6R5Q: XBP1u-paused ribosome nascent chain complex

Name: PDB 6R5Q: Structure of XBP1u-paused ribosome nascent chain complex (post-state)
Published: 2019-07-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of XBP1u-paused ribosome nascent chain complex (post-state). Determined by electron microscopy at 3.0 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Saccharomyces cerevisiae, Homo sapiens, Oryctolagus cuniculus
Chains: 85
Atoms: 215,870
Mol. weight: 3192.87 kDa
Ligands: MG, ZN
Released: 10 Jul 2019

Explore 6R5Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R5Q contains 507 α-helices and 566 β-strands across 78 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	88-92	5
β-strand	106-107	2	36
β-strand	115-116	2	36
α-helix	119	1
β-strand	120	1	37
α-helix	121	1
β-strand	131	1	37
β-strand	133-134	2	38
β-strand	139-141	3	38
β-strand	146-148	3	38

Chain 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	239-245	7

Chain 6: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	47
β-strand	10-11	2	47
α-helix	17	1
β-strand	18-22	5	48
β-strand	30-35	6	48
β-strand	41-45	5	48
β-strand	53-58	6	48
β-strand	66-71	6	49
β-strand	77-82	6	49
β-strand	87-91	5	49
β-strand	96-101	6	49
β-strand	108-113	6	50
β-strand	120-124	5	50
β-strand	129-132	4	50
β-strand	138-141	4	50
β-strand	154-156	3	21
β-strand	164-167	4	21
β-strand	173-178	6	21
β-strand	184-189	6	21
β-strand	195-200	6	51
β-strand	206-211	6	51
β-strand	215-220	6	51
β-strand	226-231	6	51
β-strand	236-241	6	52
β-strand	247-252	6	52
β-strand	255-260	6	52
β-strand	264-270	7	52
α-helix	282-285	4
β-strand	286-291	6	47
β-strand	297-302	6	47
β-strand	307-312	6	47

Chain 9: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	22
α-helix	33-35	3
β-strand	38-39	2	22
α-helix	40-50	11
β-strand	53	1	148

Chain a: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	42-48	7
β-strand	72-74	3	39
α-helix	78-80	3
α-helix	84-92	9
β-strand	98	1	128
α-helix	99	1
β-strand	100-102	3	40
α-helix	103-106	4
β-strand	110-112	3	39
β-strand	122-126	5	40
β-strand	128-129	2	39
α-helix	131-140	10
β-strand	142-146	5	40

Chain A: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-12	7
β-strand	18	1	53
α-helix	30-32	3
α-helix	34-37	4
β-strand	40-50	11	54
α-helix	51	1
β-strand	57-64	8	54
β-strand	71-77	7	54
β-strand	79	1	55
β-strand	83	1	56
β-strand	87-91	5	54
β-strand	100-103	4	54
β-strand	112-114	3	54
β-strand	116	1	57
β-strand	126	1	57
β-strand	134-140	7	54
β-strand	145-149	5	54
β-strand	155-159	5	54
β-strand	163-166	4	54
α-helix	168	1
β-strand	169	1	55
α-helix	178-179	2
α-helix	182-192	11
β-strand	193	1	53
β-strand	224-225	2	58
β-strand	237-238	2	58

Chain AA: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	84-88	5
α-helix	92-96	5
α-helix	98-101	4
α-helix	104-111	8
α-helix	112-116	5
α-helix	124-126	3

Chain b: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-19	8
α-helix	22-24	3
α-helix	37-48	12
α-helix	49-51	3
α-helix	55-75	21
α-helix	91-100	10
α-helix	106-116	11

70 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
E-tRNA	3	RNA	75	Saccharomyces cerevisiae
X-box-binding protein 1	1	protein	24	Homo sapiens	P17861 (AlphaFold model)
P-tRNA	2	RNA	76	Saccharomyces cerevisiae
28S ribosomal RNA	5	RNA	3543	Oryctolagus cuniculus
5S rRNA	7	RNA	120	Oryctolagus cuniculus
5.8S ribosomal RNA	8	RNA	151	Oryctolagus cuniculus
uL2	A	protein	248	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
uL3	B	protein	394	Oryctolagus cuniculus	G1TL06 (AlphaFold model)
uL4	C	protein	362	Oryctolagus cuniculus	G1SVW5 (AlphaFold model)
60S ribosomal protein L5	D	protein	293	Oryctolagus cuniculus	P19949
60S ribosomal protein L6	E	protein	251	Oryctolagus cuniculus	G1SKF7
uL30	F	protein	225	Oryctolagus cuniculus	G1SV32

73 more molecules are not listed.

Sequence of entity 1 (3), FASTA

>6R5Q_1 E-tRNA (chains 3)
GCCCGGAUAGCUCAGCUGUAGAGCAUCAGACUUAAAAUCUGAGGGUCCAGGGUUCAAGUC
CCUGUUCGGGCGCCA

Sequence of entity 2 (1), FASTA

>6R5Q_2 X-box-binding protein 1 (chains 1)
DPVPYQPPFLCQWGRHQPAWKPLM

Sequence of entity 3 (2), FASTA

>6R5Q_3 P-tRNA (chains 2)
GCUUCCGUAGUGCAGCGGCUAGCACGUUAGGCUCAUAAUCUAAAGGUCCUUGGUUCGAAA
CCAUCCGGGGGCACCA

Sequence of entity 4 (5), FASTA

>6R5Q_4 28S ribosomal RNA (chains 5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAA
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGAAAUGUGGCGUACGGAAGACCCACUCCCCGGCGC
CGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCGGUAGCG
GCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCAGCCCAA
AGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAACAAGUA
CCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAACCGUUA
AGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGCGCGGUC
CGGCCGUGCCGGCGGGGCGGAUCUCCCGCUCCCGUCGGCGGGGGACCGCCCCCCGGCCGG
CGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGGAC
GGCUGGGAAGGCCCCGGCGGGGAAGGUGGCCCGGGGGCCCCGGGUGUUACAGCCCCGCCC
CGGCAGCAGCAGCUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUGCGCCGCGCUCU
CCCCCCUCGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUGGGGCGGACUGUCCA
GUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGGCCACGCGUCCCCCGCGAGCGCA
CGGGGUCGGCGGCGAUGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACCAAGGAGU
CUAACACGUGCGCGAGUCGGGGGCUACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCC
GGCGGCGCGCCGCCGGCCGAGGUGGGAUCCCGAGGCCUUCCAGUCCGCCGAGGGCGCACC
ACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCC
GAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCG
UAGCGGUCCUGACGUGCGAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCG
AACCAUCUAGUAGCUGGUUCCCUCCAAAGUUUCCCUCAGGAUAGCUGGCGCUCUCCGCAG
UUUUAUCCGGUAAAGCGAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCU
CAAACUUUAAAUGGGUAAGAAGCCCGGCUCGCUGGUGUGGAGCCGGGCGUGGAAUGCGAG
UGCCUAGUGGGCCACUUUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGG
UUAAGGCGCCCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACA
GCAGGAUGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCG
AAUCAACUAGCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCU
GGCAGUCGGCAGAGCGAGAAAGAGAGUGGCGCGGACGCUACGCCGCGACGAGUAGGAGGG
CCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCAG
AUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGGU
UCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGUU
CCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCAGCCGAUCGAAAGGGAGUCGGGUUCAG
AUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGAC
CGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCAG
GGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGUU
CCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAUC
UCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUGU
UGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUUG
GCUCUAAGGGCUGGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAA
UUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAG
UGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUA
UGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUG
AACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCU
UGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAA
GAGACGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCGGGCUCUCGCUUCUGGCG
CCAAGCGCCCGGCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUG
ACUGGGGCGGUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGA
CAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAA
UACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGG
UGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGU
CGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCG
UUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGU
UAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAA
CCGCAGGUUCAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACC
AUCUGUGGGAUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUAGC
GCCGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCGGGGUCCGGUGCGGAGAGCC
CUUCGUCCCGGGAAACGGGGCGGCCGGAAAGGGGGCCGCCCUCUCGCCCGUCACGCACCG
CACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGU
UUCGUACGUAGCAGAGCAGCUGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUU
UGU

Sequence of entity 5 (7), FASTA

>6R5Q_5 5S rRNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 6 (8), FASTA

>6R5Q_6 5.8S ribosomal RNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUC
CUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 7 (A), FASTA

>6R5Q_7 uL2 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT

Sequence of entity 8 (B), FASTA

>6R5Q_8 uL3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 9 (C), FASTA

>6R5Q_9 uL4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
SD

Sequence of entity 10 (D), FASTA

>6R5Q_10 60S ribosomal protein L5 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

Sequence of entity 11 (E), FASTA

>6R5Q_11 60S ribosomal protein L6 (chains E)
KGKPHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVG
GDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRH
RGKRVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYF
KKKKLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFAL
TNGVYPHKLVF

Sequence of entity 12 (F), FASTA

>6R5Q_12 uL30 (chains F)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYNIICMEDLIHEIYTVGKHFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	299
ZN	Zinc ion	Zn	6

Primary citation

Structural and mutational analysis of the ribosome-arresting human XBP1u. Shanmuganathan, V., Schiller, N., Magoulopoulou, A. et al. Elife (2019) 8. DOI 10.7554/eLife.46267 · PubMed

Other PDB entries of the same protein (UniProt P17861 (AlphaFold model), which also has an AlphaFold model), best resolution first:

28LN 2.7 Å, XBP1u-stalled RPL4 RNC in complex with NAC
9NDP 2.82 Å, Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC
6R6P 3.1 Å, Structure of XBP1u-paused ribosome nascent chain complex (rotated state)
6R6G 3.7 Å, Structure of XBP1u-paused ribosome nascent chain complex with SRP.
6R7Q 3.9 Å, Structure of XBP1u-paused ribosome nascent chain complex with Sec61.

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