8RJD: PDB entry 8RJD

Name: PDB 8RJD: Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2
Published: 2024-01-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2. Determined by electron microscopy at 2.79 Å resolution. Released 24 Jan 2024.

Method: Electron microscopy
Resolution: 2.79 Å
Organisms: Canis lupus familiaris, Oryctolagus cuniculus, Bos taurus
Chains: 56
Atoms: 146,794
Mol. weight: 2366.69 kDa
Ligands: MG, ZN
Released: 24 Jan 2024

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

Secondary structure: helices and β-sheets

8RJD contains 415 α-helices and 349 β-strands across 52 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 1: 24 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	19	1	1
α-helix	20-22	3
α-helix	25-27	3
α-helix	28-47	20
β-strand	49	1	2
α-helix	50	1
α-helix	63-68	6
β-strand	75	1	2
α-helix	82-97	16
α-helix	106-134	29
α-helix	140-143	4
α-helix	145-168	24
α-helix	169-173	5
α-helix	178-196	19
β-strand	200-203	4	3
β-strand	206-209	4	3
α-helix	212-222	11
α-helix	226-232	7
α-helix	242-259	18
β-strand	262-269	8	4
β-strand	276-282	7	4
α-helix	289-311	23
α-helix	316-319	4
β-strand	323-327	5	5
β-strand	334-339	6	5
α-helix	341-344	4
α-helix	351-356	6
α-helix	358-383	26
α-helix	387-396	10
β-strand	399-400	2	4
α-helix	406-414	9
α-helix	417-437	21
α-helix	443-464	22

Chain 2: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	68	1	1
α-helix	70-93	24

Chain 3: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	2-24	23
α-helix	27-29	3
α-helix	30-65	36

Chain 4: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	16-20	5

Chain 5: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	78-80	3
β-strand	83-89	7	21
β-strand	95-96	2	22
β-strand	101-109	9	21
β-strand	115-126	12	23
β-strand	129-140	12	23
β-strand	144-146	3	23
β-strand	150-158	9	21
α-helix	162-164	3
β-strand	168-179	12	23
β-strand	184-195	12	23
β-strand	196-197	2	22
α-helix	198	1
α-helix	205-234	30
α-helix	258-264	7

Chain 6: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	23-29	7	30
β-strand	31	1	31
β-strand	35	1	32
β-strand	40-48	9	30
α-helix	53	1
β-strand	54-60	7	21
β-strand	69-73	5	30
β-strand	78-83	6	21
β-strand	87-97	11	30
β-strand	103-105	3	33
β-strand	109-113	5	21
β-strand	120-124	5	21
β-strand	129-131	3	33
β-strand	134	1	32
α-helix	136-143	8
α-helix	147-156	10
α-helix	158-175	18

Chain 7: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	8-20	13
α-helix	26-41	16
α-helix	43-45	3
α-helix	46-50	5
α-helix	59-91	33
α-helix	93-106	14
α-helix	114-151	38
α-helix	152-156	5
α-helix	162-183	22

Chain 8: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	30	1	36
β-strand	34-37	4	21
β-strand	40	1	37
β-strand	44	1	31
β-strand	47-54	8	21
β-strand	56	1	36
β-strand	66-70	5	38
β-strand	73-76	4	38
α-helix	77	1
β-strand	78-80	3	21
β-strand	85-92	8	21
β-strand	100-108	9	38
α-helix	109-120	12
α-helix	129-130	2
β-strand	132-138	7	38
β-strand	142	1	37
α-helix	149-172	24

44 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
Protein transport protein Sec61 subunit alpha isoform 1	1	protein	476	Canis lupus familiaris	P38377 (AlphaFold model)
Protein transport protein Sec61 subunit beta	2	protein	96	Canis lupus familiaris	P60467 (AlphaFold model)
Protein transport protein Sec61 subunit gamma	3	protein	68	Canis lupus familiaris	P60058 (AlphaFold model)
Stress-associated endoplasmic reticulum protein	4	protein	66	Canis lupus familiaris	A0A8I3PRN4 (AlphaFold model)
Translocon-associated protein subunit alpha	5	protein	286	Canis lupus familiaris	P16967
Translocon-associated protein subunit beta	6	protein	183	Canis lupus familiaris	P23438
Translocon-associated protein subunit gamma	7	protein	185	Canis lupus familiaris	A0A8C0T6I4
Translocon-associated protein subunit delta	8	protein	173	Canis lupus familiaris	A0A8I3PXW2
Calnexin	9	protein	593	Canis lupus familiaris	P24643
Ribosomal protein L8	A	protein	257	Oryctolagus cuniculus	G1TT27
Nascent chain	B	protein	229	Bos taurus	P02699
Large ribosomal subunit protein uL4	C	protein	425	Oryctolagus cuniculus	G1SVW5

44 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>8RJD_1 Protein transport protein Sec61 subunit alpha isoform 1 (chains 1)
MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFG
MIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLP
NLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSN
LYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVH
AVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTA
AAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF

Sequence of entity 2 (2), FASTA

>8RJD_2 Protein transport protein Sec61 subunit beta (chains 2)
MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYT
EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS

Sequence of entity 3 (3), FASTA

>8RJD_3 Protein transport protein Sec61 subunit gamma (chains 3)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG

Sequence of entity 4 (4), FASTA

>8RJD_4 Stress-associated endoplasmic reticulum protein (chains 4)
MVAKQRIRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQ
SIRMGM

Sequence of entity 5 (5), FASTA

>8RJD_5 Translocon-associated protein subunit alpha (chains 5)
MRVLPRLLLLLLLAFPAAVLLRGGPGGSLVAAQDLTEDEETVEDSIIEDEDDEAEVEEDE
PTDLAEDKEEEDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESL
DASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDL
NGNVFQDAVFNQTVTIIEREDGLDGETIFMYMFLAGLGLLVVVGLHQLLESRKRKRPIQK
VEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE

Sequence of entity 6 (6), FASTA

>8RJD_6 Translocon-associated protein subunit beta (chains 6)
MRLLASVLLALFAVSHAEEGARLLASKSLLNRYAVEGRDLTLQYNIYNVGSSAALDVELS
DDSFPPEDFGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATVTYLAQEDGPV
VIGFTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKS
KKN

Sequence of entity 7 (7), FASTA

>8RJD_7 Translocon-associated protein subunit gamma (chains 7)
MAPKGGSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAV
LYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDER
ILWKKNEVADYEATTFSIFYNNTLFLVLVIVASFFILKNFNPTVNYILSISASSGLIALL
STGSK

Sequence of entity 8 (8), FASTA

>8RJD_8 Translocon-associated protein subunit delta (chains 8)
MAALASLGALALLLLSSLSCCSAEACVEPQITPSYYTTSDAVISTETVFIVEISLTCKNR
VQNMALYADVSGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQR
NNEDISIIPPLFTVSVDHRGTWNGPWVSTEVLAAAIGLVIYYLAFSAKSHIQA

Sequence of entity 9 (9), FASTA

>8RJD_9 Calnexin (chains 9)
MEGKWLLCMLLVLGTTIVQAHEGHDDDMIDIEDDLDDVIEEVEDSKSKPDTSAPTSPKVT
YKAPVPTGEVYFADSFDRGTLSGWILSKAKKDDTDDEIAKYDGKWEVDEMKETKLPGDKG
LVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQF
HDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGVYEEKHAKRPDADLKTYFTDKKTHLYT
LILNPDNSFEILVDQSIVNSGNLLNDMTPPVNPSREIEDPEDQKPEDWDERPKIPDPDAV
KPDDWNEDAPAKIPDEEATKPDGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPK
CESAPGCGVWQRPMIDNPNYKGKWKPPMIDNPNYQGIWKPRKIPNPDFFEDLEPFKMTPF
SAIGLELWSMTSDIFFDNFIVCGDRRVVDDWANDGWGLKKAADGAAEPGVVGQMIEAAEE
RPWLWVVYVLTVALPVFLVILFCCSGKKQSSPVEYKKTDAPQPDVKEEEEEKEEEKDKGD
EEEEGEEKLEEKQKSDAEEDGGTASQEEDDRKPKAEEDEILNRSPRNRKPRRE

Sequence of entity 10 (A), FASTA

>8RJD_10 Ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 11 (B), FASTA

>8RJD_11 Nascent chain (chains B)
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVTASAWSHPQFEKGGGSGGGSGGSAWSH
PQFEKAGGSAGSGGGSAGGSALSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFGSAG
SGGGSAGGGSAAEPWQFSMLAAYMFLLIMLGFPINCLTLYVTVQHKKLRTPLNYILLNLA
VADLFMVFGGFTTTLYTSLHGYFVFGPTGMPGPTPSGTNVGSSGRSPSV

Sequence of entity 12 (C), FASTA

>8RJD_12 Large ribosomal subunit protein uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	218
ZN	Zinc ion	Zn	5

Primary citation

Structural analysis of the dynamic ribosome-translocon complex. Lewis, A.J.O., Zhong, F., Keenan, R.J. et al. Elife (2024) 13. DOI 10.7554/eLife.95814 · PubMed

Other PDB entries of the same protein (UniProt P38377 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Z3T 2.69 Å, Structure of canine Sec61 inhibited by mycolactone
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8RJC 2.9 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
7TM3 3.25 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in…
8OJ8 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)
8BTK 3.5 Å, Structure of the TRAP complex with the Sec translocon and a translating ribosome
3JC2 3.6 Å, The structure of the mammalian Sec61 channel opened by a signal sequence
7TUT 3.88 Å, Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in…
6R7Q 3.9 Å, Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
6FTI 4.2 Å, Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the…
6FTJ 4.7 Å, Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the…
2WWB 6.48 Å, cryo-EM structure of the mammalian SEC61 complex bound to the actively translating wheat…

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