8AGC: PDB entry 8AGC

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

Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide and non-acceptor peptide bound. Determined by electron microscopy at 3.1 Å resolution. Released 7 Dec 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae
Chains: 9
Atoms: 17,764
Mol. weight: 297.65 kDa
Ligands: ELU, CPL, PTY, MN
Released: 7 Dec 2022

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

Secondary structure: helices and β-sheets

8AGC contains 87 α-helices and 103 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: 42 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
α-helix	34-38	5
α-helix	47-60	14
α-helix	63-67	5
β-strand	70-71	2	1
β-strand	74	1	2
β-strand	80-81	2	1
α-helix	82-84	3
α-helix	89-100	12
α-helix	101-105	5
α-helix	111-116	6
α-helix	118-135	18
α-helix	140-152	13
α-helix	154-158	5
α-helix	168-188	21
α-helix	191-207	17
α-helix	212-227	16
α-helix	233-250	18
α-helix	259-262	4
β-strand	263	1	3
α-helix	264-266	3
α-helix	267-287	21
α-helix	293-319	27
β-strand	323	1	3
α-helix	324-326	3
α-helix	337-340	4
β-strand	348	1	4
α-helix	349-351	3
α-helix	358-361	4
α-helix	366-379	14
α-helix	383-401	19
α-helix	403-409	7
α-helix	410-428	19
α-helix	442-469	28
α-helix	470-474	5
β-strand	481	1	5
β-strand	493	1	5
α-helix	495-505	11
β-strand	512-514	3	2
α-helix	517-519	3
α-helix	520-522	3
α-helix	523-527	5
β-strand	530-531	2	2
α-helix	540-550	11
β-strand	553	1	6
α-helix	554-563	10
β-strand	568-572	5	2
α-helix	583-586	4
α-helix	587-597	11
α-helix	604-606	3
α-helix	622-625	4
β-strand	627	1	6
α-helix	628-633	6
β-strand	646-647	2	7
β-strand	654-655	2	7
β-strand	666-671	6	2
β-strand	677-682	6	2
α-helix	683-686	4
α-helix	692-700	9

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-32	29

Chain C: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	14-15	2	8
α-helix	16	1
α-helix	22-24	3
α-helix	25-44	20
α-helix	53-82	30

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	23-40	18
α-helix	43-68	26
α-helix	74-99	26
α-helix	109-128	20

Chain E: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	32-41	10	9
β-strand	47-56	10	9
β-strand	63-70	8	10
α-helix	72-76	5
β-strand	78-85	8	9
β-strand	91	1	9
β-strand	93-97	5	10
β-strand	113-123	11	10
α-helix	124	1
β-strand	128-137	10	9
α-helix	141	1
β-strand	142-143	2	11
β-strand	147-148	2	12
α-helix	153	1
β-strand	154-160	7	11
β-strand	170	1	9
β-strand	173-178	6	9
β-strand	183-186	4	11
β-strand	197	1	9
β-strand	203-204	2	9
β-strand	208	1	9
β-strand	211	1	9
β-strand	220-226	7	11
β-strand	231-243	13	13
β-strand	248-259	12	13
α-helix	262	1
β-strand	263-264	2	12
α-helix	270-278	9
β-strand	288	1	14
β-strand	291-294	4	15
β-strand	300-306	7	13
β-strand	309-310	2	13
β-strand	314-316	3	15
β-strand	320-323	4	15
β-strand	329	1	14
β-strand	331	1	12
β-strand	334-344	11	13
α-helix	345-347	3
β-strand	349-351	3	8
β-strand	358-364	7	8
β-strand	373-374	2	13
β-strand	377-383	7	13
β-strand	388-393	6	8
β-strand	400-406	7	13
β-strand	416-423	8	13
β-strand	426-427	2	13
β-strand	434-440	7	8
α-helix	443-446	4
α-helix	448-468	21

Chain F: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	16
β-strand	68-69	2	16
β-strand	79-85	7	17
β-strand	86	1	18
β-strand	91	1	18
β-strand	94-95	2	17
β-strand	99-101	3	16
β-strand	105-111	7	16
α-helix	119-127	9
β-strand	132-139	8	17
α-helix	144	1
β-strand	149-156	8	17
β-strand	179	1	19
α-helix	186-191	6
α-helix	192-214	23
α-helix	229-251	23
α-helix	256-280	25

Chain G: 14 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	20
α-helix	38-40	3
α-helix	41-49	9
β-strand	55-58	4	20
β-strand	69	1	21
β-strand	74	1	21
β-strand	78-81	4	20
α-helix	90-93	4
α-helix	96-104	9
β-strand	108-112	5	20
β-strand	114	1	22
β-strand	117	1	22
α-helix	120-128	9
β-strand	131-133	3	23
β-strand	138-141	4	24
β-strand	152-154	3	25
α-helix	155-157	3
β-strand	171-173	3	25
β-strand	177	1	26
β-strand	180-182	3	23
β-strand	188-190	3	20
β-strand	193	1	23
β-strand	199-202	4	24
α-helix	207-208	2
β-strand	211	1	24
β-strand	216	1	23
β-strand	218-222	5	20
β-strand	228-232	5	20
β-strand	234	1	26
α-helix	240-242	3
α-helix	248-257	10
β-strand	263-273	11	27
β-strand	285	1	28
β-strand	289-299	11	27
β-strand	304-306	3	27
β-strand	313-317	5	19
β-strand	321-326	6	19
β-strand	328-332	5	27
β-strand	337-345	9	27
α-helix	346-347	2
β-strand	351-359	9	19
β-strand	367-375	9	19
β-strand	376	1	28
α-helix	380-382	3
α-helix	384-385	2
α-helix	386-388	3
α-helix	390-415	26

Chain H: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	217-232	16
α-helix	237-240	4
α-helix	267-285	19
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 glycotransferase	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

>8AGC_1 Dolichyl-diphosphooligosaccharide--protein glycotransferase (chains A)
MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVN
NSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAP
LFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFM
FWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYT
TWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMV
SLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFF
FDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVA
LSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVV
LPSQTPDGKLALIDDFREAYYWLRMNSDEDSKVAAWWDYGYQIGGMADRTTLVDNNTWNN
THIAIVGKAMASPEEKSYEILKEHDVDYVLVIFGGLIGFGGDDINKFLWMIRISEGIWPE
EIKERDFYTAEGEYRVDARASETMRNSLLYKMSYKDFPQLFNGGQATDRVRQQMITPLDV
PPLDYFDEVFTSENWMVRIYQLKKDDAQGRTLRDVGELTRSSTKTRRSIKRPELGLRV

Sequence of entity 2 (B), FASTA

>8AGC_2 OST4 isoform 1 (chains B)
MISDEQLNSLAITFGIVMMTLIVIYHAVDSTMSPKNRTLQVDGGSGGSLEVLFQGPTETS
QVAPA

Sequence of entity 3 (C), FASTA

>8AGC_3 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (chains C)
MTYEQLYKEFHSSKSFQPFIHLDTQPKFAICGLIVTLAVLSSALFAVGSKSSYIKKLFFY
TILSVIGSLFAGLTTVFASNSFGVYV

Sequence of entity 4 (D), FASTA

>8AGC_4 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (chains D)
MAKAPKANTPKVTSTSSAVLTDFQETFKTSKRAYFAQIEKYPKLKLIDTFCFFLVLLGVI
QCTFIILIRDNFPFNAFLAGFIICVGQFVLLMSLRLQLCNSFPGISKNRAFAEFIVASLI
LHFVCLHFIN

Sequence of entity 5 (E), FASTA

>8AGC_5 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (chains E)
MRQVWFSWIVGLFLCFFNVSSAAQYEPPATWENVDYKRTIDVSNAYISETIEITIKNIAS
EPATEYFTAFESGIFSKVSFFSAYFTNEATFLNSQLLANSTTAPGDDGESEIRYGIIQFP
NAISPQEEVSLVIKSFYNTVGIPYPEHVGMSEEQHLLWETNRLPLSAYDTKKASFTLIGS
SSFEEYHPPNDESLLGKANGNSFEFGPWEDIPRFSSNETLAIVYSHNAPLNQVVNLRRDI
WLSHWASTIQFEEYYELTNKAAKLSKGFSRLELMKQIQTQNMRQTHFVTVLDMLLPEGAT
DHYFTDLVGLVSTSHAERDHFFIRPRFPIFGGWNYNFTVGWTNKLSDFLHVSSGSDEKFV
ASIPILNGPPDTVYDNVELSVFLPEGAEIFDIDSPVPFTNVSIETQKSYFDLNKGHVKLT
FSYRNLISQVANGQVLIKYDYPKSSFFKKPLSIACYIFTALMGVFVLKTLNMNVTN

Sequence of entity 6 (F), FASTA

>8AGC_6 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (chains F)
MQFFKTLAALVSCISFVLAYVAQDVHVSFPSTAGKSRVMIGKVEPRIGIDETVPTTITVE
DPNEVIQVNFAIESTNKPFQNTLLIGLPNKNLEMAFEPEIKDNGKLSMYKYRIDLAKLDA
ALLQEASRSPEPIKATLILASSTAKPKENLFREILQLNLNFDVDHSDSSLVDKFGIKPEI
HHIFHAEPKRVAKPIAVIFVLIIFITILSLIVTWLNSCAAAFNNIPTGVTAVYFLGFIAT
IVGFEVIFARYYLGTSIFETLFSSLYLGAPGLLTSTKFLRSFG

Sequence of entity 7 (G), FASTA

>8AGC_7 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains G)
MRTDWNFFFCILLQAIFVVGTQTSRTLVLYDQSTEPLEEYSVYLKDLEQRNYKLEYLDIN
STSTTVDLYDKEQRLFDNIIVFPTKGGKNLARQIPVKQLIKFFENEGNILCMSSPGAVPN
TIRLFLNELGIYPSPKGHVIRDYFSPSSEELVVSSNHLLNKYVYNARKSEDFVFGESSAA
LLENREQIVPILNAPRTSFTESKGKCNSWTSGSQGFLVVGFQNLNNARLVWIGSSDFLKN
KNQDSNQEFAKELLKWTFNEKSVIKSVHAVHSHADGTSYDEEPYKIKDKVIYSVGFSEWN
GEEWLPHIADDIQFELRQVDPYYRLTLSPSGNDSETQYYTTGEFILPDRHGVFTFLTDYR
KIGLSFTTDKDVKAIRHLANDEYPRSWEISNSWVYISAICGVIVAWIFFVVSFVTTSSVG
KKLETFKKTN

Sequence of entity 8 (H), FASTA

>8AGC_8 OST3 isoform 1 (chains H)
MNWLFLVSLVFFCGVSTHPALAMSSNRLLKLANKSPKKIIPLKDSSFENILAPPHENAYI
VALFTATAPEIGCSLCLELESEYDTIVASWFDDHPDAKSSNSDTSIFFTKVNLEDPSKTI
PKAFQFFQLNNVPRLFIFKPNSPSILDHSVISISTDTGSERMKQIIQAIKQFSQVNDFSL
HLPMDWTPIITSTIITFITVLLFKKQSKLMFSIISSRIIWATLSTFFIICMISAYMFNQI
RNTQLAGVGPKGEVMYFLPNEFQHQFAIETQVMVLIYGTLAALVVVLVKGIQFLRSHLYP
ETKKAYFIDAILASFCALFIYVFFAALTTVFTIKSPAYPFPLLRLSAPFK

Sequence of entity 9 (P), FASTA

>8AGC_9 PEPTIDE (chains P)
YAAATSA

Ligands and cofactors

ID	Name	Formula	Copies
ELU	phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl]…	C20 H38 O7 P2	1
CPL	1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine	C42 H80 N O8 P	4
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	2
MN	Manganese (II) ion	Mn	1
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

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:

8AGE 2.8 Å, Structure of yeast oligosaccharylransferase complex with acceptor peptide bound
8AGB 3.0 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

Browse structure collections

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