28ZV: Human 48S PIC with mRNA

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

human 48S PIC with mRNA (non-Kozak). Determined by electron microscopy at 2.9 Å resolution. Released 10 Jun 2026.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 41
Atoms: 85,772
Mol. weight: 1420.08 kDa
Ligands: MET, GNP, ZN, MG
Released: 10 Jun 2026

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

Secondary structure: helices and β-sheets

28ZV contains 242 α-helices and 281 β-strands across 37 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 D: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	19-22	4	51
β-strand	32-36	5	51
β-strand	42-46	5	51
α-helix	48-50	3
β-strand	69-75	7	51
β-strand	83-86	4	51
α-helix	92-118	27
α-helix	124-140	17
α-helix	147-158	12
α-helix	161-164	4
α-helix	170-183	14
β-strand	189-191	3	52
β-strand	194-196	3	53
β-strand	198	1	54
α-helix	207-218	12
β-strand	227-231	5	53
β-strand	234-237	4	53
β-strand	239-241	3	52
α-helix	244-263	20
β-strand	268	1	54
β-strand	271-273	3	53
α-helix	280-292	13

Chain E: 16 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	42-43	2	58
β-strand	46-47	2	59
α-helix	54-62	9
α-helix	70-73	4
β-strand	86-91	6	58
α-helix	97	1
β-strand	104-105	2	58
β-strand	114	1	60
β-strand	123	1	60
β-strand	124-131	8	58
α-helix	139-141	3
α-helix	142-146	5
α-helix	147-150	4
β-strand	155-160	6	59
α-helix	168-178	11
β-strand	185-190	6	59
α-helix	197-210	14
α-helix	219-220	2
β-strand	221-223	3	59
α-helix	226-228	3
α-helix	232-242	11
α-helix	253-254	2
β-strand	255-258	4	61
β-strand	262	1	62
β-strand	278	1	62
β-strand	281-283	3	61
β-strand	294-296	3	63
β-strand	297	1	61
β-strand	298-303	6	63
β-strand	309-316	8	63
β-strand	322-323	2	64
β-strand	326-327	2	64
β-strand	336-337	2	61
β-strand	338	1	64
β-strand	357-359	3	61
β-strand	360	1	63
α-helix	365-366	2
β-strand	367-373	7	65
β-strand	376-377	2	65
α-helix	390-392	3
α-helix	398-399	2
β-strand	403-408	6	65
β-strand	411-420	10	65
β-strand	425-434	10	65
β-strand	440-447	8	65
β-strand	450-462	13	65

Chain H: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	33-43	11	73
β-strand	46-51	6	73
β-strand	55-60	6	73
α-helix	63-65	3
β-strand	76-81	6	73
β-strand	88-94	7	73
α-helix	97-106	10

Chain Ln: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21

Chain Sa: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	48
β-strand	29-31	3	48
β-strand	36-43	8	49
α-helix	49-54	6
β-strand	57	1	50
α-helix	62-65	4
β-strand	66-73	8	49
α-helix	75-81	7
α-helix	91-93	3
α-helix	97-100	4

Chain SA: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	12-20	9
β-strand	25	1	17
β-strand	38-41	4	18
α-helix	46	1
β-strand	47-49	3	18
α-helix	51-67	17
α-helix	71-73	3
β-strand	74-78	5	19
α-helix	81-94	14
β-strand	97-100	4	19
β-strand	121-124	4	19
α-helix	131-137	7
β-strand	144-148	5	19
β-strand	159-162	4	19
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-202	4
α-helix	207-218	12

Chain Sb: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	76
β-strand	44-47	4	76
β-strand	54-55	2	77
β-strand	62-65	4	77
α-helix	71	1
β-strand	72-73	2	77
α-helix	74	1
β-strand	78-81	4	76

Chain SB: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	21
β-strand	43-50	8	21
β-strand	53	1	22
β-strand	56	1	22
α-helix	58-62	5
β-strand	66-70	5	21
α-helix	72-75	4
β-strand	82-91	10	21
β-strand	95-105	11	21
α-helix	107-113	7
β-strand	118	1	23
β-strand	120-125	6	21
β-strand	128	1	21
β-strand	134-142	9	21
β-strand	143	1	24
β-strand	154	1	23
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-201	10
β-strand	207	1	24
β-strand	211-219	9	21
α-helix	221-223	3
α-helix	225-231	7

29 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

29 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>28ZV_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

>28ZV_2 60S ribosomal protein L41 (chains Ln)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 3 (SE), FASTA

>28ZV_3 Small ribosomal subunit protein eS4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 4 (SA), FASTA

>28ZV_4 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 5 (SB), FASTA

>28ZV_5 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 6 (SH), FASTA

>28ZV_6 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 7 (SI), FASTA

>28ZV_7 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 8 (SL), FASTA

>28ZV_8 Small ribosomal subunit protein uS17 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 9 (SV), FASTA

>28ZV_9 40S ribosomal protein S21 (chains SV)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 10 (SX), FASTA

>28ZV_10 40S ribosomal protein S23 (chains SX)
MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAK
QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRF
KVVKVANVSLLALYKGKKERPRS

Sequence of entity 11 (Sa), FASTA

>28ZV_11 40S ribosomal protein S26 (chains Sa)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 12 (SC), FASTA

>28ZV_12 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Ligands and cofactors

ID	Name	Formula	Copies
MET	Methionine	C5 H11 N O2 S	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	70

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

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