6FTI: Mammalian Oligosaccharyltransferase

Name: PDB 6FTI: Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome
Published: 2018-03-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: protein transport

Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome. Determined by electron microscopy at 4.2 Å resolution. Released 21 Mar 2018.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Oryctolagus cuniculus, Canis lupus familiaris
Chains: 60
Atoms: 153,850
Mol. weight: 2289.7 kDa
Ligands: MG, ZN, 9UB
Released: 21 Mar 2018

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

Secondary structure: helices and β-sheets

6FTI contains 389 α-helices and 323 β-strands across 56 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 0: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-23	22

Chain 1: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	439-458	20
α-helix	468-503	36
α-helix	510-536	27
α-helix	544-572	29
α-helix	583-605	23

Chain 2: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	18-41	24
α-helix	53-75	23

Chain 3: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-46	16
α-helix	49-52	4
β-strand	59	1	15
β-strand	71	1	15
α-helix	84-103	20
α-helix	104-108	5
α-helix	118-145	28

Chain 4: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-31	28

Chain 5: 28 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	14-33	20
α-helix	36-40	5
α-helix	50-62	13
α-helix	91-105	15
α-helix	113-116	4
α-helix	119-136	18
α-helix	141-152	12
α-helix	155-159	5
α-helix	172-187	16
α-helix	192-208	17
α-helix	212-228	17
α-helix	234-252	19
α-helix	265-285	21
α-helix	295-316	22
α-helix	365-369	5
α-helix	371-380	10
α-helix	386-399	14
α-helix	405-408	4
α-helix	410-429	20
α-helix	457-481	25
α-helix	504-514	11
α-helix	526-528	3
α-helix	529-535	7
α-helix	550-556	7
α-helix	563-572	10
β-strand	577-578	2	25
β-strand	581	1	26
α-helix	596-601	6
β-strand	618-619	2	27
β-strand	623-624	2	27
α-helix	632-636	5
α-helix	639-642	4
β-strand	678-680	3	25
β-strand	689	1	26
β-strand	692-694	3	25

Chain 6: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	6-18	13
α-helix	22-44	23
α-helix	56-77	22
α-helix	91-99	9
α-helix	101-104	4
α-helix	106-109	4

Chain 7: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	416-437	22

48 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
uL2	A	protein	244	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
uL3	B	protein	394	Oryctolagus cuniculus	G1TL06 (AlphaFold model)
Ribosomal protein L4	C	protein	362	Oryctolagus cuniculus	G1SVW5 (AlphaFold model)
60S ribosomal protein L5	D	protein	292	Oryctolagus cuniculus	P19949 (AlphaFold model)
60S ribosomal protein L6	E	protein	248	Oryctolagus cuniculus	G1TG04
uL30	F	protein	225	Oryctolagus cuniculus	G1SV32
eL8	G	protein	241	Oryctolagus cuniculus	G1STW0
uL6	H	protein	190	Oryctolagus cuniculus	G1SWI6
Ribosomal protein L10 (Predicted)	I	protein	213	Oryctolagus cuniculus	B7NZQ2
Ribosomal protein L11	J	protein	169	Oryctolagus cuniculus	G1TUB8
eL13	L	protein	210	Oryctolagus cuniculus
Ribosomal protein L14	M	protein	138	Oryctolagus cuniculus	G1SZ12

48 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6FTI_1 uL2 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGR

Sequence of entity 2 (B), FASTA

>6FTI_2 uL3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 3 (C), FASTA

>6FTI_3 Ribosomal protein L4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
KS

Sequence of entity 4 (D), FASTA

>6FTI_4 60S ribosomal protein L5 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

Sequence of entity 5 (E), FASTA

>6FTI_5 60S ribosomal protein L6 (chains E)
PHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDK
NGGTRVVKLRKMPRYYPTEDVPRKLLSHGRKPFSQHVRKLRASITPGTILIILTGRHRGK
RVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKK
QLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNG
VYPHKLVF

Sequence of entity 6 (F), FASTA

>6FTI_6 uL30 (chains F)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGEDAGNREDQINRLIRRMN

Sequence of entity 7 (G), FASTA

>6FTI_7 eL8 (chains G)
KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQ
VLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTT
LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFT
QVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKL
G

Sequence of entity 8 (H), FASTA

>6FTI_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA

Sequence of entity 9 (I), FASTA

>6FTI_9 Ribosomal protein L10 (Predicted) (chains I)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 10 (J), FASTA

>6FTI_10 Ribosomal protein L11 (chains J)
ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKI
AVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGL
DFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG

Sequence of entity 11 (L), FASTA

>6FTI_11 eL13 (chains L)
APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPASGPLRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (M), FASTA

>6FTI_12 Ribosomal protein L14 (chains M)
VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFI
LKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRNR
IIKNEVKKLQRAALLKAS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	159
ZN	Zinc ion	Zn	5
9UB	[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl…	C29 H51 N O11 P2	1

Primary citation

Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. Braunger, K., Pfeffer, S., Shrimal, S. et al. Science (2018) 360:215-219. DOI 10.1126/science.aar7899 · PubMed

Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:

11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
9BDL 2.8 Å, 80S ribosome with angiogenin
9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1

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