6R6P: XBP1u-paused ribosome nascent chain complex

Name: PDB 6R6P: Structure of XBP1u-paused ribosome nascent chain complex (rotated state)
Published: 2019-07-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of XBP1u-paused ribosome nascent chain complex (rotated state). Determined by electron microscopy at 3.1 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Saccharomyces cerevisiae
Chains: 85
Atoms: 218,067
Mol. weight: 3222.21 kDa
Ligands: ZN, MG
Released: 10 Jul 2019

Explore 6R6P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R6P contains 481 α-helices and 573 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	106-108	3	53
β-strand	114-116	3	53
α-helix	119	1
β-strand	120	1	54
α-helix	121	1
β-strand	131	1	54
β-strand	133-134	2	55
β-strand	139-141	3	55
β-strand	146-148	3	55

Chain 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	238-244	7

Chain 6: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	67
β-strand	10-11	2	67
α-helix	17	1
β-strand	18-22	5	68
β-strand	30-35	6	68
β-strand	41-45	5	68
β-strand	53-58	6	68
β-strand	66-71	6	69
β-strand	77-82	6	69
β-strand	86-91	6	69
β-strand	97-102	6	69
β-strand	108-113	6	70
β-strand	120-124	5	70
β-strand	129-132	4	70
β-strand	138-142	5	70
β-strand	154-156	3	71
β-strand	164-168	5	71
β-strand	174-178	5	71
β-strand	184-189	6	71
β-strand	195-200	6	72
β-strand	206-211	6	72
β-strand	215-220	6	72
β-strand	226-231	6	72
β-strand	236-241	6	73
β-strand	247-252	6	73
β-strand	255-260	6	73
β-strand	266-270	5	73
α-helix	282-285	4
β-strand	286-291	6	67
β-strand	297-302	6	67
β-strand	307-312	6	67

Chain 9: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	17	1	179
β-strand	20	1	179
α-helix	22-26	5
α-helix	30-36	7
α-helix	39-47	9
α-helix	51-66	16
α-helix	72-74	3
β-strand	75-78	4	180
β-strand	84	1	181
β-strand	93-97	5	180
β-strand	102-106	5	180
α-helix	109-111	3
β-strand	115	1	181

Chain a: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	42-47	6
β-strand	53	1	149
β-strand	72-74	3	16
α-helix	84-88	5
β-strand	100-102	3	17
α-helix	103-106	4
β-strand	110-112	3	16
β-strand	123-126	4	17
β-strand	128-129	2	16
α-helix	131-140	10
β-strand	143-146	4	17

Chain A: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	9-11	3
β-strand	18	1	27
α-helix	29-32	4
α-helix	34-37	4
β-strand	40-50	11	28
α-helix	51	1
β-strand	57-64	8	28
β-strand	71-77	7	28
β-strand	79	1	29
β-strand	82-83	2	30
β-strand	87-91	5	28
β-strand	101	1	28
β-strand	102-103	2	31
α-helix	108	1
β-strand	112-114	3	32
β-strand	116	1	33
β-strand	126	1	33
β-strand	134-140	7	32
β-strand	145-149	5	32
β-strand	155-159	5	32
β-strand	163-164	2	31
β-strand	165-166	2	32
α-helix	168	1
β-strand	169	1	29
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	27
β-strand	224-225	2	34
α-helix	229-230	2
β-strand	237-238	2	34

Chain AA: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	84-88	5
α-helix	90-91	2
α-helix	93-96	4
α-helix	98-101	4
α-helix	104-111	8
α-helix	112-116	5
α-helix	124-126	3

Chain b: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	37-49	13
α-helix	54-75	22

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
28S ribosomal RNA	5	RNA	3662	Oryctolagus cuniculus
5S ribosomal RNA	7	RNA	120	Oryctolagus cuniculus
5.8S ribosomal RNA	8	RNA	156	Oryctolagus cuniculus
uL2	A	protein	244	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	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

73 more molecules are not listed.

Sequence of entity 1 (5), FASTA

>6R6P_1 28S ribosomal RNA (chains 5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCGCGGGGGACCGUCCCCCGACC
GGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGG
ACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGCCGAGUGUUACAGCCCCCCCGGCAG
CAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUC
CCGGCGCCGCCGGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCGGGGCGGACU
GUCCCCAGUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGAGGGGCCACGCGCGCG
UCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCC
ACCCGACCCGUCUUGAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCG
CACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGG
AUCCCGAGGCCUCUCCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCC
GGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGC
AGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGU
CGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCC
GAAGUUUCCCUCAGGAUAGCUGGCGCUCUCGCACACGCAGUUUUAUCCGGUAAAGCGAAU
GAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAGA
AGCCCGGCUCGCUGGCGUGAGCCGGGCGUGGAAUGGAGUGCCUAGUGGGCCACUUUUGGU
AAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGACGC
UCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGU
CGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGG
AUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGGGAG
CGGCGGGGGCGGCGCGCGCGCGCGCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGAC
GAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGC
CGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAG
UGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGG
CGAGCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGA
GUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGC
GGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUU
GUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAA
GCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGA
GGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGC
CUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGG
GAUAAGGAUUGGCUCUAAGGGCUGGGUCGGUCGUCGGCCGGCGCCUAGCAGCCGACUUAG
AACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCG
CGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAU
UCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCC
UCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUA
CUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGAC
CCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGUUUUUUCACUGACCCGGU
GAGGCGGGGGGGCGAGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCGCG
CCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUA
CACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCC
GUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGA
AAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGU
UACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUC
CUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCA
CCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCU
ACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAG
ACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUU
AUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCGCGG
AGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCGGGGUCCGGUGCGGAGUGCCCUUCGU
CCUGGGAAACGGGGCGCGGCCGGAGAGGCGGCCGCCCCCUCGCCCGUCACGCACGCCGUU
CGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUA
CGUAGCAGAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUU
GU

Sequence of entity 2 (7), FASTA

>6R6P_2 5S ribosomal RNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 3 (8), FASTA

>6R6P_3 5.8S ribosomal RNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 4 (A), FASTA

>6R6P_4 uL2 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGR

Sequence of entity 5 (B), FASTA

>6R6P_5 uL3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 6 (C), FASTA

>6R6P_6 uL4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
SD

Sequence of entity 7 (D), FASTA

>6R6P_7 60S ribosomal protein L5 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

Sequence of entity 8 (E), FASTA

>6R6P_8 60S ribosomal protein L6 (chains E)
PHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDK
NGGTRVVKLRKMPRYYPTEDVPRKLLSHGRKPFSQHVRKLRASITPGTILIILTGRHRGK
RVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKK
QLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNG
VYPHKLVF

Sequence of entity 9 (F), FASTA

>6R6P_9 uL30 (chains F)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGEDAGNREDQINRLIRRMN

Sequence of entity 10 (G), FASTA

>6R6P_10 eL8 (chains G)
KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQ
VLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTT
LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFT
QVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKL
G

Sequence of entity 11 (H), FASTA

>6R6P_11 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA

Sequence of entity 12 (I), FASTA

>6R6P_12 Ribosomal protein L10 (Predicted) (chains I)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5
MG	Magnesium ion	Mg	159

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 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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