9B0Q: In situ human top-back di-ribosome structure

Name: PDB 9B0Q: In situ human top-back di-ribosome structure (Composite map)
Published: 2025-03-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ human top-back di-ribosome structure (Composite map). Determined by electron microscopy at 3.2 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 172
Atoms: 459,641
Mol. weight: 6815.73 kDa
Ligands: ZN, MG
Released: 19 Mar 2025

Explore 9B0Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B0Q contains 1,157 α-helices and 1,264 β-strands across 160 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: 42 helices, 45 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
β-strand	19-26	8	44
α-helix	32-42	11
β-strand	73-80	8	44
α-helix	83-88	6
β-strand	97-104	8	44
α-helix	114-120	7
β-strand	124-128	5	44
β-strand	130	1	45
α-helix	137-148	12
β-strand	152-157	6	44
β-strand	158	1	45
α-helix	160-161	2
α-helix	162-166	5
α-helix	171-190	20
β-strand	212-216	5	44
α-helix	217-219	3
β-strand	221-223	3	44
α-helix	225-235	11
α-helix	248-260	13
β-strand	265-267	3	46
β-strand	272-274	3	46
β-strand	278	1	47
β-strand	284	1	47
β-strand	287	1	46
α-helix	288-289	2
α-helix	290-294	5
α-helix	295-305	11
α-helix	309-318	10
α-helix	333-343	11
β-strand	345	1	44
α-helix	346-357	12
α-helix	359-360	2
α-helix	361-368	8
α-helix	369-371	3
β-strand	373	1	48
α-helix	380-387	8
β-strand	395-403	9	49
β-strand	410-415	6	49
β-strand	418	1	49
β-strand	420-422	3	50
β-strand	427-430	4	49
β-strand	442-445	4	49
β-strand	450-454	5	49
β-strand	457-461	5	49
β-strand	463-465	3	50
β-strand	469-473	5	49
β-strand	483-486	4	49
α-helix	493	1
β-strand	494	1	48
α-helix	495-498	4
β-strand	505-511	7	51
α-helix	514-516	3
α-helix	517-530	14
β-strand	535-538	4	51
β-strand	544-548	5	51
α-helix	551-560	10
α-helix	561-565	5
β-strand	570-573	4	51
α-helix	574-578	5
β-strand	580-583	4	52
β-strand	591-594	4	53
β-strand	601-608	8	53
α-helix	613-619	7
α-helix	628-639	12
α-helix	644-647	4
β-strand	649-651	3	53
α-helix	654-656	3
β-strand	660-664	5	53
α-helix	671-674	4
α-helix	676-688	13
β-strand	697	1	52
β-strand	700-708	9	53
α-helix	718-735	18
β-strand	738-742	5	52
β-strand	744-752	9	54
α-helix	753-755	3
α-helix	756-765	10
β-strand	769-775	7	54
β-strand	781-789	9	54
α-helix	790-792	3
α-helix	796-804	9
β-strand	809-812	4	54
β-strand	818-819	2	52
α-helix	830-841	12
α-helix	848-849	2
α-helix	851-854	4

Chain CB: 42 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
β-strand	20-26	7	147
α-helix	32-42	11
β-strand	73-80	8	147
α-helix	83-88	6
β-strand	97-104	8	147
α-helix	114-121	8
β-strand	124-128	5	147
β-strand	129-130	2	148
α-helix	137-148	12
α-helix	151	1
β-strand	152	1	147
α-helix	153	1
β-strand	157-158	2	148
α-helix	160-161	2
α-helix	162-167	6
α-helix	171-192	22
β-strand	214-216	3	148
β-strand	221-223	3	148
α-helix	225-235	11
α-helix	248-260	13
β-strand	265-267	3	149
β-strand	272-274	3	149
β-strand	278	1	150
β-strand	284	1	150
β-strand	287	1	149
α-helix	288-289	2
α-helix	290-294	5
α-helix	295-306	12
α-helix	309-319	11
α-helix	333-343	11
β-strand	345	1	148
α-helix	346-357	12
α-helix	359-360	2
α-helix	361-368	8
α-helix	369-371	3
β-strand	373	1	151
α-helix	380-387	8
β-strand	395-403	9	152
α-helix	404	1
β-strand	410-418	9	152
β-strand	420-422	3	153
β-strand	426-430	5	152
β-strand	442-446	5	152
β-strand	449-453	5	152
β-strand	458-461	4	152
β-strand	463-465	3	153
β-strand	468-473	6	152
β-strand	480	1	154
β-strand	482	1	154
β-strand	483-486	4	152
β-strand	494	1	151
α-helix	495-497	3
β-strand	505-511	7	155
α-helix	517-530	14
β-strand	535-538	4	155
α-helix	543	1
β-strand	544-548	5	155
α-helix	551-560	10
α-helix	561-565	5
β-strand	570-573	4	155
α-helix	574-578	5
β-strand	580-583	4	156
β-strand	591	1	157
β-strand	594	1	158
β-strand	601-603	3	158
β-strand	604	1	157
β-strand	606-608	3	159
α-helix	613-618	6
α-helix	628-638	11
α-helix	645-647	3
β-strand	649-652	4	159
α-helix	654-656	3
β-strand	660-664	5	159
α-helix	672-686	15
β-strand	696-697	2	156
β-strand	700-704	5	159
β-strand	706-708	3	158
α-helix	718-735	18
β-strand	738-740	3	156
β-strand	741-742	2	160
β-strand	745-752	8	161
α-helix	753-755	3
α-helix	756-765	10
β-strand	770-775	6	161
β-strand	781-788	8	161
α-helix	790-792	3
α-helix	796-804	9
β-strand	809-813	5	161
β-strand	818-819	2	160
α-helix	830-841	12
α-helix	848-849	2
α-helix	851-854	4

Chain cH: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-32	8
β-strand	42	1	24
β-strand	49	1	25
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 CH: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-32	8
β-strand	39-40	2	1
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
β-strand	131	1	2
β-strand	139	1	2

Chain la: 7 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	212
β-strand	72-74	3	342
α-helix	78-81	4
α-helix	84-92	9
β-strand	98	1	124
β-strand	100-102	3	343
α-helix	103-106	4
β-strand	110-112	3	342
β-strand	123-126	4	343
β-strand	128-129	2	342
α-helix	131-139	9
β-strand	143-146	4	343

Chain lA: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	34-36	3
β-strand	41-50	10	363
α-helix	51	1
β-strand	57-64	8	363
β-strand	71-74	4	363
β-strand	77	1	363
β-strand	79	1	364
β-strand	83	1	175
β-strand	87-90	4	363
β-strand	101	1	363
α-helix	104-106	3
β-strand	112-113	2	365
β-strand	116	1	366
β-strand	120	1	367
β-strand	122	1	367
β-strand	126	1	366
β-strand	134-140	7	365
α-helix	142-144	3
β-strand	145-149	5	365
β-strand	155-159	5	365
β-strand	165	1	363
β-strand	166	1	365
β-strand	169	1	364
β-strand	171	1	368
α-helix	182-192	11
α-helix	206-208	3
β-strand	225	1	369
α-helix	229-230	2
β-strand	238	1	369

Chain La: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-11	5
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-74	3	55
α-helix	75-77	3
α-helix	84-91	8
β-strand	97-98	2	272
β-strand	100-102	3	56
α-helix	103-106	4
β-strand	110-112	3	55
β-strand	123-126	4	56
β-strand	128-129	2	55
α-helix	131-139	9
β-strand	143-146	4	56

Chain LA: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	9-12	4
α-helix	14-16	3
α-helix	30-32	3
α-helix	34-38	5
β-strand	41-44	4	81
β-strand	45-49	5	82
β-strand	58-64	7	82
β-strand	71-77	7	82
β-strand	79	1	83
β-strand	83	1	84
β-strand	87-90	4	81
β-strand	101-103	3	81
β-strand	112-113	2	85
β-strand	116-117	2	86
β-strand	124-126	3	86
β-strand	134-140	7	85
α-helix	142-144	3
β-strand	145-149	5	85
β-strand	155-159	5	85
β-strand	163-165	3	81
β-strand	166	1	85
β-strand	169	1	83
β-strand	171	1	87
α-helix	174-176	3
α-helix	182-192	11
β-strand	224-225	2	88
α-helix	229-230	2
β-strand	237-238	2	88

150 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, 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	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

75 more molecules are not listed.

Sequence of entity 1 (CH, cH), FASTA

>9B0Q_1 Endothelial differentiation-related factor 1 (chains CH, cH)
QAILAARRAAAGEDVETSKKWAAGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQ
GRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKDIGKPIEK
GPRAK

Sequence of entity 2 (SE, sE), FASTA

>9B0Q_2 Small ribosomal subunit protein eS4, X isoform (chains SE, sE)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRLAAKQSSG

Sequence of entity 3 (SI, sI), FASTA

>9B0Q_3 40S ribosomal protein S8 (chains SI, sI)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 4 (SL, sL), FASTA

>9B0Q_4 40S ribosomal protein S11 (chains SL, sL)
ADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCP
FTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQ
IGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQ

Sequence of entity 5 (SX, sX), FASTA

>9B0Q_5 40S ribosomal protein S23 (chains SX, sX)
GKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQ
PNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFK
VVKVANVSLLALYKGKKERPR

Sequence of entity 6 (SG, sG), FASTA

>9B0Q_6 40S ribosomal protein S6 (chains SG, sG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Sequence of entity 7 (SJ, sJ), FASTA

>9B0Q_7 40S ribosomal protein S9 (chains SJ, sJ)
PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELL
TLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAK
SIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKG
QGGAG

Sequence of entity 8 (SY, sY), FASTA

>9B0Q_8 40S ribosomal protein S24 (chains SY, sY)
NDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFR
THFGGGKTTGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTA
KANVGAGKKPK

Sequence of entity 9 (se), FASTA

>9B0Q_9 Small ribosomal subunit protein eS30 (chains se)
VHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

Sequence of entity 10 (SA, sA), FASTA

>9B0Q_10 40S ribosomal protein SA (chains SA, sA)
GALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA
RAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLL
VVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREV
LRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVT

Sequence of entity 11 (SB, sB), FASTA

>9B0Q_11 40S ribosomal protein S3a (chains SB, sB)
VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVA
FRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKA
CQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGE

Sequence of entity 12 (SH, sH), FASTA

>9B0Q_12 Small ribosomal subunit protein eS7 (chains SH, sH)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQ

Ligands and cofactors

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

Primary citation

In situ human top-top di-ribosome structure (Composite map). 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
9B0S 3.8 Å, In situ human top-top di-ribosome structure (Composite map)
1X57 Solution structures of the HTH domain of human EDF-1 protein

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