9B0S: In situ human top-top di-ribosome structure

Name: PDB 9B0S: In situ human top-top di-ribosome structure (Composite map)
Published: 2025-03-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ human top-top di-ribosome structure (Composite map). Determined by electron microscopy at 3.8 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 171
Atoms: 456,973
Mol. weight: 6765.24 kDa
Ligands: MG, ZN
Released: 19 Mar 2025

Explore 9B0S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B0S contains 1,149 α-helices and 1,220 β-strands across 158 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 cB: 41 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
β-strand	19-26	8	20
α-helix	32-42	11
β-strand	73-80	8	20
α-helix	81-82	2
α-helix	83-88	6
β-strand	97-104	8	20
α-helix	114-120	7
β-strand	124-130	7	20
α-helix	137-148	12
β-strand	152-158	7	20
α-helix	160-161	2
α-helix	162-166	5
α-helix	171-191	21
α-helix	207-209	3
β-strand	212-216	5	20
β-strand	221-223	3	20
α-helix	225-235	11
α-helix	249-260	12
β-strand	265-267	3	21
β-strand	272-274	3	21
β-strand	278	1	22
β-strand	284	1	22
β-strand	287	1	21
α-helix	288	1
α-helix	289-294	6
α-helix	295-305	11
α-helix	309-318	10
α-helix	333-343	11
β-strand	345	1	20
α-helix	346-357	12
α-helix	359-360	2
α-helix	361-368	8
β-strand	373	1	23
α-helix	380-387	8
β-strand	395-403	9	24
β-strand	410-418	9	24
β-strand	420-422	3	25
β-strand	426-430	5	24
β-strand	442-446	5	24
β-strand	450-454	5	24
β-strand	457-460	4	24
β-strand	463-465	3	25
β-strand	469-472	4	24
β-strand	480	1	26
β-strand	482	1	26
β-strand	483-486	4	24
α-helix	491-493	3
β-strand	494	1	23
α-helix	495-497	3
β-strand	505-511	7	27
α-helix	514-516	3
α-helix	517-530	14
β-strand	535-538	4	27
β-strand	544-548	5	27
α-helix	551-560	10
α-helix	561-565	5
β-strand	570-573	4	27
α-helix	574-578	5
β-strand	580-583	4	28
β-strand	591-594	4	29
β-strand	601-607	7	29
α-helix	613-619	7
α-helix	628-638	11
α-helix	646-648	3
β-strand	649-651	3	29
α-helix	654-656	3
β-strand	660-664	5	29
α-helix	671-674	4
α-helix	676-688	13
β-strand	700-708	9	29
α-helix	713-715	3
α-helix	718-735	18
β-strand	738-742	5	28
β-strand	745-752	8	30
α-helix	753-755	3
α-helix	756-765	10
β-strand	769-775	7	30
β-strand	781-788	8	30
α-helix	796-804	9
β-strand	809-813	5	30
β-strand	818-819	2	28
α-helix	830-841	12
α-helix	848-849	2

Chain CF: 14 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	177
α-helix	20-30	11
α-helix	36-49	14
α-helix	52-54	3
α-helix	64-68	5
β-strand	77-81	5	177
β-strand	86-91	6	177
α-helix	99-106	8
β-strand	111-117	7	177
α-helix	123-126	4
α-helix	133-143	11
β-strand	149-153	5	177
α-helix	164-181	18
β-strand	190-193	4	177
β-strand	194	1	178
β-strand	199	1	178
β-strand	214-218	5	179
β-strand	221-225	5	179
α-helix	228-231	4
α-helix	235-240	6
α-helix	245-246	2
β-strand	247	1	180
β-strand	248-249	2	181
β-strand	252-256	5	182
β-strand	260-266	7	182
β-strand	269	1	180
β-strand	272	1	183
β-strand	277-280	4	181
β-strand	285-288	4	181
β-strand	289-294	6	182
β-strand	297-298	2	182
β-strand	302	1	183
β-strand	307-312	6	182
β-strand	325-328	4	181
α-helix	332-334	3
β-strand	337-346	10	184
β-strand	353	1	185
α-helix	359	1
β-strand	360-363	4	184
β-strand	366-379	14	184
β-strand	386-389	4	184
β-strand	394	1	185
β-strand	399-406	8	184
α-helix	419-422	4
β-strand	423-428	6	184
β-strand	431-443	13	184

Chain cH: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	25-32	8
α-helix	60-63	4
α-helix	75-88	14
α-helix	92-99	8
α-helix	103-111	9
α-helix	118-127	10

Chain la: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-9	3
α-helix	42-48	7
β-strand	53	1	168
β-strand	72-74	3	304
α-helix	78-80	3
α-helix	84-92	9
β-strand	97-98	2	96
β-strand	100-101	2	305
α-helix	103-106	4
β-strand	110-112	3	304
β-strand	123-126	4	305
β-strand	128-129	2	304
α-helix	131-140	10
β-strand	143-146	4	305

Chain lA: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	14-16	3
β-strand	18	1	322
α-helix	30-32	3
α-helix	34-37	4
β-strand	41-50	10	323
α-helix	51	1
β-strand	57-64	8	323
β-strand	71-73	3	323
β-strand	77	1	323
β-strand	79	1	324
β-strand	83	1	134
β-strand	87-90	4	323
β-strand	101-103	3	323
α-helix	104-106	3
β-strand	112-113	2	325
β-strand	116	1	326
β-strand	126	1	326
β-strand	134-140	7	325
β-strand	145-149	5	325
β-strand	155-159	5	325
β-strand	163-165	3	323
β-strand	166	1	325
β-strand	169	1	324
β-strand	171	1	327
α-helix	182-190	9
β-strand	193	1	322
α-helix	201-203	3
β-strand	225	1	328
α-helix	229-230	2
β-strand	238	1	328

Chain La: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-11	5
α-helix	42-48	7
β-strand	53	1	301
α-helix	65-68	4
β-strand	72-74	3	31
α-helix	75-78	4
α-helix	79-81	3
α-helix	84-92	9
β-strand	97-98	2	230
β-strand	100-102	3	32
α-helix	103-106	4
β-strand	110-112	3	31
β-strand	123-126	4	32
β-strand	128-129	2	31
α-helix	131-139	9
β-strand	143-146	4	32

Chain LA: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-12	4
α-helix	14-16	3
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	54
β-strand	58-64	7	54
β-strand	71-77	7	54
β-strand	79	1	55
β-strand	83	1	56
β-strand	87-91	5	54
β-strand	101-103	3	54
β-strand	112-113	2	57
β-strand	116	1	58
β-strand	126	1	58
β-strand	134-140	7	57
α-helix	142-144	3
β-strand	145-149	5	57
β-strand	155-159	5	57
β-strand	163-165	3	54
β-strand	166	1	57
β-strand	169	1	55
β-strand	171	1	59
α-helix	174-176	3
α-helix	182-190	9
α-helix	198-200	3
β-strand	224-225	2	60
α-helix	229-230	2
β-strand	237-238	2	60

Chain lb: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-24	3
α-helix	37-48	12
α-helix	49-51	3
α-helix	54-72	19
α-helix	92-100	9
α-helix	106-115	10

148 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
Endothelial differentiation-related factor 1	cH	protein	125	Homo sapiens	O60869 (AlphaFold model)
Small ribosomal subunit protein eS4, X isoform	SE, sE	protein	262	Homo sapiens	P62701 (AlphaFold model)
40S ribosomal protein S8	SI, sI	protein	206	Homo sapiens	P62241 (AlphaFold model)
40S ribosomal protein S11	SL, sL	protein	153	Homo sapiens	P62280 (AlphaFold model)
40S ribosomal protein S23	SX, sX	protein	141	Homo sapiens	P62266
40S ribosomal protein S6	SG, sG	protein	237	Homo sapiens	P62753
40S ribosomal protein S9	SJ, sJ	protein	185	Homo sapiens	P46781
40S ribosomal protein S24	SY, sY	protein	131	Homo sapiens	P62847
Small ribosomal subunit protein eS30	Se, se	protein	58	Homo sapiens	P62861
40S ribosomal protein SA	SA, sA	protein	221	Homo sapiens	P08865
40S ribosomal protein S3a	SB, sB	protein	214	Homo sapiens	P61247
Small ribosomal subunit protein eS7	SH, sH	protein	189	Homo sapiens	P62081

77 more molecules are not listed.

Sequence of entity 1 (cH), FASTA

>9B0S_1 Endothelial differentiation-related factor 1 (chains cH)
QAILAARRAAAGEDVETSKKWAAGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQ
GRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKDIGKPIEK
GPRAK

Sequence of entity 2 (SE, sE), FASTA

>9B0S_2 Small ribosomal subunit protein eS4, X isoform (chains SE, sE)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRLAAKQSSG

Sequence of entity 3 (SI, sI), FASTA

>9B0S_3 40S ribosomal protein S8 (chains SI, sI)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 4 (SL, sL), FASTA

>9B0S_4 40S ribosomal protein S11 (chains SL, sL)
ADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCP
FTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQ
IGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQ

Sequence of entity 5 (SX, sX), FASTA

>9B0S_5 40S ribosomal protein S23 (chains SX, sX)
GKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQ
PNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFK
VVKVANVSLLALYKGKKERPR

Sequence of entity 6 (SG, sG), FASTA

>9B0S_6 40S ribosomal protein S6 (chains SG, sG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Sequence of entity 7 (SJ, sJ), FASTA

>9B0S_7 40S ribosomal protein S9 (chains SJ, sJ)
PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELL
TLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAK
SIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKG
QGGAG

Sequence of entity 8 (SY, sY), FASTA

>9B0S_8 40S ribosomal protein S24 (chains SY, sY)
NDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFR
THFGGGKTTGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTA
KANVGAGKKPK

Sequence of entity 9 (Se, se), FASTA

>9B0S_9 Small ribosomal subunit protein eS30 (chains Se, se)
VHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

Sequence of entity 10 (SA, sA), FASTA

>9B0S_10 40S ribosomal protein SA (chains SA, sA)
GALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA
RAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLL
VVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREV
LRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVT

Sequence of entity 11 (SB, sB), FASTA

>9B0S_11 40S ribosomal protein S3a (chains SB, sB)
VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVA
FRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKA
CQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGE

Sequence of entity 12 (SH, sH), FASTA

>9B0S_12 Small ribosomal subunit protein eS7 (chains SH, sH)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	510
ZN	Zinc ion	Zn	12

Primary citation

In situ human top-back di-ribosome structure. Wei, Z., Yong, X. To be published.

Other PDB entries of the same protein (UniProt O60869 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RPV 2.35 Å, Structure of the ZAK-bound human disome
9P73 2.66 Å, In situ human eEF2-A/P-P/E state 80S ribosome
6ZVH 2.9 Å, EDF1-ribosome complex
9P8H 2.98 Å, In situ human A/P-P/E state 80S ribosome
9B0Q 3.2 Å, In situ human top-back di-ribosome structure (Composite map)
1X57 Solution structures of the HTH domain of human EDF-1 protein

Browse structure collections

About this viewer

MolViewer shows 9B0S 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.