6R7Q: 40S ribosomal protein S30

Name: PDB 6R7Q: Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
Published: 2019-07-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of XBP1u-paused ribosome nascent chain complex with Sec61. Determined by electron microscopy at 3.9 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Saccharomyces cerevisiae
Chains: 88
Atoms: 219,898
Mol. weight: 3256.77 kDa
Ligands: ZN, MG
Released: 10 Jul 2019

Explore 6R7Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R7Q contains 545 α-helices and 587 β-strands across 81 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	116
β-strand	115-116	2	116
α-helix	119	1
β-strand	120	1	117
α-helix	121	1
β-strand	131	1	117
β-strand	133-134	2	118
β-strand	139-141	3	118
β-strand	146-148	3	118

Chain 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	239-241	3

Chain 6: 2 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	145
β-strand	10-11	2	145
α-helix	17-18	2
β-strand	21-22	2	146
β-strand	32-33	2	146
β-strand	41-44	4	146
β-strand	54-58	5	146
β-strand	66-71	6	147
β-strand	77-82	6	147
β-strand	87-91	5	147
β-strand	96-101	6	147
β-strand	108-112	5	148
β-strand	120-124	5	148
β-strand	129-132	4	148
β-strand	140-142	3	148
β-strand	154-156	3	149
β-strand	165-167	3	149
β-strand	173	1	150
β-strand	175-176	2	149
β-strand	186	1	149
β-strand	189	1	150
β-strand	195	1	151
β-strand	199-200	2	152
β-strand	206-208	3	152
β-strand	211	1	151
β-strand	215-220	6	152
β-strand	226-231	6	152
β-strand	236-241	6	153
β-strand	247-252	6	153
β-strand	255-260	6	153
β-strand	265-270	6	153
α-helix	282-284	3
β-strand	286-291	6	145
β-strand	297-302	6	145
β-strand	307-312	6	145

Chain 9: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	165
α-helix	33-35	3
β-strand	38-39	2	165
α-helix	40-45	6
α-helix	47-50	4
β-strand	53	1	64

Chain a: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-9	3
α-helix	42-47	6
β-strand	72-74	3	46
α-helix	84-92	9
β-strand	97-98	2	125
β-strand	100-102	3	47
β-strand	110-112	3	46
β-strand	122-126	5	47
β-strand	128-129	2	46
α-helix	131-140	10
β-strand	142-146	5	47

Chain A: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
β-strand	18	1	23
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-50	11	24
α-helix	51	1
β-strand	57-64	8	24
β-strand	71-77	7	24
α-helix	78	1
β-strand	79	1	25
β-strand	83	1	26
β-strand	87-91	5	24
β-strand	101	1	24
β-strand	102-103	2	27
β-strand	112-114	3	28
β-strand	116	1	29
β-strand	126	1	29
β-strand	134-140	7	28
β-strand	145-149	5	28
β-strand	155-159	5	28
β-strand	163-164	2	27
β-strand	165-166	2	28
α-helix	168	1
β-strand	169	1	25
α-helix	174-176	3
α-helix	178-179	2
α-helix	182-190	9
β-strand	193	1	23
α-helix	201-203	3
β-strand	224-225	2	30
β-strand	237-238	2	30

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	12-18	7
α-helix	22-26	5
α-helix	37-48	12
α-helix	49-51	3
α-helix	54-75	22
α-helix	91-100	10
α-helix	102-115	14

73 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
40S ribosomal protein S30	AA	protein	55	Oryctolagus cuniculus	G1T8A2 (AlphaFold model)
40S ribosomal protein S7	BB	protein	189	Oryctolagus cuniculus	G1SVB0 (AlphaFold model)
40S ribosomal protein S8	CC	protein	206	Oryctolagus cuniculus	G1TJW1 (AlphaFold model)
Ribosomal protein S9 (Predicted)	DD	protein	185	Oryctolagus cuniculus	B7NZS8 (AlphaFold model)
Ribosomal protein S11	EE	protein	151	Oryctolagus cuniculus	G1TRM4
Ribosomal protein S28	FF	protein	62	Oryctolagus cuniculus	G1TIB4
uS10	GG	protein	100	Oryctolagus cuniculus
eS21	HH	protein	83	Oryctolagus cuniculus
uS13	II	protein	144	Oryctolagus cuniculus	G1TPG3
40S ribosomal protein S27	JJ	protein	83	Oryctolagus cuniculus	G1TZ76
eS17	KK	protein	132	Oryctolagus cuniculus	G1TU13
eS26	LL	protein	101	Oryctolagus cuniculus

76 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>6R7Q_1 40S ribosomal protein S30 (chains AA)
SLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

Sequence of entity 2 (BB), FASTA

>6R7Q_2 40S ribosomal protein S7 (chains BB)
AKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVP
VPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAV
HDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDV
NFEFPEFQL

Sequence of entity 3 (CC), FASTA

>6R7Q_3 40S ribosomal protein S8 (chains CC)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 4 (DD), FASTA

>6R7Q_4 Ribosomal protein S9 (Predicted) (chains DD)
PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELL
TLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAK
SIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKG
QGGAG

Sequence of entity 5 (EE), FASTA

>6R7Q_5 Ribosomal protein S11 (chains EE)
DIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPF
TGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQI
GDIVTVGECRPLSKTVRFNVLKVTKAAGTKK

Sequence of entity 6 (FF), FASTA

>6R7Q_6 Ribosomal protein S28 (chains FF)
QPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREAR
RL

Sequence of entity 7 (GG), FASTA

>6R7Q_7 uS10 (chains GG)
HRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCGEGSKTW
DRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIA

Sequence of entity 8 (HH), FASTA

>6R7Q_8 eS21 (chains HH)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 9 (II), FASTA

>6R7Q_9 uS13 (chains II)
SLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTE
DEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHR
GLRHFWGLRVRGQHTKTTGRRGRT

Sequence of entity 10 (JJ), FASTA

>6R7Q_10 40S ribosomal protein S27 (chains JJ)
PLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCST
VLCQPTGGKARLTEGCSFRRKQH

Sequence of entity 11 (KK), FASTA

>6R7Q_11 eS17 (chains KK)
GRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKRI
QRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVTQ
PTVGMNFKTPRG

Sequence of entity 12 (LL), FASTA

>6R7Q_12 eS26 (chains LL)
TKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDA
YVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFR

Ligands and cofactors

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

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 G1T8A2 (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…
7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
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…
7JQB 2.7 Å, SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
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
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon

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