29IZ: Large ribosomal subunit protein uL30

Name: PDB 29IZ: Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
Published: 2026-09-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2. Determined by electron microscopy at 2.08 Å resolution. Released 30 Sept 2026.

Method: Electron microscopy
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 82
Atoms: 214,840
Mol. weight: 3958.13 kDa
Ligands: A1JQ4, SPM, SPD, ZN
Released: 30 Sept 2026

Explore 29IZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

29IZ contains 634 α-helices and 583 β-strands across 77 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	33
β-strand	10	1	33
β-strand	18	1	34
β-strand	25	1	34
β-strand	34-41	8	35
β-strand	48-57	10	35
α-helix	59-64	6
α-helix	67-78	12

Chain Aa: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	5
β-strand	30-34	5	5
α-helix	35-39	5
α-helix	41-42	2
β-strand	43	1	6
α-helix	44	1
β-strand	52	1	6
α-helix	53	1
α-helix	61-66	6
α-helix	69-72	4
α-helix	84-109	26

Chain AA: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	29-78	50
β-strand	81-83	3	1
α-helix	84-87	4
β-strand	89-94	6	2
α-helix	103-112	10
β-strand	119-124	6	2
α-helix	127-135	9
α-helix	137-139	3
β-strand	140-143	4	2
α-helix	147-157	11
β-strand	159-162	4	3
β-strand	165-168	4	3
α-helix	172-179	8
α-helix	180-182	3
α-helix	187-196	10
α-helix	201-207	7
β-strand	208	1	3
α-helix	209-210	2
β-strand	211-212	2	2
α-helix	213-215	3
β-strand	226	1	4
α-helix	227-229	3
β-strand	233	1	4
β-strand	234-237	4	2
α-helix	240-247	8

Chain Ab: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	14-36	23
α-helix	41-73	33
α-helix	89-92	4
α-helix	97-101	5
α-helix	105-113	9
α-helix	115-118	4
β-strand	119-121	3	52

Chain AB: 17 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	45-47	3
α-helix	52-54	3
β-strand	56	1	12
α-helix	59-73	15
β-strand	75-76	2	13
α-helix	78-81	4
α-helix	82-84	3
α-helix	89-100	12
α-helix	103-106	4
α-helix	107-116	10
α-helix	132-134	3
β-strand	137-138	2	14
α-helix	140-148	9
β-strand	154-158	5	14
α-helix	165-168	4
α-helix	170-177	8
β-strand	181-184	4	14
α-helix	187-193	7
β-strand	201-204	4	14
α-helix	212-222	11
α-helix	223-227	5
α-helix	230-235	6
β-strand	238-239	2	13
α-helix	244-258	15

Chain Ac: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	22
β-strand	13	1	22
α-helix	18	1
β-strand	19	1	51
α-helix	20-21	2
α-helix	23-25	3
α-helix	26-29	4
α-helix	32-34	3
α-helix	35-48	14
α-helix	52-62	11
α-helix	66-77	12
α-helix	80-101	22

Chain AC: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
β-strand	17-21	5	19
β-strand	24-29	6	19
β-strand	32-37	6	19
β-strand	44-48	5	18
β-strand	53-62	10	18
α-helix	64-85	22
β-strand	88-95	8	20
β-strand	102-106	5	21
β-strand	111-115	5	21
α-helix	117-119	3
β-strand	124-127	4	21
α-helix	128-129	2
β-strand	133-136	4	20
β-strand	143-148	6	20
α-helix	151-164	14
β-strand	178-185	8	20

Chain Ad: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-17	2	32
β-strand	27-28	2	32
β-strand	33-34	2	32
α-helix	44-45	2
α-helix	51-57	7
α-helix	67-74	8
α-helix	84-86	3

69 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
Large ribosomal subunit protein uL30	AA	protein	248	Homo sapiens	P18124 (AlphaFold model)
60S ribosomal protein L7a	AB	protein	266	Homo sapiens	P62424 (AlphaFold model)
60S ribosomal protein L9	AC	protein	192	Homo sapiens	P32969 (AlphaFold model)
Ribosomal protein uL16-like	AD	protein	214	Homo sapiens	Q96L21 (AlphaFold model)
60S ribosomal protein L11	AE	protein	178	Homo sapiens	P62913
60S ribosomal protein L13	AF	protein	211	Homo sapiens	P26373
60S ribosomal protein L14	AG	protein	215	Homo sapiens	P50914
60S ribosomal protein L15	AH	protein	204	Homo sapiens	P61313
60S ribosomal protein L13a	AI	protein	203	Homo sapiens	P40429
60S ribosomal protein L17	AJ	protein	184	Homo sapiens	P18621
60S ribosomal protein L18	AK	protein	188	Homo sapiens	Q07020
60S ribosomal protein L19	AL	protein	196	Homo sapiens	P84098

70 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>29IZ_1 Large ribosomal subunit protein uL30 (chains AA)
MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKE
YRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNG
TFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLG
KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQI
NRLIRRMN

Sequence of entity 2 (AB), FASTA

>29IZ_2 60S ribosomal protein L7a (chains AB)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG

Sequence of entity 3 (AC), FASTA

>29IZ_3 60S ribosomal protein L9 (chains AC)
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 4 (AD), FASTA

>29IZ_4 Ribosomal protein uL16-like (chains AD)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLGGHMVSDEYEQL
SSEALEAARICANKYMVKSCGRDGFHMRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNEEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAKKCLIPDGCGVKYVPSHGPLDKWRVLHS

Sequence of entity 5 (AE), FASTA

>29IZ_5 60S ribosomal protein L11 (chains AE)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 6 (AF), FASTA

>29IZ_6 60S ribosomal protein L13 (chains AF)
MAPSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPVRNVYKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 7 (AG), FASTA

>29IZ_7 60S ribosomal protein L14 (chains AG)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTQVRRQAMPFKCMQLTDF
ILKFPHSAHQKYVRQAWQKADINTKWAATRWAKKIEARERKAKMTDFDRFKVMKAKKMRN
RIIKNEVKKLQKAALLKASPKKAPGTKGTAAAAAAAAAAKVPAKKITAASKKAPAQKVPA
QKATGQKAAPAPKAQKGQKAPAQKAPAPKASGKKA

Sequence of entity 8 (AH), FASTA

>29IZ_8 60S ribosomal protein L15 (chains AH)
MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYV
IYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYW
VGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKF
HHTIGGSRRAAWRRRNTLQLHRYR

Sequence of entity 9 (AI), FASTA

>29IZ_9 60S ribosomal protein L13a (chains AI)
MAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRK
RMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVV
PAALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQ
AEKNVEKKIDKYTEVLKTHGLLV

Sequence of entity 10 (AJ), FASTA

>29IZ_10 60S ribosomal protein L17 (chains AJ)
MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF
RRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVN
KAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKL
MARE

Sequence of entity 11 (AK), FASTA

>29IZ_11 60S ribosomal protein L18 (chains AK)
MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPP
LSLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRARSRILRAGGKI
LTFDQLALDSPKGCGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGR
RASRGYKN

Sequence of entity 12 (AL), FASTA

>29IZ_12 60S ribosomal protein L19 (chains AL)
MSMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSR
ARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMY
HSLYLKVKGNVFKNKRILMEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAK
KEEIIKTLSKEEETKK

Ligands and cofactors

ID	Name	Formula	Copies
A1JQ4	Toxin NT-2	C17 H24 O7	1
SPM	Spermine	C10 H26 N4	5
SPD	Spermidine	C7 H19 N3	6
ZN	Zinc ion	Zn	8
PUT	1,4-diaminobutane	C4 H12 N2	4
MG	Magnesium ion	Mg	252

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

Primary citation

Toxin NT-2 bound to human ribosome. Rabl, J., Karousis, E.D. To be published.

Other PDB entries of the same protein (UniProt P18124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
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.
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)
29IX 2.2 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. NT-2 added to purified…

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