7QWS: Ribosome translating beta-tubulin

Name: PDB 7QWS: Structure of ribosome translating beta-tubulin in complex with TTC5 and NAC
Published: 2022-03-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of ribosome translating beta-tubulin in complex with TTC5 and NAC. Determined by electron microscopy at 3.4 Å resolution. Released 9 Mar 2022.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Oryctolagus cuniculus
Chains: 49
Atoms: 137,913
Mol. weight: 2592.41 kDa
Ligands: ZN, MG
Released: 9 Mar 2022

Explore 7QWS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QWS contains 342 α-helices and 312 β-strands across 45 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 a: 6 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	53	1	36
β-strand	72-74	3	90
α-helix	75-81	7
α-helix	84-89	6
β-strand	100-102	3	91
β-strand	110-112	3	90
β-strand	123-126	4	91
β-strand	128-129	2	90
α-helix	131-140	10
β-strand	143-146	4	91

Chain A: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	9-11	3
α-helix	14-16	3
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	6
β-strand	58-64	7	6
β-strand	71-77	7	6
β-strand	79	1	7
β-strand	83	1	8
β-strand	87-91	5	6
β-strand	101-103	3	6
α-helix	108	1
β-strand	112-114	3	6
β-strand	116	1	9
β-strand	126	1	9
β-strand	134-140	7	6
α-helix	142-144	3
β-strand	145-149	5	6
β-strand	155-159	5	6
β-strand	163-166	4	6
β-strand	169	1	7
α-helix	182-190	9
α-helix	198-200	3
α-helix	201-203	3
β-strand	224-225	2	10
α-helix	229-230	2
β-strand	237-238	2	10

Chain b: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	37-48	12
α-helix	49-51	3
α-helix	54-75	22

Chain B: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	27-29	3
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	18
β-strand	45-59	15	19
β-strand	60	1	20
β-strand	68	1	20
β-strand	71-80	10	19
α-helix	82-83	2
β-strand	84-95	12	21
β-strand	98-106	9	21
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-165	7	21
α-helix	168-170	3
α-helix	177-179	3
β-strand	180-184	5	21
β-strand	185-186	2	18
α-helix	190-199	10
β-strand	204-205	2	21
α-helix	207-209	3
β-strand	216-222	7	19
α-helix	223-225	3
β-strand	227-229	3	22
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-272	3	22
β-strand	276-286	11	19
β-strand	292-293	2	23
β-strand	297-298	2	23
α-helix	300-302	3
β-strand	320	1	24
β-strand	324	1	24
β-strand	330-335	6	19
β-strand	344-349	6	19
β-strand	365-368	4	19
α-helix	382-389	8

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-23	10
β-strand	26-29	4	29
α-helix	31-39	9
β-strand	45-49	5	29
α-helix	54-67	14
β-strand	70-74	5	29
α-helix	78-84	7
β-strand	93-98	6	29

Chain C: 24 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	30
α-helix	10	1
β-strand	11	1	31
β-strand	12-13	2	32
β-strand	15	1	32
β-strand	21-23	3	30
α-helix	24-25	2
α-helix	26-29	4
α-helix	31-32	2
α-helix	34-44	11
α-helix	49-51	3
β-strand	64-66	3	33
β-strand	77-79	3	33
α-helix	117-131	15
α-helix	134-139	6
β-strand	152-154	3	31
α-helix	156-160	5
α-helix	164-173	10
α-helix	178-185	8
β-strand	188-189	2	34
α-helix	190-191	2
α-helix	193-197	5
β-strand	201-202	2	34
β-strand	208-211	4	31
α-helix	217-222	6
β-strand	228-231	4	31
α-helix	237-240	4
α-helix	242-244	3
β-strand	250-253	4	31
α-helix	254-263	10
α-helix	279-282	4
α-helix	289-293	5
α-helix	296-299	4
α-helix	303-305	3
α-helix	322-328	7
α-helix	331-337	7
α-helix	341-362	22

Chain d: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	37
α-helix	29-32	4
α-helix	38-40	3
α-helix	41-56	16
β-strand	62-64	3	37
α-helix	66-73	8
β-strand	83-90	8	37
β-strand	104-108	5	37
β-strand	121	1	37

Chain D: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	21-25	5
α-helix	30-36	7
α-helix	38-40	3
β-strand	50-55	6	40
β-strand	60-66	7	40
α-helix	72	1
β-strand	73-79	7	40
α-helix	80-82	3
α-helix	83-86	4
α-helix	95-112	18
α-helix	139-141	3
β-strand	142-143	2	41
β-strand	145-147	3	40
α-helix	158-169	12
β-strand	171-172	2	41
β-strand	183-184	2	42
β-strand	189-190	2	42
α-helix	194-200	7
α-helix	202-214	13
α-helix	216-222	7
α-helix	224-227	4
α-helix	233-249	17
α-helix	255-258	4
α-helix	273-291	19

37 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
Nascent chain tubulin beta	s	protein	24	Homo sapiens
Nascent polypeptide-associated complex subunit alpha	t	protein	215	Oryctolagus cuniculus	Q13765 (AlphaFold model)
Transcription factor BTF3	u	protein	162	Oryctolagus cuniculus	G1TKK2 (AlphaFold model)
60S ribosomal protein L8	A	protein	245	Oryctolagus cuniculus	A0A5F9D5B2 (AlphaFold model)
60S ribosomal protein L29	b	protein	223	Oryctolagus cuniculus	G1SGR6 (AlphaFold model)
Ribosomal protein L3	B	protein	403	Oryctolagus cuniculus	G1TL06
60S ribosomal protein L30	c	protein	115	Oryctolagus cuniculus	G1TDL2
60S ribosomal protein L4	C	protein	413	Oryctolagus cuniculus	G1SVW5
Ribosomal protein L31	d	protein	125	Oryctolagus cuniculus	G1SHG0
Ribosomal_L18_c domain-containing protein	D	protein	297	Oryctolagus cuniculus	P19949
Ribosomal protein L32	e	protein	157	Oryctolagus cuniculus	G1TUN8
60S ribosomal protein L6	E	protein	291	Oryctolagus cuniculus	G1SKF7

37 more molecules are not listed.

Sequence of entity 1 (s), FASTA

>7QWS_1 Nascent chain tubulin beta (chains s)
XXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (t), FASTA

>7QWS_2 Nascent polypeptide-associated complex subunit alpha (chains t)
MPGEATETVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQATTQQAQLAAAAEID
EEPVSKAKQSRSEKKARKAMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTY
IVFGEAKIEDLSQQAQLAAAEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVKD
IELVMSQANVSRAKAVRALKNNSNDIVNAIMELTM

Sequence of entity 3 (u), FASTA

>7QWS_3 Transcription factor BTF3 (chains u)
MKETIMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIE
EVNMFTNQGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRR
LAEALPKQSVDGKAPLATGEDDDDEVPDLVENFDEASKNEAN

Sequence of entity 4 (A), FASTA

>7QWS_4 60S ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGR

Sequence of entity 5 (b), FASTA

>7QWS_5 60S ribosomal protein L29 (chains b)
MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQAN
NAKAMAARAEAIKALVKPKEVKPTIPKGVSRKLDRLAYIAHPKLGRRARARIARGLRLSR
PQTKAKAKTEPQIKGKVKAQIKAQAQAQIKSKGKGKAQAETKPKAQAQAKPKAQAQGKPK
AQAQAKPKAHAQAKPKAQAQAKPKAQAQTKRTGVTPGLLSAWG

Sequence of entity 6 (B), FASTA

>7QWS_6 Ribosomal protein L3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 7 (c), FASTA

>7QWS_7 60S ribosomal protein L30 (chains c)
MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKSEI
EYYAMLAKTGVHHYSGNNIELGTACGKYYRVCTLSIIDPGDSDIIRSMPEQTGEK

Sequence of entity 8 (C), FASTA

>7QWS_8 60S ribosomal protein L4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKKKPVVGRKAAAAKKPAADKKAADKRAGPEDKKPAA

Sequence of entity 9 (d), FASTA

>7QWS_9 Ribosomal protein L31 (chains d)
MAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTP
DVRIDTRLNKAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTV
NVDEN

Sequence of entity 10 (D), FASTA

>7QWS_10 Ribosomal_L18_c domain-containing protein (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 11 (e), FASTA

>7QWS_11 Ribosomal protein L32 (chains e)
MCLLLISFLYLKEKKGCPLLGTIAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKP
RGIDNRVRRRFKGQILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAE
IAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE

Sequence of entity 12 (E), FASTA

>7QWS_12 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGRKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKQLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5
MG	Magnesium ion	Mg	97

Primary citation

Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting. Jomaa, A., Gamerdinger, M., Hsieh, H.H. et al. Science (2022) 375:839-844. DOI 10.1126/science.abl6459 · PubMed

Other PDB entries of the same protein (UniProt Q13765 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MCB 1.9 Å, Crystal structure of NAC domains of human nascent polypeptide-associated complex (NAC)
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9S3D 2.32 Å, NAC bound human RNC with 58 amino acid ARF1-linker
9S3B 2.38 Å, NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1
3MCE 2.4 Å, Crystal structure of the NAC domain of alpha subunit of nascent polypeptide-associated…
9S3C 2.42 Å, NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2
9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
3LKX 2.5 Å, Human nac dimerization domain
9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9T6D 2.67 Å, NAA40-NAC bound human 80S (combined translation states)
28LN 2.7 Å, XBP1u-stalled RPL4 RNC in complex with NAC

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