-strand	93-96	4	8
β-strand	113-118	6	8
β-strand	128-137	10	7
α-helix	141	1
β-strand	142-143	2	9
β-strand	147-148	2	10
β-strand	155-161	7	9
α-helix	164-165	2
β-strand	170	1	7
β-strand	174-178	5	7
β-strand	183-185	3	9
β-strand	197-199	3	7
β-strand	202-204	3	7
β-strand	211	1	7
β-strand	219-225	7	9
β-strand	231-243	13	11
β-strand	248-259	12	11
α-helix	262	1
β-strand	263-264	2	10
α-helix	270-278	9
β-strand	288	1	12
β-strand	291-294	4	13
α-helix	295-296	2
β-strand	300-306	7	11
β-strand	309-310	2	11
β-strand	314-317	4	13
β-strand	320-323	4	13
β-strand	329	1	12
β-strand	334-344	11	11
α-helix	345-347	3
β-strand	349-351	3	6
β-strand	358-364	7	6
β-strand	373-374	2	11
β-strand	377-383	7	11
β-strand	388-393	6	6
β-strand	400-406	7	11
β-strand	416-423	8	11
β-strand	426-427	2	11
β-strand	434-440	7	6
α-helix	443-467	25

Chain F: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	25-32	8	14
β-strand	66-67	2	14
β-strand	77-84	8	15
β-strand	89-90	2	15
β-strand	93	1	15
β-strand	97-99	3	14
β-strand	104-111	8	14
α-helix	117-125	9
β-strand	130-137	8	15
α-helix	142	1
β-strand	147-154	8	15
α-helix	173-176	4
β-strand	177	1	16
α-helix	184-186	3
α-helix	190-213	24
α-helix	227-250	24
α-helix	254-278	25

Chain G: 17 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	17
α-helix	38-40	3
α-helix	41-49	9
β-strand	54-58	5	17
α-helix	65-66	2
β-strand	69	1	18
β-strand	74	1	18
β-strand	78-81	4	17
α-helix	88-93	6
α-helix	96-104	9
β-strand	108-112	5	17
β-strand	114	1	19
β-strand	117	1	19
α-helix	121-128	8
β-strand	131-133	3	17
β-strand	138-141	4	20
β-strand	152-154	3	21
α-helix	155-157	3
β-strand	158	1	17
β-strand	171-173	3	21
β-strand	177	1	22
β-strand	180-182	3	17
β-strand	188-193	6	17
α-helix	194-195	2
β-strand	199-202	4	20
α-helix	206-208	3
β-strand	211	1	20
α-helix	212-214	3
β-strand	216-222	7	17
β-strand	228-232	5	17
β-strand	234	1	22
α-helix	240-242	3
α-helix	247-256	10
β-strand	263-273	11	23
β-strand	285	1	24
β-strand	289-299	11	23
β-strand	304-306	3	23
β-strand	313-317	5	16
β-strand	321-326	6	16
β-strand	328-332	5	23
β-strand	337-345	9	23
β-strand	351-359	9	16
β-strand	367-375	9	16
β-strand	376	1	24
α-helix	377-378	2
α-helix	380-382	3
α-helix	384-385	2
α-helix	386-388	3
α-helix	392-414	23

Chain H: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	217-232	16
α-helix	237-240	4
β-strand	248	1	25
β-strand	254	1	25
α-helix	268-285	18
α-helix	286-290	5
α-helix	291-298	8
α-helix	306-334	29

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3	A	protein	718	Saccharomyces cerevisiae	P39007 (AlphaFold model)
OST4 isoform 1	B	protein	65	Saccharomyces cerevisiae	Q99380 (AlphaFold model)
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5	C	protein	86	Saccharomyces cerevisiae	Q92316 (AlphaFold model)
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2	D	protein	130	Saccharomyces cerevisiae	P46964 (AlphaFold model)
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1	E	protein	476	Saccharomyces cerevisiae	P41543
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2	F	protein	283	Saccharomyces cerevisiae	Q02795
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1	G	protein	430	Saccharomyces cerevisiae	P33767
OST3 isoform 1	H	protein	350	Saccharomyces cerevisiae	P48439
Peptide	P	protein	7	Saccharomyces cerevisiae

Sequence of entity 1 (A), FASTA

>8AGE_1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (chains A)
MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVN
NSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAP
LFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFM
FWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYT
TWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMV
SLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFF
FDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVA
LSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVV
LPSQTPDGKLALIDDFREAYYWLRMNSDEDSKVAAWWDYGYQIGGMADRTTLVDNNTWNN
THIAIVGKAMASPEEKSYEILKEHDVDYVLVIFGGLIGFGGDDINKFLWMIRISEGIWPE
EIKERDFYTAEGEYRVDARASETMRNSLLYKMSYKDFPQLFNGGQATDRVRQQMITPLDV
PPLDYFDEVFTSENWMVRIYQLKKDDAQGRTLRDVGELTRSSTKTRRSIKRPELGLRV

Sequence of entity 2 (B), FASTA

>8AGE_2 OST4 isoform 1 (chains B)
MISDEQLNSLAITFGIVMMTLIVIYHAVDSTMSPKNRTLQVDGGSGGSLEVLFQGPTETS
QVAPA

Sequence of entity 3 (C), FASTA

>8AGE_3 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (chains C)
MTYEQLYKEFHSSKSFQPFIHLDTQPKFAICGLIVTLAVLSSALFAVGSKSSYIKKLFFY
TILSVIGSLFAGLTTVFASNSFGVYV

Sequence of entity 4 (D), FASTA

>8AGE_4 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (chains D)
MAKAPKANTPKVTSTSSAVLTDFQETFKTSKRAYFAQIEKYPKLKLIDTFCFFLVLLGVI
QCTFIILIRDNFPFNAFLAGFIICVGQFVLLMSLRLQLCNSFPGISKNRAFAEFIVASLI
LHFVCLHFIN

Sequence of entity 5 (E), FASTA

>8AGE_5 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (chains E)
MRQVWFSWIVGLFLCFFNVSSAAQYEPPATWENVDYKRTIDVSNAYISETIEITIKNIAS
EPATEYFTAFESGIFSKVSFFSAYFTNEATFLNSQLLANSTTAPGDDGESEIRYGIIQFP
NAISPQEEVSLVIKSFYNTVGIPYPEHVGMSEEQHLLWETNRLPLSAYDTKKASFTLIGS
SSFEEYHPPNDESLLGKANGNSFEFGPWEDIPRFSSNETLAIVYSHNAPLNQVVNLRRDI
WLSHWASTIQFEEYYELTNKAAKLSKGFSRLELMKQIQTQNMRQTHFVTVLDMLLPEGAT
DHYFTDLVGLVSTSHAERDHFFIRPRFPIFGGWNYNFTVGWTNKLSDFLHVSSGSDEKFV
ASIPILNGPPDTVYDNVELSVFLPEGAEIFDIDSPVPFTNVSIETQKSYFDLNKGHVKLT
FSYRNLISQVANGQVLIKYDYPKSSFFKKPLSIACYIFTALMGVFVLKTLNMNVTN

Sequence of entity 6 (F), FASTA

>8AGE_6 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (chains F)
MQFFKTLAALVSCISFVLAYVAQDVHVSFPSTAGKSRVMIGKVEPRIGIDETVPTTITVE
DPNEVIQVNFAIESTNKPFQNTLLIGLPNKNLEMAFEPEIKDNGKLSMYKYRIDLAKLDA
ALLQEASRSPEPIKATLILASSTAKPKENLFREILQLNLNFDVDHSDSSLVDKFGIKPEI
HHIFHAEPKRVAKPIAVIFVLIIFITILSLIVTWLNSCAAAFNNIPTGVTAVYFLGFIAT
IVGFEVIFARYYLGTSIFETLFSSLYLGAPGLLTSTKFLRSFG

Sequence of entity 7 (G), FASTA

>8AGE_7 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains G)
MRTDWNFFFCILLQAIFVVGTQTSRTLVLYDQSTEPLEEYSVYLKDLEQRNYKLEYLDIN
STSTTVDLYDKEQRLFDNIIVFPTKGGKNLARQIPVKQLIKFFENEGNILCMSSPGAVPN
TIRLFLNELGIYPSPKGHVIRDYFSPSSEELVVSSNHLLNKYVYNARKSEDFVFGESSAA
LLENREQIVPILNAPRTSFTESKGKCNSWTSGSQGFLVVGFQNLNNARLVWIGSSDFLKN
KNQDSNQEFAKELLKWTFNEKSVIKSVHAVHSHADGTSYDEEPYKIKDKVIYSVGFSEWN
GEEWLPHIADDIQFELRQVDPYYRLTLSPSGNDSETQYYTTGEFILPDRHGVFTFLTDYR
KIGLSFTTDKDVKAIRHLANDEYPRSWEISNSWVYISAICGVIVAWIFFVVSFVTTSSVG
KKLETFKKTN

Sequence of entity 8 (H), FASTA

>8AGE_8 OST3 isoform 1 (chains H)
MNWLFLVSLVFFCGVSTHPALAMSSNRLLKLANKSPKKIIPLKDSSFENILAPPHENAYI
VALFTATAPEIGCSLCLELESEYDTIVASWFDDHPDAKSSNSDTSIFFTKVNLEDPSKTI
PKAFQFFQLNNVPRLFIFKPNSPSILDHSVISISTDTGSERMKQIIQAIKQFSQVNDFSL
HLPMDWTPIITSTIITFITVLLFKKQSKLMFSIISSRIIWATLSTFFIICMISAYMFNQI
RNTQLAGVGPKGEVMYFLPNEFQHQFAIETQVMVLIYGTLAALVVVLVKGIQFLRSHLYP
ETKKAYFIDAILASFCALFIYVFFAALTTVFTIKSPAYPFPLLRLSAPFK

Sequence of entity 9 (P), FASTA

>8AGE_9 PEPTIDE (chains P)
YANATSA

Ligands and cofactors

ID	Name	Formula	Copies
CPL	1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine	C42 H80 N O8 P	4
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	1
KZB	(2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5…	C33 H54 O10	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
323	2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate	C25 H22 N2 O4	1
MN	Manganese (II) ion	Mn	1

Primary citation

Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase. Ramirez, A.S., de Capitani, M., Pesciullesi, G. et al. Nat Commun (2022) 13:7296-7296. DOI 10.1038/s41467-022-35067-x · PubMed

Other PDB entries of the same protein (UniProt P39007 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AGB 3.0 Å, Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide…
8AGC 3.1 Å, Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide…
6EZN 3.3 Å, Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex
7OCI 3.46 Å, Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex
6C26 3.5 Å, The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex
2LGZ Solution structure of STT3P

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