8AGB: PDB entry 8AGB

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

Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide bound. Determined by electron microscopy at 3.0 Å resolution. Released 7 Dec 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 17,202
Mol. weight: 296.93 kDa
Ligands: CPL, PTY, MN, ELU
Released: 7 Dec 2022

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

Secondary structure: helices and β-sheets

8AGB contains 75 α-helices and 104 β-strands across 8 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: 34 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
α-helix	46-60	15
α-helix	64-67	4
β-strand	71	1	1
β-strand	80	1	1
α-helix	90-104	15
α-helix	111-116	6
α-helix	118-137	20
α-helix	140-152	13
α-helix	154-160	7
α-helix	167-188	22
α-helix	191-205	15
α-helix	209-212	4
α-helix	214-227	14
α-helix	233-250	18
α-helix	259-262	4
α-helix	267-288	22
α-helix	356-362	7
α-helix	366-380	15
α-helix	383-401	19
α-helix	406-428	23
α-helix	442-472	31
β-strand	481	1	2
β-strand	493	1	2
α-helix	495-505	11
β-strand	512	1	3
β-strand	513-514	2	4
α-helix	520-525	6
β-strand	530	1	3
α-helix	540-548	9
α-helix	554-563	10
β-strand	568-572	5	4
α-helix	587-593	7
α-helix	604-606	3
α-helix	622-626	5
α-helix	628-633	6
α-helix	638-640	3
α-helix	642-644	3
β-strand	646-647	2	5
β-strand	654-655	2	5
α-helix	657-659	3
α-helix	661-663	3
β-strand	666-671	6	4
β-strand	677-682	6	4
α-helix	683-686	4
α-helix	692-700	9

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-31	28

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	15	1	6
α-helix	22-24	3
α-helix	25-46	22
α-helix	53-81	29

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	22-40	19
α-helix	42-68	27
α-helix	74-99	26
α-helix	107-128	22

Chain E: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	7
β-strand	33	1	8
β-strand	36-41	6	9
β-strand	47-53	7	9
β-strand	56-57	2	7
β-strand	63-70	8	10
α-helix	72-76	5
β-strand	80-85	6	9
β-strand	91	1	9
β-strand	93-96	4	10
β-strand	113-123	11	10
α-helix	124	1
β-strand	128	1	7
β-strand	131-137	7	9
α-helix	141	1
β-strand	142-143	2	11
β-strand	147-148	2	12
β-strand	154-161	8	11
β-strand	170	1	8
β-strand	176-178	3	9
β-strand	183-185	3	11
β-strand	197-199	3	9
β-strand	202-204	3	9
β-strand	211	1	8
β-strand	219-226	8	11
β-strand	231-236	6	13
β-strand	239-243	5	13
β-strand	248-259	12	13
β-strand	263-264	2	12
α-helix	270-279	10
β-strand	288	1	14
β-strand	291-294	4	15
α-helix	295-296	2
β-strand	300-306	7	13
β-strand	310	1	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	6
β-strand	358-364	7	6
β-strand	373-374	2	13
β-strand	377-383	7	13
β-strand	388-393	6	6
β-strand	400-406	7	13
β-strand	416-423	8	13
β-strand	426-427	2	13
β-strand	434-440	7	6
α-helix	443-446	4
α-helix	448-468	21

Chain F: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	16
β-strand	43-44	2	17
β-strand	60-63	4	16
β-strand	68-71	4	16
β-strand	81-87	7	17
α-helix	89-91	3
β-strand	96-97	2	17
α-helix	99	1
β-strand	100-101	2	18
β-strand	110-111	2	18
β-strand	113-114	2	16
α-helix	121-129	9
β-strand	134-141	8	17
α-helix	146	1
β-strand	151-159	9	17
β-strand	181	1	19
α-helix	185-190	6
α-helix	194-216	23
α-helix	232-253	22
α-helix	258-282	25

Chain G: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	20
β-strand	31	1	21
β-strand	35	1	21
α-helix	38-40	3
α-helix	41-49	9
β-strand	54-56	3	20
β-strand	69	1	22
β-strand	74	1	22
β-strand	78-81	4	20
α-helix	88-93	6
α-helix	96-104	9
β-strand	108-112	5	20
α-helix	120-129	10
β-strand	131-133	3	23
β-strand	139-142	4	24
β-strand	151-154	4	25
α-helix	155-157	3
β-strand	171-174	4	25
β-strand	177	1	26
β-strand	180-182	3	23
β-strand	188-190	3	20
β-strand	198-201	4	24
β-strand	211	1	24
α-helix	212-214	3
β-strand	216	1	23
β-strand	218-222	5	20
β-strand	228-232	5	20
β-strand	234	1	26
α-helix	243-257	15
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	337-340	4	27
β-strand	344-345	2	27
α-helix	346	1
β-strand	351-360	10	19
β-strand	362	1	29
β-strand	364	1	29
β-strand	366-375	10	19
β-strand	376	1	28
α-helix	386-388	3
α-helix	393-415	23

Chain H: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	217-232	16
α-helix	236-240	5
α-helix	268-288	21
α-helix	291-298	8
α-helix	305-334	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3	A	protein	718	Saccharomyces cerevisiae	P39007 (AlphaFold model)
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4	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 SWP1	F	protein	285	Saccharomyces cerevisiae	Q02795
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1	G	protein	430	Saccharomyces cerevisiae	P33767
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3	H	protein	350	Saccharomyces cerevisiae	P48439

Sequence of entity 1 (A), FASTA

>8AGB_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

>8AGB_2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (chains B)
MISDEQLNSLAITFGIVMMTLIVIYHAVDSTMSPKNRTLQVDGGSGGSLEVLFQGPTETS
QVAPA

Sequence of entity 3 (C), FASTA

>8AGB_3 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (chains C)
MTYEQLYKEFHSSKSFQPFIHLDTQPKFAICGLIVTLAVLSSALFAVGSKSSYIKKLFFY
TILSVIGSLFAGLTTVFASNSFGVYV

Sequence of entity 4 (D), FASTA

>8AGB_4 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (chains D)
MAKAPKANTPKVTSTSSAVLTDFQETFKTSKRAYFAQIEKYPKLKLIDTFCFFLVLLGVI
QCTFIILIRDNFPFNAFLAGFIICVGQFVLLMSLRLQLCNSFPGISKNRAFAEFIVASLI
LHFVCLHFIN

Sequence of entity 5 (E), FASTA

>8AGB_5 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (chains E)
MRQVWFSWIVGLFLCFFNVSSAAQYEPPATWENVDYKRTIDVSNAYISETIEITIKNIAS
EPATEYFTAFESGIFSKVSFFSAYFTNEATFLNSQLLANSTTAPGDDGESEIRYGIIQFP
NAISPQEEVSLVIKSFYNTVGIPYPEHVGMSEEQHLLWETNRLPLSAYDTKKASFTLIGS
SSFEEYHPPNDESLLGKANGNSFEFGPWEDIPRFSSNETLAIVYSHNAPLNQVVNLRRDI
WLSHWASTIQFEEYYELTNKAAKLSKGFSRLELMKQIQTQNMRQTHFVTVLDMLLPEGAT
DHYFTDLVGLVSTSHAERDHFFIRPRFPIFGGWNYNFTVGWTNKLSDFLHVSSGSDEKFV
ASIPILNGPPDTVYDNVELSVFLPEGAEIFDIDSPVPFTNVSIETQKSYFDLNKGHVKLT
FSYRNLISQVANGQVLIKYDYPKSSFFKKPLSIACYIFTALMGVFVLKTLNMNVTN

Sequence of entity 6 (F), FASTA

>8AGB_6 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (chains F)
MQFFKTLAALVSCISFVLAYVAQDVHVSFPSTAGKSRVMIGKVEPRIGIDETVPTTITVE
DPNEVIQVNFAIESTNKPFQNTLLIGLPNKNLEMAFEPEIKDNGKLSMYKYRIDLAKLDA
ALLQEASRSPEPIKATLILASSTAKPKENLFREILQLNLNFDVDHSDSSLVDKFGIKPEI
HHIFHAEPKRVAKPIAVIFVLIIFITILSLIVTWLNSCAAAFNNIPTGVTAVYFLGFIAT
IVGFEVIFARYYLGTSIFETLFSSLYLGAPGLLTSTKFLRSFGTI

Sequence of entity 7 (G), FASTA

>8AGB_7 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains G)
MRTDWNFFFCILLQAIFVVGTQTSRTLVLYDQSTEPLEEYSVYLKDLEQRNYKLEYLDIN
STSTTVDLYDKEQRLFDNIIVFPTKGGKNLARQIPVKQLIKFFENEGNILCMSSPGAVPN
TIRLFLNELGIYPSPKGHVIRDYFSPSSEELVVSSNHLLNKYVYNARKSEDFVFGESSAA
LLENREQIVPILNAPRTSFTESKGKCNSWTSGSQGFLVVGFQNLNNARLVWIGSSDFLKN
KNQDSNQEFAKELLKWTFNEKSVIKSVHAVHSHADGTSYDEEPYKIKDKVIYSVGFSEWN
GEEWLPHIADDIQFELRQVDPYYRLTLSPSGNDSETQYYTTGEFILPDRHGVFTFLTDYR
KIGLSFTTDKDVKAIRHLANDEYPRSWEISNSWVYISAICGVIVAWIFFVVSFVTTSSVG
KKLETFKKTN

Sequence of entity 8 (H), FASTA

>8AGB_8 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 (chains H)
MNWLFLVSLVFFCGVSTHPALAMSSNRLLKLANKSPKKIIPLKDSSFENILAPPHENAYI
VALFTATAPEIGCSLCLELESEYDTIVASWFDDHPDAKSSNSDTSIFFTKVNLEDPSKTI
PKAFQFFQLNNVPRLFIFKPNSPSILDHSVISISTDTGSERMKQIIQAIKQFSQVNDFSL
HLPMDWTPIITSTIITFITVLLFKKQSKLMFSIISSRIIWATLSTFFIICMISAYMFNQI
RNTQLAGVGPKGEVMYFLPNEFQHQFAIETQVMVLIYGTLAALVVVLVKGIQFLRSHLYP
ETKKAYFIDAILASFCALFIYVFFAALTTVFTIKSPAYPFPLLRLSAPFK

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	2
MN	Manganese (II) ion	Mn	1
ELU	phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl]…	C20 H38 O7 P2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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
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

Browse structure collections

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