11JJ: IFRD2

Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveled. Determined by electron microscopy at 2.9 Å resolution. Released 2 Sept 2026.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Oryctolagus cuniculus
Chains: 86
Atoms: 224,036
Mol. weight: 5510.97 kDa
Ligands: ZN, GDP
Released: 2 Sept 2026

Explore 11JJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

11JJ contains 688 α-helices and 641 β-strands across 81 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 10: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	11	1	118
β-strand	18	1	118
α-helix	26-29	4
β-strand	35-37	3	119
α-helix	43-45	3
β-strand	48-54	7	119
β-strand	58-61	4	118
α-helix	62-80	19
β-strand	85-89	5	119
β-strand	95-99	5	118
β-strand	121-129	9	118
β-strand	134-140	7	119
α-helix	142-144	3
α-helix	145-156	12
β-strand	163-167	5	119
β-strand	170	1	120
β-strand	177	1	120
α-helix	178-186	9
β-strand	190-193	4	121
β-strand	196-199	4	121
α-helix	206-212	7

Chain 11: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	16-25	10	207
α-helix	31-44	14
β-strand	49-52	4	207
β-strand	57	1	208
β-strand	62	1	208
β-strand	67-74	8	207
α-helix	76-89	14
β-strand	93-95	3	209
α-helix	96-98	3
β-strand	99	1	207
β-strand	105-109	5	207
α-helix	112-115	4
α-helix	117-119	3
β-strand	128-135	8	207
α-helix	139-143	5
α-helix	159-170	12
β-strand	173-175	3	209

Chain 13: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
β-strand	22-24	3	128
α-helix	28-45	18
β-strand	55	1	129
β-strand	58-60	3	130
β-strand	70-72	3	130
β-strand	76	1	131
α-helix	78-84	7
α-helix	88-91	4
α-helix	92-94	3
β-strand	96	1	129
β-strand	98	1	131
β-strand	106	1	132
α-helix	107-123	17
β-strand	124-126	3	133
α-helix	139-140	2
α-helix	141-144	4
α-helix	149-151	3
β-strand	167	1	134
α-helix	168-170	3
α-helix	171-175	5
α-helix	178-210	33

Chain 14: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	139
β-strand	11-15	5	140
β-strand	24-30	7	140
β-strand	35-40	6	140
β-strand	45-51	7	140
α-helix	52-54	3
β-strand	55-61	7	140
α-helix	70-80	11
α-helix	82-88	7
α-helix	90-102	13
α-helix	106-138	33

Chain 15: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
α-helix	17-32	16
β-strand	36-39	4	144
α-helix	45-50	6
β-strand	59-67	9	144
α-helix	84-86	3
α-helix	98-109	12
β-strand	114-123	10	144
β-strand	127-135	9	144
α-helix	140-143	4
α-helix	154-156	3
α-helix	166-172	7
α-helix	178-183	6
α-helix	188-195	8
β-strand	198-200	3	128

Chain 17: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-22	9	158
α-helix	26-36	11
β-strand	40	1	158
α-helix	41-52	12
α-helix	57	1
β-strand	58-59	2	159
α-helix	67-68	2
β-strand	69	1	160
α-helix	71-76	6
β-strand	80	1	160
β-strand	81-82	2	159
α-helix	85-104	20
α-helix	109-111	3
β-strand	112-121	10	158
α-helix	122-124	3
β-strand	125	1	161
α-helix	126	1
β-strand	128-130	3	162
α-helix	132-134	3
β-strand	136-138	3	162
β-strand	141	1	161
β-strand	144-152	9	158

Chain 19: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-21	3
β-strand	22-24	3	164
α-helix	29-33	5
α-helix	38-46	9
β-strand	50-52	3	164
α-helix	53-57	5
α-helix	61-71	11
α-helix	78-80	3
α-helix	85-88	4
α-helix	91-111	21
α-helix	117-128	12
α-helix	135-180	46

Chain 20: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-16	9	169
α-helix	17-18	2
α-helix	25-27	3
β-strand	28-34	7	169
α-helix	37-51	15
β-strand	59-67	9	169
α-helix	68-69	2
β-strand	76-85	10	170
β-strand	90-99	10	170
α-helix	102-117	16
α-helix	121-123	3
β-strand	125-132	8	170
α-helix	134-136	3
α-helix	140-143	4
β-strand	151-152	2	139
β-strand	168	1	150
α-helix	171-172	2

73 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
IFRD2	IF	protein	442	Oryctolagus cuniculus
40S_SA_C domain-containing protein	BB	protein	217	Oryctolagus cuniculus	G1TJH8 (AlphaFold model)
40S ribosomal protein S2	S2	protein	221	Oryctolagus cuniculus	O18789 (AlphaFold model)
eS21	PP	protein	83	Oryctolagus cuniculus
Small ribosomal subunit protein uS17	DD	protein	151	Oryctolagus cuniculus	G1TRM4 (AlphaFold model)
5.8S rRNA	58	RNA	156	Oryctolagus cuniculus
5S rRNA	6	RNA	120	Oryctolagus cuniculus
60S ribosomal protein L8	L8	protein	248	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
60S ribosomal protein L3	L3	protein	394	Oryctolagus cuniculus	G1TL06
60S ribosomal protein L4	L4	protein	362	Oryctolagus cuniculus	A0A5F9DCT1
60S ribosomal protein L5	L5	protein	293	Oryctolagus cuniculus	P19949
60S ribosomal protein L6	L6	protein	291	Oryctolagus cuniculus	G1SKF7

74 more molecules are not listed.

Sequence of entity 1 (IF), FASTA

>11JJ_1 IFRD2 (chains IF)
MPRARKGNTLRKGGQRRGGGARSSAQADSGSSDDEAASEARSTASECPSLLSTTAEDSLG
GDVVDEQGQQEDLEEKLKEYVDCLTDKSAKTRQGALESLRLALASRLLPDFLLERRLTLA
DALEKCLKKGKGEEQALAAAVLGLLCVQLGPGPKGEELFHSLQPLLVSVLSDSTASPAAR
LHCASALGLGCYVAAADIQDLVSCLACLESVFSRFYGLGGSSTSPVVPASLHGLLSAALQ
AWALLLTICPSTQISHILDRQLPRLPQLLSSESVNLRIAAGETIALLFELARDLEEEFVY
EDMEALCSVLRTLATDSNKYRAKADRRRQRSTFRAVLHSVEGGECEEEIVRFGFEVLYMD
SWARHRIYAAFKEVLGSGMHHHLQNNELLRDIFGLGPVLLLDATALKACKVPRFEKHLYN
AAAFKARTKARSRVRDKRADIL

Sequence of entity 2 (BB), FASTA

>11JJ_2 40S_SA_C domain-containing protein (chains BB)
SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLA
ARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPRL
LVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLARE
VLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAA

Sequence of entity 3 (S2), FASTA

>11JJ_3 40S ribosomal protein S2 (chains S2)
KEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTR
AGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP
HTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFA
KATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT

Sequence of entity 4 (PP), FASTA

>11JJ_4 eS21 (chains PP)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 5 (DD), FASTA

>11JJ_5 Small ribosomal subunit protein uS17 (chains DD)
DIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPF
TGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQI
GDIVTVGECRPLSKTVRFNVLKVTKAAGTKK

Sequence of entity 6 (58), FASTA

>11JJ_6 5.8S rRNA (chains 58)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 7 (6), FASTA

>11JJ_7 5S rRNA (chains 6)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 8 (L8), FASTA

>11JJ_8 60S ribosomal protein L8 (chains L8)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT

Sequence of entity 9 (L3), FASTA

>11JJ_9 60S ribosomal protein L3 (chains L3)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 10 (L4), FASTA

>11JJ_10 60S ribosomal protein L4 (chains L4)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
SD

Sequence of entity 11 (L5), FASTA

>11JJ_11 60S ribosomal protein L5 (chains L5)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

Sequence of entity 12 (L6), FASTA

>11JJ_12 60S ribosomal protein L6 (chains L6)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles. Seraj, Z., Zottig, X., Huang, C. et al. Elife (2026) 15. DOI 10.7554/eLife.110114 · PubMed

Other PDB entries of the same protein (UniProt G1TJH8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
9BDL 2.8 Å, 80S ribosome with angiogenin
11HG 2.9 Å, Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveled
9Q1S 3.0 Å, NediV IRES (P site) in complex with Rabbit 80S ribosome
9Q2P 3.0 Å, Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E…
7UCJ 3.1 Å, Mammalian 80S translation initiation complex with mRNA and Harringtonine
9BDN 3.1 Å, 80S ribosome with angiogenin and tRNAAla
9Q2M 3.3 Å, Rabbit ribosomal 80S elongation complex with eEF2, partial P site Ala-tRNA, E site…
6ZVK 3.49 Å, The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the…
9Q1Q 3.5 Å, NediV IRES (A site) in complex with Rabbit 80S ribosome
7A01 3.6 Å, The Halastavi arva virus intergenic region IRES promotes translation by the simplest…
9BDP 3.7 Å, 80S ribosome bound with angiogenin and complex of eEF1A and Ala-tRNAAla

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