9PKD: Transcription factor BTF3

Name: PDB 9PKD: In situ CHX and HHT treated 80S consensus ribosome
Published: 2026-07-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ CHX and HHT treated 80S consensus ribosome. Determined by electron microscopy at 2.42 Å resolution. Released 15 Jul 2026.

Method: Electron microscopy
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 82
Atoms: 216,861
Mol. weight: 3209.72 kDa
Ligands: 3HE, HMT, ZN, SPD
Released: 15 Jul 2026

Explore 9PKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PKD contains 563 α-helices and 569 β-strands across 78 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 CI: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	52-62	11
α-helix	70-72	3

Chain La: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-10	4
α-helix	42-48	7
β-strand	72-74	3	23
α-helix	75-81	7
α-helix	84-91	8
β-strand	97-98	2	110
β-strand	100-102	3	24
α-helix	103-106	4
β-strand	110-112	3	23
β-strand	123-126	4	24
β-strand	128-129	2	23
α-helix	131-139	9
β-strand	143-146	4	24

Chain LA: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	18	1	35
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	36
α-helix	50-51	2
β-strand	58-64	7	36
β-strand	71-77	7	36
β-strand	79	1	37
β-strand	83	1	38
β-strand	87-91	5	36
β-strand	101-103	3	36
α-helix	104-106	3
β-strand	112-113	2	39
β-strand	116-117	2	40
β-strand	124-126	3	40
β-strand	134-140	7	39
α-helix	142-144	3
β-strand	145-149	5	39
β-strand	155-159	5	39
β-strand	163-165	3	36
β-strand	166	1	39
β-strand	169	1	37
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	35
α-helix	201-203	3
β-strand	224-225	2	41
α-helix	229-230	2
β-strand	237-238	2	41

Chain Lb: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-24	3
α-helix	37-48	12
α-helix	54-73	20
α-helix	92-99	8
α-helix	106-117	12

Chain LB: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	44
β-strand	45-59	15	45
β-strand	71-80	10	45
α-helix	82-83	2
β-strand	84-95	12	44
β-strand	98-106	9	44
α-helix	107	1
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-165	7	44
α-helix	168-170	3
β-strand	180-186	7	44
α-helix	190-199	10
β-strand	204-205	2	44
α-helix	207-209	3
β-strand	216-222	7	45
α-helix	223-224	2
β-strand	225-229	5	46
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-273	4	46
β-strand	276-287	12	45
β-strand	292-293	2	47
β-strand	297-298	2	47
α-helix	300-303	4
α-helix	316	1
β-strand	320	1	48
β-strand	324	1	48
β-strand	330-334	5	45
β-strand	344-349	6	45
β-strand	365-368	4	45
α-helix	382-389	8
α-helix	393-401	9

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-21	12
β-strand	26-29	4	49
α-helix	31-40	10
β-strand	45-49	5	49
α-helix	54-67	14
β-strand	70-74	5	49
α-helix	78-84	7
β-strand	93-98	6	49

Chain LC: 25 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	50
β-strand	17-23	7	50
α-helix	24-25	2
α-helix	26-29	4
α-helix	31-32	2
α-helix	34-44	11
β-strand	65-66	2	51
β-strand	77-78	2	51
β-strand	90	1	51
α-helix	100-101	2
α-helix	117-130	14
α-helix	134-138	5
β-strand	152-154	3	50
α-helix	156-160	5
α-helix	164-173	10
α-helix	177-185	9
β-strand	188-189	2	52
α-helix	190-191	2
α-helix	193-197	5
β-strand	201-202	2	52
β-strand	208-211	4	50
α-helix	217-220	4
β-strand	228-231	4	50
α-helix	232-234	3
α-helix	237-240	4
β-strand	250-253	4	50
α-helix	254-258	5
α-helix	260-264	5
α-helix	279-282	4
α-helix	289-293	5
α-helix	296-300	5
α-helix	302-305	4
α-helix	311-314	4
α-helix	316-317	2
α-helix	322-328	7
α-helix	332-365	34

Chain Ld: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	53
α-helix	29-33	5
α-helix	38-40	3
α-helix	41-57	17
β-strand	62-64	3	53
α-helix	66-72	7
β-strand	83-92	10	53
β-strand	102-108	7	53
β-strand	120-122	3	53

70 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
Transcription factor BTF3	CI	protein	31	Homo sapiens	P20290 (AlphaFold model)
28S rRNA	L5	RNA	3655	Homo sapiens
5S rRNA	L7	RNA	120	Homo sapiens
5.8S rRNA	L8	RNA	156	Homo sapiens
60S ribosomal protein L8	LA	protein	248	Homo sapiens	P62917 (AlphaFold model)
Large ribosomal subunit protein uL3	LB	protein	402	Homo sapiens	P39023 (AlphaFold model)
60S ribosomal protein L4	LC	protein	368	Homo sapiens	P36578 (AlphaFold model)
Large ribosomal subunit protein uL18	LD	protein	293	Homo sapiens	P46777
Large ribosomal subunit protein eL6	LE	protein	250	Homo sapiens	Q02878
60S ribosomal protein L7	LF	protein	225	Homo sapiens	P18124
60S ribosomal protein L7a	LG	protein	241	Homo sapiens	P62424
60S ribosomal protein L9	LH	protein	190	Homo sapiens	P32969

70 more molecules are not listed.

Sequence of entity 1 (CI), FASTA

>9PKD_1 Transcription factor BTF3 (chains CI)
IMNQEKLAKLQAQVRIGGKGTARRKKKVVHR

Sequence of entity 2 (L5), FASTA

>9PKD_2 28S rRNA (chains L5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCGCGGGGGACCGUCCCCCGACC
GGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGG
ACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGCCCCCGAGUGUUACAGCCCCCC
CGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCC
CCCCUCGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCGGGGCGGACUGUCCCC
AGUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGAGGCCACGCGCGCGUCCCCCGA
AGAGGGGGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACC
CGUCUUGAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAG
CCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAG
GCCUCUCCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGU
GGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAA
GCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGAC
CUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUC
CCUCAGGAUAGCUGGCGCUCUCGCAGACCCGAGCCACGCAGUUUUAUCCGGUAAAGCGAA
UGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAG
AAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUGGGCCACUUUU
GGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGA
CGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGA
AGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAA
UGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGG
GAGCGGCGGCCGGAGCCCCGCGGACGCUACGCCGCGACGAGUAGGAGGGCCGCUGCGGUG
AGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCAGAUCUUGGUGGU
AGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGGUUCCAUGUGAAC
AGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGUUCCGAAGGGACG
GGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUCGGGUUCAGAUCCCCGAAUC
CGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGACCGAUCCCGGAG
AAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCAGGGCGCCCUGGA
AUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGUUCCGGCGGCGUC
CGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAUCUCGCGCCGGGC
CGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUGUUGGAACAAUGU
AGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGC
UGGGUCGGUCGCGGCCGGCGCCUAGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUC
CGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGA
UUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGC
GGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGC
AUGAAXGGAUGAACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAA
GGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCU
GGCACGGUGAAGAGACAUGAGAACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGG
GGCGAGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCGCGCCGGCCGGGC
GCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUACACCUGUCAA
ACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGA
AGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGAAAGCGGGGCC
UCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGUUACCACAGGG
AUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUC
GGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUA
GGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUG
UGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUG
UAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAAC
GCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCGCGGAGCCUCGGUU
GGCCUCGGAUAGCCGGUCCCCCGCCGGGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAA
CGGGGCGCGGCCGGAGAGGCGGCCGCCCCCUCGCCCGUCACGCACCGCACGUUCGUGGGG
AACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUACGUAGCA
GAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGU

Sequence of entity 3 (L7), FASTA

>9PKD_3 5S rRNA (chains L7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 4 (L8), FASTA

>9PKD_4 5.8S rRNA (chains L8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 5 (LA), FASTA

>9PKD_5 60S ribosomal protein L8 (chains LA)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT

Sequence of entity 6 (LB), FASTA

>9PKD_6 Large ribosomal subunit protein uL3 (chains LB)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 7 (LC), FASTA

>9PKD_7 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEK

Sequence of entity 8 (LD), FASTA

>9PKD_8 Large ribosomal subunit protein uL18 (chains LD)
GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDII
CQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEG
QVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFP
GYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYK
KAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

Sequence of entity 9 (LE), FASTA

>9PKD_9 Large ribosomal subunit protein eL6 (chains LE)
KGKPHCSRNPVLVRGIGRYSRSAMYSRKAMYKRKYSAAKSKVEKKKKEKVLATVTKPVGG
DKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHR
GKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDISNVKIPKHLTDAYFK
KKKLRKPRHQEGEIFDTEKEKYEITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALT
NGIYPHKLVF

Sequence of entity 10 (LF), FASTA

>9PKD_10 60S ribosomal protein L7 (chains LF)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN

Sequence of entity 11 (LG), FASTA

>9PKD_11 60S ribosomal protein L7a (chains LG)
KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQ
ALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTT
LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFT
QVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKL
G

Sequence of entity 12 (LH), FASTA

>9PKD_12 60S ribosomal protein L9 (chains LH)
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA

Ligands and cofactors

ID	Name	Formula	Copies
3HE	4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2…	C15 H23 N O4	1
HMT	(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cep…	C29 H39 N O9	1
ZN	Zinc ion	Zn	6
SPD	Spermidine	C7 H19 N3	10
SPM	Spermine	C10 H26 N4	7
MG	Magnesium ion	Mg	219

Primary citation

In situ CHX and HHT treated 80S consensus ribosome. Wei, Z., Yong, X. To be published.

Other PDB entries of the same protein (UniProt P20290 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MCB 1.9 Å, Crystal structure of NAC domains of human nascent polypeptide-associated complex (NAC)
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)
9S3D 2.32 Å, NAC bound human RNC with 58 amino acid ARF1-linker
9S3B 2.38 Å, NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1
9S3C 2.42 Å, NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2
9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
9P8B 2.48 Å, In situ human eEF1A-A/T-P-E state 80S ribosome
3LKX 2.5 Å, Human nac dimerization domain
9P7D 2.57 Å, In situ human Hibernating class4 80S ribosome
9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
9P7E 2.59 Å, In situ human Hibernating class5 80S ribosome

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