6ZVJ: 40S ribosomal protein SA

Structure of a human ABCE1-bound 43S pre-initiation complex - State II. Determined by electron microscopy at 3.8 Å resolution. Released 7 Oct 2020.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 51
Atoms: 115,020
Mol. weight: 1804.82 kDa
Ligands: ZN, SF4, MG, ATP
Released: 7 Oct 2020

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

Secondary structure: helices and β-sheets

6ZVJ contains 430 α-helices and 443 β-strands across 50 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 1: 27 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	108
α-helix	24-28	5
α-helix	32-34	3
β-strand	39-40	2	109
β-strand	49-50	2	109
α-helix	60-63	4
β-strand	70-75	6	108
β-strand	85-86	2	110
β-strand	93-94	2	110
β-strand	105-110	6	111
α-helix	118-123	6
α-helix	137-139	3
α-helix	140-143	4
α-helix	152-160	9
β-strand	166-169	4	111
α-helix	176-178	3
β-strand	183	1	112
α-helix	184-188	5
β-strand	213	1	112
α-helix	219-231	13
β-strand	237-241	5	111
α-helix	249-260	12
β-strand	268-272	5	111
α-helix	279-281	3
β-strand	285-290	6	111
β-strand	296-297	2	110
β-strand	298-299	2	111
β-strand	303-304	2	111
α-helix	305-314	10
β-strand	316	1	113
β-strand	322	1	108
β-strand	323	1	113
β-strand	349-350	2	114
β-strand	354-356	3	115
β-strand	361-364	4	115
α-helix	365-366	2
β-strand	367-368	2	114
β-strand	374-378	5	116
α-helix	385-391	7
α-helix	403-405	3
β-strand	410-411	2	116
β-strand	423	1	117
α-helix	424-427	4
α-helix	442-446	5
α-helix	447-449	3
β-strand	458	1	117
α-helix	464-477	14
β-strand	482-486	5	116
α-helix	495-497	3
α-helix	499-508	10
β-strand	514-518	5	116
α-helix	522-528	7
β-strand	531-534	4	116
β-strand	535-538	4	115
β-strand	542-545	4	115
α-helix	546-548	3
β-strand	549	1	116
α-helix	551-562	12
β-strand	566-568	3	118
β-strand	575-577	3	118
α-helix	578-579	2
α-helix	583-591	9

Chain a: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	1
β-strand	38-41	4	2
α-helix	46	1
β-strand	47-49	3	2
α-helix	50	1
α-helix	51-66	16
β-strand	74-78	5	3
α-helix	84-94	11
β-strand	97-100	4	3
β-strand	121-124	4	3
α-helix	131-136	6
β-strand	144-148	5	3
β-strand	159-162	4	3
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-201	3
α-helix	207-214	8

Chain A: 33 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	10-21	12
α-helix	25-35	11
α-helix	47-60	14
α-helix	64-77	14
α-helix	83-115	33
α-helix	124-130	7
α-helix	137-144	8
α-helix	147-163	17
α-helix	171-188	18
α-helix	192-210	19
α-helix	223-242	20
α-helix	246-262	17
α-helix	269-285	17
α-helix	290-302	13
α-helix	313-326	14
α-helix	338-341	4
α-helix	353-357	5
α-helix	367-375	9
α-helix	379-381	3
α-helix	390	1
α-helix	391-396	6
α-helix	403-414	12
α-helix	422-424	3
α-helix	430-443	14
β-strand	447-451	5	87
α-helix	452-458	7
α-helix	464-476	13
β-strand	483-485	3	87
β-strand	490-492	3	87
α-helix	500-502	3
α-helix	523-537	15
α-helix	540-559	20
α-helix	565-599	35
α-helix	605-639	35
α-helix	643-684	42
α-helix	708-724	17

Chain b: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	128
β-strand	45-52	8	128
α-helix	56-59	4
α-helix	64-76	13
β-strand	84-90	7	128
α-helix	91	1
α-helix	98-111	14
α-helix	115-129	15
β-strand	133-139	7	129
β-strand	140	1	130
β-strand	148	1	130
β-strand	151-155	5	129
α-helix	162-164	3
β-strand	168-177	10	129
β-strand	180-189	10	129
α-helix	190-191	2
β-strand	209-210	2	119
α-helix	211-214	4
β-strand	223-226	4	56

Chain B: 9 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	188-189	2	71
α-helix	192-194	3
α-helix	200-211	12
β-strand	219-221	3	72
β-strand	224-225	2	73
β-strand	228-229	2	73
β-strand	233	1	71
β-strand	234-236	3	72
α-helix	241-245	5
β-strand	254	1	74
β-strand	260	1	74
β-strand	263-264	2	71
β-strand	308-310	3	75
β-strand	315-317	3	75
β-strand	353	1	76
β-strand	356	1	76
β-strand	357-361	5	77
β-strand	366-371	6	77
β-strand	378-381	4	78
β-strand	387	1	79
β-strand	388-391	4	78
α-helix	395-397	3
β-strand	404-407	4	78
β-strand	408	1	79
β-strand	414-418	5	78
β-strand	445-446	2	80
α-helix	455-457	3
β-strand	464-465	2	80
β-strand	470	1	81
β-strand	480-481	2	81
α-helix	490	1
β-strand	491-497	7	81
β-strand	502-509	8	81
β-strand	515-519	5	82
β-strand	525-530	6	82
β-strand	542-548	7	82
β-strand	556-561	6	82
β-strand	565	1	83
β-strand	569	1	83
β-strand	576-581	6	83
β-strand	588-593	6	83
β-strand	602	1	83
β-strand	613-616	4	84
α-helix	617	1
β-strand	622-626	5	84
β-strand	633-634	2	85
β-strand	635-639	5	84
β-strand	644-645	2	84
β-strand	650-651	2	85
β-strand	654-659	6	86
β-strand	666-670	5	86
β-strand	681-684	4	86
β-strand	690	1	86
α-helix	714-719	6
α-helix	734-742	9

Chain c: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	22-35	14
α-helix	41-60	20
α-helix	68-84	17
α-helix	94-96	3
β-strand	109	1	61
α-helix	110-115	6
α-helix	123-131	9
β-strand	135-136	2	62
β-strand	141	1	62
β-strand	148	1	61
β-strand	158-159	2	62
α-helix	172-177	6

Chain C: 31 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	52-72	21
α-helix	76-90	15
α-helix	97-99	3
α-helix	105-120	16
α-helix	137-145	9
α-helix	329-336	8
α-helix	349-360	12
α-helix	368-383	16
α-helix	395-414	20
β-strand	418-419	2	88
β-strand	421	1	89
β-strand	438-439	2	88
β-strand	442	1	89
α-helix	445-456	12
α-helix	476-489	14
α-helix	503-510	8
α-helix	545-557	13
α-helix	563-578	16
α-helix	583-592	10
α-helix	594-597	4
α-helix	598-600	3
α-helix	603-621	19
α-helix	628-632	5
α-helix	644-646	3
α-helix	670-672	3
α-helix	679-701	23
α-helix	712-722	11
α-helix	734-745	12
α-helix	749-753	5
α-helix	761	1
α-helix	762-766	5
α-helix	772-794	23
β-strand	799-803	5	87
α-helix	804-810	7
α-helix	815-827	13
β-strand	833-836	4	87
β-strand	841-844	4	87
α-helix	851-877	27

Chain d: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-70	6
α-helix	79-83	5
α-helix	86-88	3
α-helix	92-97	6
α-helix	99-101	3
β-strand	103-116	14	15
β-strand	119-132	14	15
β-strand	136-144	9	15
α-helix	147-160	14
β-strand	163-164	2	15
α-helix	165-166	2
β-strand	168	1	16
β-strand	179	1	16
β-strand	184-188	5	17
β-strand	191-196	6	17
β-strand	204-205	2	17
α-helix	208-216	9
β-strand	222-227	6	17
α-helix	233-244	12
α-helix	253-255	3
α-helix	258-261	4
α-helix	265-268	4

42 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 SA	a	protein	216	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	p	protein	211	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S2	d	protein	216	Homo sapiens	P15880 (AlphaFold model)
40S ribosomal protein S26	Q	protein	101	Homo sapiens	P62854 (AlphaFold model)
40S ribosomal protein S4, X isoform	q	protein	255	Homo sapiens	P62701
60S ribosomal protein L41	W	protein	24	Homo sapiens	P62945
40S ribosomal protein S6	r	protein	222	Homo sapiens	P62753
40S ribosomal protein S7	s	protein	181	Homo sapiens	P62081
40S ribosomal protein S8	t	protein	205	Homo sapiens	P62241
40S ribosomal protein S9	c	protein	180	Homo sapiens	P46781
40S ribosomal protein S11	n	protein	144	Homo sapiens	P62280
40S ribosomal protein S13	m	protein	149	Homo sapiens	P62277

38 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>6ZVJ_1 40S ribosomal protein SA (chains a)
SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLA
ARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRL
LVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLARE
VLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAA

Sequence of entity 2 (p), FASTA

>6ZVJ_2 40S ribosomal protein S3a (chains p)
DPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFR
KFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGF
TKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQ
SIYPLHDVFVRKVKMLKKPKFELGKLMELHG

Sequence of entity 3 (d), FASTA

>6ZVJ_3 40S ribosomal protein S2 (chains d)
WMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAG
QRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHT
VPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKA
TFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVK

Sequence of entity 4 (Q), FASTA

>6ZVJ_4 40S ribosomal protein S26 (chains Q)
TKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDA
YVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFR

Sequence of entity 5 (q), FASTA

>6ZVJ_5 40S ribosomal protein S4, X isoform (chains q)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRL

Sequence of entity 6 (W), FASTA

>6ZVJ_6 60S ribosomal protein L41 (chains W)
MRAKWRKKRMRRLKRKRRKMRQRS

Sequence of entity 7 (r), FASTA

>6ZVJ_7 40S ribosomal protein S6 (chains r)
KLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGF
PMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDI
PGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVT
PRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEK

Sequence of entity 8 (s), FASTA

>6ZVJ_8 40S ribosomal protein S7 (chains s)
IVKPNEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSF
QKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILED
LVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEF
Q

Sequence of entity 9 (t), FASTA

>6ZVJ_9 40S ribosomal protein S8 (chains t)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARK

Sequence of entity 10 (c), FASTA

>6ZVJ_10 40S ribosomal protein S9 (chains c)
PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELL
TLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAK
SIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKG

Sequence of entity 11 (n), FASTA

>6ZVJ_11 40S ribosomal protein S11 (chains n)
IQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFT
GNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIG
DIVTVGECRPLSKTVRFNVLKVTK

Sequence of entity 12 (m), FASTA

>6ZVJ_12 40S ribosomal protein S13 (chains m)
GRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVA
QVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESR
IHRLARYYKTKRVLPPNWKYESSTASALV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SF4	Iron/sulfur cluster	Fe4 S4	2
MG	Magnesium ion	Mg	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Kratzat, H., Mackens-Kiani, T., Ameismeier, M. et al. EMBO J (2021) 40:e105179-e105179. DOI 10.15252/embj.2020105179 · PubMed

Other PDB entries of the same protein (UniProt P08865 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
3BCH 2.15 Å, Crystal Structure of the Human Laminin Receptor Precursor
7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)
8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline

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