28ZU: 60S ribosomal protein L41

Name: PDB 28ZU: human 48S PIC with Kozak mRNA and eIF1A W70A mutant
Published: 2026-06-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

human 48S PIC with Kozak mRNA and eIF1A W70A mutant. Determined by electron microscopy at 3.2 Å resolution. Released 10 Jun 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 41
Atoms: 85,890
Mol. weight: 1420.48 kDa
Ligands: MG, ZN, MET, GNP
Released: 10 Jun 2026

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

Secondary structure: helices and β-sheets

28ZU contains 252 α-helices and 285 β-strands across 38 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: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	19-24	6	49
β-strand	31	1	50
β-strand	34-36	3	49
β-strand	42-46	5	49
β-strand	47	1	50
α-helix	48-50	3
α-helix	59-61	3
β-strand	68-77	10	49
α-helix	78-80	3
β-strand	82-86	5	49
α-helix	92-118	27
α-helix	124-131	8
α-helix	132-136	5
α-helix	137-142	6
α-helix	147-158	12
α-helix	162-165	4
α-helix	170-183	14
α-helix	188	1
β-strand	189-198	10	51
α-helix	205-218	14
β-strand	225-228	4	51
β-strand	234-241	8	51
α-helix	244-264	21
β-strand	268-271	4	51
α-helix	280-293	14

Chain E: 18 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	55
β-strand	19	1	55
α-helix	33-38	6
β-strand	42-47	6	56
α-helix	54-61	8
α-helix	70-73	4
β-strand	87-91	5	57
α-helix	97	1
β-strand	102-105	4	57
β-strand	113	1	57
β-strand	124-128	5	57
β-strand	130-134	5	56
α-helix	142-149	8
β-strand	154-160	7	56
α-helix	167	1
α-helix	168-177	10
β-strand	185-190	6	56
α-helix	197-211	15
β-strand	221-223	3	56
β-strand	225	1	58
α-helix	226-228	3
β-strand	230	1	58
α-helix	232-241	10
α-helix	244-247	4
α-helix	253-254	2
β-strand	255-257	3	59
β-strand	278	1	60
β-strand	281	1	61
β-strand	282-285	4	59
β-strand	288-289	2	62
β-strand	293-303	11	59
β-strand	309-317	9	59
β-strand	318-323	6	60
β-strand	326-327	2	60
β-strand	330-331	2	62
β-strand	337	1	61
β-strand	338-341	4	60
α-helix	345-348	4
α-helix	349-351	3
α-helix	356	1
β-strand	357-359	3	59
α-helix	364-367	4
β-strand	368-373	6	63
β-strand	376-377	2	63
β-strand	380	1	64
α-helix	390-393	4
β-strand	394	1	64
α-helix	395-398	4
β-strand	402-408	7	63
β-strand	411-420	10	63
β-strand	425-433	9	63
β-strand	440-447	8	63
β-strand	450-461	12	63
β-strand	464	1	63

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	176-178	3
α-helix	180-182	3

Chain H: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	33-38	6	70
β-strand	43	1	70
β-strand	46-51	6	70
β-strand	55-60	6	70
β-strand	76-81	6	70
β-strand	88-94	7	70
α-helix	97-106	10

Chain Ln: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-21	19

Chain Sa: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	46
β-strand	30-31	2	46
β-strand	36-43	8	47
α-helix	47-56	10
β-strand	57	1	48
α-helix	63-65	3
β-strand	66-73	8	47
α-helix	75-80	6
α-helix	97-99	3

Chain SA: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	32-37	6
β-strand	38-41	4	17
α-helix	46	1
β-strand	47-49	3	17
α-helix	51-66	16
α-helix	71-73	3
β-strand	74-78	5	18
α-helix	84-94	11
β-strand	97-100	4	18
β-strand	121-124	4	18
α-helix	131-137	7
β-strand	144-148	5	18
β-strand	159-162	4	18
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-202	4
α-helix	212-218	7

Chain Sb: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	75
β-strand	43-47	5	75
α-helix	54	1
β-strand	55	1	76
α-helix	56	1
β-strand	62	1	76
β-strand	64-65	2	77
β-strand	72-73	2	77
α-helix	74	1
β-strand	78-81	4	75

30 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

>28ZU_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

>28ZU_2 60S ribosomal protein L41 (chains Ln)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 3 (SE), FASTA

>28ZU_3 Small ribosomal subunit protein eS4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 4 (SA), FASTA

>28ZU_4 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 5 (SB), FASTA

>28ZU_5 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 6 (SH), FASTA

>28ZU_6 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 7 (SI), FASTA

>28ZU_7 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 8 (SL), FASTA

>28ZU_8 Small ribosomal subunit protein uS17 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 9 (SV), FASTA

>28ZU_9 40S ribosomal protein S21 (chains SV)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 10 (SX), FASTA

>28ZU_10 40S ribosomal protein S23 (chains SX)
MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAK
QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRF
KVVKVANVSLLALYKGKKERPRS

Sequence of entity 11 (Sa), FASTA

>28ZU_11 40S ribosomal protein S26 (chains Sa)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 12 (SC), FASTA

>28ZU_12 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	83
ZN	Zinc ion	Zn	3
MET	Methionine	C5 H11 N O2 S	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	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

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