7R4X: 60S ribosomal protein L41

Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map. Determined by electron microscopy at 2.15 Å resolution. Released 22 Feb 2023.

Method: Electron microscopy
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 35
Atoms: 77,936
Mol. weight: 1231.51 kDa
Ligands: ZN, MG
Released: 22 Feb 2023

Explore 7R4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R4X contains 244 α-helices and 243 β-strands across 34 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 a: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	64
β-strand	29-31	3	64
β-strand	36-43	8	65
α-helix	47-54	8
β-strand	57	1	1
α-helix	62-65	4
β-strand	66-73	8	65
α-helix	75-80	6
α-helix	91-93	3
α-helix	97-99	3

Chain A: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-11	2
α-helix	12-21	10
β-strand	25	1	41
α-helix	32-37	6
β-strand	38	1	42
α-helix	46-47	2
β-strand	48	1	41
β-strand	49	1	42
α-helix	51-66	16
α-helix	71-73	3
β-strand	74-78	5	43
α-helix	81-83	3
α-helix	84-91	8
α-helix	96	1
β-strand	97-100	4	43
α-helix	102-104	3
β-strand	121-124	4	43
α-helix	131-137	7
β-strand	144	1	43
β-strand	148	1	44
β-strand	162	1	44
α-helix	168-182	15
α-helix	194-195	2
α-helix	199-202	4

Chain b: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	20-22	3
β-strand	32-36	5	20
α-helix	42	1
β-strand	43-47	5	20
β-strand	54-55	2	21
α-helix	56	1
β-strand	62-65	4	21
β-strand	72-73	2	21
α-helix	74	1
β-strand	78-81	4	20

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	4
β-strand	43-50	8	4
α-helix	51-52	2
α-helix	58-62	5
β-strand	66-70	5	4
α-helix	71-73	3
β-strand	82-92	11	4
β-strand	95-105	11	4
α-helix	107-113	7
β-strand	118	1	5
β-strand	120-128	9	4
β-strand	134-143	10	4
β-strand	154	1	5
α-helix	155-157	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-201	10
β-strand	207-219	13	4
α-helix	221-223	3
α-helix	225-230	6

Chain c: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	24
β-strand	27-34	8	24
β-strand	41-47	7	24
β-strand	55-58	4	24

Chain C: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	78-83	6
α-helix	91-98	8
β-strand	103-116	14	67
β-strand	119-131	13	67
β-strand	136-144	9	67
α-helix	147-160	14
β-strand	163-164	2	67
β-strand	168	1	68
β-strand	179	1	68
β-strand	184-188	5	69
β-strand	191-196	6	69
β-strand	204-205	2	69
α-helix	208-216	9
β-strand	222-227	6	69
α-helix	233-245	13
α-helix	247-249	3
α-helix	253-255	3
α-helix	258-259	2
α-helix	265-268	4
α-helix	270-276	7

Chain d: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	30-31	2	66
α-helix	33-35	3
β-strand	38-39	2	66
α-helix	40-50	11
β-strand	53-54	2	59

Chain D: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
α-helix	30-32	3
β-strand	34-41	8	7
β-strand	46-52	7	7
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-89	6	7
α-helix	94-96	3
α-helix	98-109	12
α-helix	115-128	14
β-strand	133-140	8	8
β-strand	148-155	8	8
α-helix	163-167	5
β-strand	168-177	10	8
β-strand	180-189	10	8
α-helix	190-192	3
α-helix	203-204	2
β-strand	209-210	2	9
α-helix	211-213	3
α-helix	216-219	4
β-strand	226	1	10

26 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
60S ribosomal protein L41	n	protein	25	Homo sapiens	P62945 (AlphaFold model)
18S ribosomal RNA	2	RNA	1868	Homo sapiens
40S ribosomal protein S3a	B	protein	264	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S3	D	protein	243	Homo sapiens	P23396 (AlphaFold model)
40S ribosomal protein S4, X isoform	E	protein	263	Homo sapiens	P62701 (AlphaFold model)
40S ribosomal protein S5	F	protein	204	Homo sapiens	P46782
40S ribosomal protein S7	H	protein	194	Homo sapiens	P62081
40S ribosomal protein S8	I	protein	208	Homo sapiens	P62241
40S ribosomal protein S10	K	protein	165	Homo sapiens	P46783
40S ribosomal protein S11	L	protein	158	Homo sapiens	P62280
40S ribosomal protein S15	P	protein	145	Homo sapiens	P62841
40S ribosomal protein S16	Q	protein	146	Homo sapiens	P62249

23 more molecules are not listed.

Sequence of entity 1 (n), FASTA

>7R4X_1 60S ribosomal protein L41 (chains n)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 2 (2), FASTA

>7R4X_2 18S ribosomal RNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCCGCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUCCACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGCCCUGGCGGAGCGCUGAGAAGACGGUCGAA
CUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGAAG
GAUCAUUA

Sequence of entity 3 (B), FASTA

>7R4X_3 40S ribosomal protein S3a (chains B)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (D), FASTA

>7R4X_4 40S ribosomal protein S3 (chains D)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 5 (E), FASTA

>7R4X_5 40S ribosomal protein S4, X isoform (chains E)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 6 (F), FASTA

>7R4X_6 40S ribosomal protein S5 (chains F)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 7 (H), FASTA

>7R4X_7 40S ribosomal protein S7 (chains H)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 8 (I), FASTA

>7R4X_8 40S ribosomal protein S8 (chains I)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 9 (K), FASTA

>7R4X_9 40S ribosomal protein S10 (chains K)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 10 (L), FASTA

>7R4X_10 40S ribosomal protein S11 (chains L)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 11 (P), FASTA

>7R4X_11 40S ribosomal protein S15 (chains P)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK

Sequence of entity 12 (Q), FASTA

>7R4X_12 40S ribosomal protein S16 (chains Q)
MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGK
ERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLL
VADPRRCESKKFGGPGARARYQKSYR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
MG	Magnesium ion	Mg	88

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

Primary citation

Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 angstrom resolution. Pellegrino, S., Dent, K.C., Spikes, T. et al. Nucleic Acids Res (2023) 51:4043-4054. DOI 10.1093/nar/gkad194 · 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
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
9O3Y 2.2 Å, Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chain

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