6R6G: ES31

Name: PDB 6R6G: Structure of XBP1u-paused ribosome nascent chain complex with SRP.
Published: 2019-07-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of XBP1u-paused ribosome nascent chain complex with SRP. Determined by electron microscopy at 3.7 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Saccharomyces cerevisiae
Chains: 92
Atoms: 227,187
Mol. weight: 3366.39 kDa
Ligands: MG, ZN
Released: 10 Jul 2019

Explore 6R6G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R6G contains 532 α-helices and 583 β-strands across 83 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	1
β-strand	115-116	2	1
α-helix	119	1
β-strand	120	1	2
α-helix	121	1
β-strand	131	1	2
β-strand	133-134	2	3
β-strand	139-141	3	3
β-strand	146-148	3	3

Chain 6: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	54
β-strand	10-11	2	54
α-helix	17	1
β-strand	18-22	5	55
β-strand	30-35	6	55
β-strand	41-45	5	55
β-strand	53-58	6	55
β-strand	66-71	6	56
β-strand	77-82	6	56
β-strand	87-91	5	56
β-strand	96-101	6	56
β-strand	108-113	6	57
β-strand	120-124	5	57
β-strand	129-132	4	57
β-strand	138-141	4	57
β-strand	154-156	3	58
β-strand	164-167	4	58
β-strand	173-178	6	58
β-strand	184-189	6	58
β-strand	195-200	6	59
β-strand	206-211	6	59
β-strand	215-220	6	59
β-strand	226-231	6	59
β-strand	236-241	6	60
β-strand	247-252	6	60
β-strand	255-260	6	60
β-strand	266-270	5	60
α-helix	282-285	4
β-strand	286-291	6	54
β-strand	297-302	6	54
β-strand	307-312	6	54

Chain 9: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	30-31	2	84
α-helix	33-35	3
β-strand	38-39	2	84
α-helix	40-50	11
β-strand	53	1	85

Chain a: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	12	1	78
β-strand	14	1	78
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-74	3	79
α-helix	78-80	3
α-helix	84-92	9
β-strand	98	1	67
α-helix	99	1
β-strand	100-102	3	80
α-helix	103-106	4
β-strand	110-112	3	79
β-strand	122-126	5	80
β-strand	128-129	2	79
α-helix	131-140	10
β-strand	142-146	5	80

Chain A: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	18	1	90
α-helix	30-32	3
α-helix	34-37	4
β-strand	40-50	11	91
α-helix	51	1
β-strand	57-64	8	91
β-strand	71-77	7	91
β-strand	79	1	92
β-strand	83	1	93
β-strand	87-91	5	91
β-strand	100-103	4	91
β-strand	112-114	3	91
β-strand	116	1	94
β-strand	126	1	94
β-strand	134-140	7	91
α-helix	142-144	3
β-strand	145-149	5	91
β-strand	155-159	5	91
β-strand	163-166	4	91
α-helix	168	1
β-strand	169	1	92
α-helix	178-179	2
α-helix	182-192	11
β-strand	193	1	90
β-strand	224-225	2	95
β-strand	237-238	2	95

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 AB: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	25-42	18
α-helix	46-59	14
α-helix	73-85	13
β-strand	103-107	5	81
α-helix	114-128	15
β-strand	132-137	6	81
α-helix	142-152	11
α-helix	168-179	12
β-strand	186-191	6	81
α-helix	201-212	12
β-strand	216-222	7	81
α-helix	229-239	11
β-strand	244-248	5	81
α-helix	256-265	10
β-strand	270-274	5	81
β-strand	282-284	3	81
α-helix	287-295	9
α-helix	329-341	13
α-helix	346-349	4
α-helix	367-380	14
α-helix	384-388	5
α-helix	392-398	7
α-helix	400-410	11
α-helix	414-433	20

Chain AC: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	87
α-helix	20-22	3
β-strand	24	1	88
α-helix	37-39	3
β-strand	41	1	88
α-helix	46-54	9
β-strand	60-63	4	87
α-helix	76-78	3
β-strand	81-84	4	87
β-strand	87	1	89
β-strand	93	1	89
α-helix	101-111	11
α-helix	113-116	4

75 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
eS31	0	protein	68	Oryctolagus cuniculus	G1SK22 (AlphaFold model)
X-box-binding protein 1	1	protein	24	Homo sapiens	P17861 (AlphaFold model)
P-tRNA	2	RNA	75	Saccharomyces cerevisiae
E-tRNA	3	RNA	75	Saccharomyces cerevisiae
mRNA	4	RNA	6	Homo sapiens
28S ribosomal RNA	5	RNA	3544	Oryctolagus cuniculus
ribosomal protein RACK1	6	protein	313	Oryctolagus cuniculus	G1SJB4 (AlphaFold model)
5S ribosomal RNA	7	RNA	120	Oryctolagus cuniculus
5.8S ribosomal RNA	8	RNA	151	Oryctolagus cuniculus
uS14	9	protein	55	Oryctolagus cuniculus	G1U7M4 (AlphaFold model)
uL2	A	protein	248	Oryctolagus cuniculus	G1TT27
40S ribosomal protein S30	AA	protein	55	Oryctolagus cuniculus	G1T8A2

80 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>6R6G_1 eS31 (chains 0)
KSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRHYCG
KCCLTYCF

Sequence of entity 2 (1), FASTA

>6R6G_2 X-box-binding protein 1 (chains 1)
DPVPYQPPFLCQWGRHQPAWKPLM

Sequence of entity 3 (2), FASTA

>6R6G_3 P-tRNA (chains 2)
GCUUCCGUAGUGCAGCGGCAGCACGUUAGGCUCAUAAUCUAAAGGUCCUUGGUUCGAAAC
CAUCCGGGGGCACCA

Sequence of entity 4 (3), FASTA

>6R6G_4 E-tRNA (chains 3)
GCCCGGAUAGCUCAGCUGUAGAGCAUCAGACUUAAAAUCUGAGGGUCCAGGGUUCAAGUC
CCUGUUCGGGCGCCA

Sequence of entity 5 (4), FASTA

>6R6G_5 mRNA (chains 4)
UUAAUG

Sequence of entity 6 (5), FASTA

>6R6G_6 28S ribosomal RNA (chains 5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAA
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGAAAUGUGGCGUACGGAAGACCCACUCCCCGGCGC
CGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCGGUAGCG
GCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCAGCCCAA
AGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAACAAGUA
CCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAACCGUUA
AGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGCGCGGUC
CGGCCGUGCCGGCGGGGCGGAUCUCCCGCUCCCGUCGGCGGGGGACCGCCCCCCGGCCGG
CGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGGAC
GGCUGGGAAGGCCCCGGCGGGGAAGGUGGCCCGGGGGCCCCGGGUGUUACAGCCCCGCCC
CGGCAGCAGCAGCUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUGCGCCGCGCUCU
CCCCCCUCGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUGGGGCGGACUGUCCA
GUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGGCCACGCGUCCCCCGCGAGCGCA
CGGGGUCGGCGGCGAUGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACCAAGGAGU
CUAACACGUGCGCGAGUCGGGGGCUACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCC
GGCGCGCGCGCCGCCGGCCGAGGUGGGAUCCCGAGGCCUUCCAGUCCGCCGAGGGCGCAC
CACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUGUUAGGACC
CGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCC
GUAGCGGUCCUGACGUGCGAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUC
GAACCAUCUAGUAGCUGGUUCCCUCCAAAGUUUCCCUCAGGAUAGCUGGCGCUCUCCGCA
GUUUUAUCCGGUAAAGCGAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUC
UCAAACUUUAAAUGGGUAAGAAGCCCGGCUCGCUGGUGUGGAGCCGGGCGUGGAAUGCGA
GUGCCUAGUGGGCCACUUUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGG
GUUAAGGCGCCCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGAC
AGCAGGAUGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCC
GAAUCAACUAGCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGC
UGGCAGUCGGCAGAGCGAGAAAGAGAGUGGCGCGGACGCUACGCCGCGACGAGUAGGAGG
GCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCA
GAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGG
UUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGU
UCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCAGCCGAUCGAAAGGGAGUCGGGUUCA
GAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGA
CCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCA
GGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGU
UCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAU
CUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUG
UUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUU
GGCUCUAAGGGCUGGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUA
AUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCA
GUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACU
AUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAU
GAACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGC
UUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGA
AGAGACGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCGGGCUCUCGCUUCUGGC
GCCAAGCGCCCGGCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUU
GACUGGGGCGGUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGG
ACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGA
AUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAG
GUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACG
UCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGC
GUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGG
UUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGA
ACCGCAGGUUCAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUAC
CAUCUGUGGGAUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUAG
CGCCGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCGGGGUCCGGUGCGGAGAGC
CCUUCGUCCCGGGAAACGGGGCGGCCGGAAAGGGGGCCGCCCUCUCGCCCGUCACGCACC
GCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGG
UUUCGUACGUAGCAGAGCAGCUGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGU
UUGU

Sequence of entity 7 (6), FASTA

>6R6G_7 ribosomal protein RACK1 (chains 6)
TEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRG
HSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIV
SGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLAN
CKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCF
SPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFAG
YTDNLVRVWQVTI

Sequence of entity 8 (7), FASTA

>6R6G_8 5S ribosomal RNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 9 (8), FASTA

>6R6G_9 5.8S ribosomal RNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUC
CUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 10 (9), FASTA

>6R6G_10 uS14 (chains 9)
GHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 11 (A), FASTA

>6R6G_11 uL2 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT

Sequence of entity 12 (AA), FASTA

>6R6G_12 40S ribosomal protein S30 (chains AA)
SLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	299
ZN	Zinc ion	Zn	5

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 G1SK22 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
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…
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
9NDP 2.82 Å, Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC
9Q7Q 2.86 Å, ABCE1-eRF1-rnc-AMD1C
11HG 2.9 Å, Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveled

Browse structure collections

About this viewer

MolViewer shows 6R6G 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.