8RJB: PDB entry 8RJB

Name: PDB 8RJB: Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4
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-RAMP4. Determined by electron microscopy at 2.69 Å resolution. Released 24 Jan 2024.

Method: Electron microscopy
Resolution: 2.69 Å
Organisms: Canis lupus familiaris, Oryctolagus cuniculus, Bos taurus
Chains: 51
Atoms: 141,192
Mol. weight: 2206.83 kDa
Ligands: MG, ZN
Released: 24 Jan 2024

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

Secondary structure: helices and β-sheets

8RJB contains 388 α-helices and 309 β-strands across 47 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: 25 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	17-19	3	1
α-helix	20-21	2
α-helix	28-47	20
α-helix	49-50	2
α-helix	63-69	7
α-helix	76-78	3
α-helix	82-96	15
α-helix	106-130	25
α-helix	131-135	5
α-helix	140-143	4
α-helix	145-170	26
α-helix	178-196	19
β-strand	200-203	4	2
β-strand	206-209	4	2
α-helix	212-222	11
α-helix	226-234	9
α-helix	242-259	18
β-strand	262-267	6	3
β-strand	268-269	2	4
β-strand	277-282	6	3
α-helix	289-312	24
α-helix	316-321	6
β-strand	323-327	5	5
β-strand	334-339	6	5
α-helix	341-345	5
α-helix	347-348	2
α-helix	351-356	6
α-helix	358-383	26
α-helix	387-396	10
β-strand	399-400	2	4
α-helix	406-408	3
α-helix	409-438	30
α-helix	444-467	24

Chain 2: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	66-68	3	1
α-helix	70-95	26

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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	5-15	11
α-helix	16-20	5
α-helix	40-64	25

Chain a: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-10	4
α-helix	42-48	7
β-strand	72-74	3	19
α-helix	75-81	7
α-helix	84-92	9
β-strand	97-98	2	67
α-helix	99	1
β-strand	100-102	3	20
β-strand	110-112	3	19
β-strand	123-126	4	20
β-strand	128-129	2	19
α-helix	131-139	9
β-strand	143-146	4	20

Chain A: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
α-helix	14-16	3
α-helix	30-32	3
α-helix	34-38	5
β-strand	40-49	10	14
β-strand	58-64	7	14
β-strand	71-77	7	14
β-strand	79	1	15
β-strand	83	1	16
β-strand	87-91	5	14
β-strand	101-103	3	14
α-helix	104-106	3
α-helix	108	1
β-strand	112-114	3	14
β-strand	116	1	17
β-strand	126	1	17
β-strand	134-140	7	14
β-strand	145-149	5	14
β-strand	155-159	5	14
β-strand	163-166	4	14
β-strand	169	1	15
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	18
α-helix	229-230	2
β-strand	237-238	2	18

Chain b: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	22-25	4
α-helix	37-48	12
α-helix	50-53	4
α-helix	54-75	22
α-helix	91-99	9
α-helix	106-116	11

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3

39 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)
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
Ribosomal_L18_c domain-containing protein	D	protein	297	Oryctolagus cuniculus	P19949
60S ribosomal protein L6	E	protein	291	Oryctolagus cuniculus	G1SKF7
Ribosomal Protein uL30	F	protein	247	Oryctolagus cuniculus	G1SV32
60S ribosomal protein L7a	G	protein	319	Oryctolagus cuniculus	G1STW0
60S ribosomal protein L9	H	protein	192	Oryctolagus cuniculus	G1SWI6

39 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>8RJB_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

>8RJB_2 Protein transport protein Sec61 subunit beta (chains 2)
MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYT
EDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS

Sequence of entity 3 (3), FASTA

>8RJB_3 Protein transport protein Sec61 subunit gamma (chains 3)
MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIP
INNIIVGG

Sequence of entity 4 (4), FASTA

>8RJB_4 Stress-associated endoplasmic reticulum protein (chains 4)
MVAKQRIRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQ
SIRMGM

Sequence of entity 5 (A), FASTA

>8RJB_5 Ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 6 (B), FASTA

>8RJB_6 Nascent chain (chains B)
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVTASAWSHPQFEKGGGSGGGSGGSAWSH
PQFEKAGGSAGSGGGSAGGSALSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFGSAG
SGGGSAGGGSAAEPWQFSMLAAYMFLLIMLGFPINCLTLYVTVQHKKLRTPLNYILLNLA
VADLFMVFGGFTTTLYTSLHGYFVFGPTGMPGPTPSGTNVGSSGRSPSV

Sequence of entity 7 (C), FASTA

>8RJB_7 Large ribosomal subunit protein uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA

Sequence of entity 8 (D), FASTA

>8RJB_8 Ribosomal_L18_c domain-containing protein (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 9 (E), FASTA

>8RJB_9 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 10 (F), FASTA

>8RJB_10 Ribosomal Protein uL30 (chains F)
MEGAEEKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEY
RQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT
FVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGK
YNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN
RLIRRMN

Sequence of entity 11 (G), FASTA

>8RJB_11 60S ribosomal protein L7a (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG

Sequence of entity 12 (H), FASTA

>8RJB_12 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

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
8RJD 2.79 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…

Browse structure collections

About this viewer

MolViewer shows 8RJB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.