28ZY: Human 48S PIC with mRNA

Name: PDB 28ZY: human 48S PIC with mRNA (Kozak_2)
Published: 2026-06-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

human 48S PIC with mRNA (Kozak_2). Determined by electron microscopy at 3.0 Å resolution. Released 10 Jun 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 50
Atoms: 108,768
Mol. weight: 2021.5 kDa
Ligands: MG, ZN, GNP, MET
Released: 10 Jun 2026

Explore 28ZY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

28ZY contains 447 α-helices and 347 β-strands across 47 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 3f: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	92-94	3	84
α-helix	96-108	13
β-strand	119-122	4	85
β-strand	125	1	86
β-strand	128	1	86
β-strand	129-131	3	84
β-strand	133-135	3	85
α-helix	150-159	10
β-strand	168-172	5	85
α-helix	181-192	12
β-strand	199-200	2	87
β-strand	215-216	2	87
β-strand	217	1	88
β-strand	231	1	88
α-helix	245-253	9
α-helix	266-293	28
α-helix	295-298	4
α-helix	299-301	3
α-helix	306-314	9
α-helix	320-356	37

Chain a: 38 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-21	14
α-helix	24-36	13
α-helix	47-60	14
α-helix	65-77	13
α-helix	80-82	3
α-helix	83-99	17
α-helix	100-106	7
α-helix	107-115	9
α-helix	126-132	7
α-helix	137-141	5
α-helix	142-146	5
α-helix	147-164	18
α-helix	171-187	17
α-helix	191-211	21
α-helix	223-243	21
α-helix	246-260	15
α-helix	272-285	14
α-helix	289-306	18
α-helix	312-326	15
α-helix	334-338	5
α-helix	339-342	4
α-helix	351-358	8
α-helix	367-371	5
α-helix	372-375	4
α-helix	377-378	2
α-helix	390-395	6
α-helix	400-415	16
α-helix	422-427	6
α-helix	428-446	19
β-strand	451	1	72
α-helix	452-458	7
α-helix	464-477	14
β-strand	482-485	4	72
β-strand	490-493	4	72
α-helix	519-535	17
α-helix	540-544	5
α-helix	545-547	3
α-helix	548-553	6
α-helix	554-565	12
α-helix	573-582	10
α-helix	583-587	5

Chain c: 35 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	52-73	22
α-helix	76-97	22
α-helix	104-120	17
α-helix	134-148	15
α-helix	153-156	4
α-helix	329-339	11
α-helix	347-363	17
α-helix	368-384	17
α-helix	392-394	3
α-helix	395-414	20
α-helix	444-461	18
α-helix	467-473	7
α-helix	476-492	17
α-helix	496-510	15
α-helix	516-519	4
α-helix	546-557	12
α-helix	564-578	15
α-helix	583-591	9
α-helix	594-596	3
α-helix	603-622	20
α-helix	627-638	12
α-helix	642-645	4
α-helix	661-667	7
α-helix	670-672	3
α-helix	679-697	19
α-helix	698-702	5
α-helix	712-723	12
α-helix	733-745	13
α-helix	750-756	7
α-helix	759-764	6
α-helix	766-768	3
α-helix	772-795	24
β-strand	799-803	5	72
α-helix	804-810	7
α-helix	815-826	12
β-strand	832-835	4	72
β-strand	840-843	4	72
α-helix	852-860	9

Chain d: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	79	1	82
β-strand	169-175	7	77
α-helix	176-180	5
α-helix	188-190	3
β-strand	191-196	6	77
α-helix	198	1
β-strand	199	1	78
α-helix	200	1
β-strand	201	1	79
β-strand	202	1	80
α-helix	204-207	4
β-strand	216	1	79
α-helix	217-219	3
α-helix	233-239	7
β-strand	245-247	3	77
α-helix	253-256	4
α-helix	258-260	3
β-strand	266-272	7	77
β-strand	275-280	6	77
α-helix	309-326	18
β-strand	328	1	80
β-strand	335	1	78
β-strand	339	1	77
β-strand	357-363	7	77
β-strand	371-377	7	77
β-strand	379-383	5	79
β-strand	387-398	12	79
α-helix	401-404	4
α-helix	409-412	4
α-helix	417-427	11
α-helix	429-442	14
β-strand	446-454	9	79
β-strand	463-471	9	79
α-helix	473-480	8
α-helix	484-498	15
β-strand	505-509	5	77
β-strand	516-521	6	77
α-helix	522	1
α-helix	523-525	3

Chain D: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-27	9	53
β-strand	31-36	6	53
α-helix	37-39	3
β-strand	42-47	6	53
α-helix	48-50	3
α-helix	55-56	2
α-helix	59-61	3
β-strand	68-77	10	53
β-strand	82-86	5	53
α-helix	92-118	27
α-helix	124-131	8
α-helix	132-136	5
α-helix	137-140	4
α-helix	145-158	14
α-helix	170-182	13
α-helix	186-188	3
β-strand	189-198	10	54
α-helix	204-217	14
β-strand	225-231	7	54
β-strand	234-241	8	54
α-helix	244-264	21
β-strand	268-270	3	54
α-helix	283-293	11

Chain e: 24 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	39-41	3
α-helix	50-55	6
α-helix	62-70	9
α-helix	77-83	7
α-helix	84-87	4
α-helix	96-111	16
α-helix	131-139	9
α-helix	147-150	4
α-helix	165-179	15
α-helix	182-197	16
α-helix	204-217	14
α-helix	225-228	4
α-helix	238-245	8
α-helix	251-263	13
α-helix	276-279	4
α-helix	294-302	9
α-helix	305-307	3
α-helix	312-321	10
α-helix	326-328	3
α-helix	329-347	19
β-strand	348-349	2	72
α-helix	353-357	5
β-strand	358	1	73
β-strand	362	1	73
α-helix	364-376	13
α-helix	377-379	3
β-strand	383	1	74
β-strand	392	1	74
α-helix	403-421	19

Chain E: 19 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	33-38	6
β-strand	42-47	6	58
α-helix	54-62	9
α-helix	65-67	3
α-helix	70-73	4
β-strand	86-91	6	58
α-helix	97	1
β-strand	102-105	4	58
β-strand	124-133	10	58
α-helix	142-149	8
β-strand	154-160	7	58
α-helix	166-167	2
α-helix	168-180	13
β-strand	185-190	6	58
α-helix	197-210	14
α-helix	219-221	3
β-strand	222-223	2	58
α-helix	226-228	3
α-helix	232-242	11
α-helix	245-247	3
α-helix	253-254	2
β-strand	255-257	3	59
β-strand	281-285	5	59
β-strand	288-289	2	60
β-strand	293-303	11	59
β-strand	309-317	9	59
β-strand	320-322	3	61
β-strand	323	1	62
β-strand	326	1	62
β-strand	330-331	2	60
β-strand	336-337	2	59
β-strand	338-340	3	61
α-helix	345-348	4
α-helix	349-351	3
β-strand	357-360	4	59
α-helix	364-366	3
β-strand	367-377	11	63
α-helix	397-399	3
β-strand	402-408	7	63
β-strand	411-420	10	63
β-strand	424-434	11	63
β-strand	440-447	8	63
β-strand	450-463	14	63
α-helix	466-468	3

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	180-182	3
α-helix	184-189	6

39 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
18S ribosomal RNA	S2	RNA	1869	Homo sapiens
60S ribosomal protein L41	Ln	protein	25	Homo sapiens	P62945 (AlphaFold model)
Small ribosomal subunit protein eS4, X isoform	SE	protein	263	Homo sapiens	P62701 (AlphaFold model)
40S ribosomal protein SA	SA	protein	295	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	264	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S7	SH	protein	194	Homo sapiens	P62081
40S ribosomal protein S8	SI	protein	208	Homo sapiens	P62241
Small ribosomal subunit protein uS17	SL	protein	158	Homo sapiens	P62280
40S ribosomal protein S21	SV	protein	83	Homo sapiens	P63220
40S ribosomal protein S23	SX	protein	143	Homo sapiens	P62266
40S ribosomal protein S26	Sa	protein	115	Homo sapiens	P62854
40S ribosomal protein S2	SC	protein	293	Homo sapiens	P15880

38 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>28ZY_1 18S ribosomal RNA (chains S2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGXGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGXAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGAA
GGAUCAUUA

Sequence of entity 2 (Ln), FASTA

>28ZY_2 60S ribosomal protein L41 (chains Ln)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 3 (SE), FASTA

>28ZY_3 Small ribosomal subunit protein eS4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 4 (SA), FASTA

>28ZY_4 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 5 (SB), FASTA

>28ZY_5 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 6 (SH), FASTA

>28ZY_6 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 7 (SI), FASTA

>28ZY_7 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 8 (SL), FASTA

>28ZY_8 Small ribosomal subunit protein uS17 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 9 (SV), FASTA

>28ZY_9 40S ribosomal protein S21 (chains SV)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 10 (SX), FASTA

>28ZY_10 40S ribosomal protein S23 (chains SX)
MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAK
QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRF
KVVKVANVSLLALYKGKKERPRS

Sequence of entity 11 (Sa), FASTA

>28ZY_11 40S ribosomal protein S26 (chains Sa)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 12 (SC), FASTA

>28ZY_12 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	87
ZN	Zinc ion	Zn	3
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
MET	Methionine	C5 H11 N O2 S	1

Water and common crystallization additives (K) are not listed.

Primary citation

Translation initiation by the Kozak mRNA sequence is based on a conformational readout on the ribosome. von Loeffelholz, O., Barchet, C., Holvec, S. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-73969-2 · PubMed

Other PDB entries of the same protein (UniProt P62945 (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
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
9O3V 2.2 Å, Human 80S ribosome stalled on MYC nascent chain

Browse structure collections

About this viewer

MolViewer shows 28ZY 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.