9P7O: In situ human AT-P-Z state ribosome

In situ human AT-P-Z state ribosome. Determined by electron microscopy at 2.65 Å resolution. Released 24 Dec 2025.

Method
Electron microscopy
Resolution
2.65 Å
Organism
Homo sapiens
Chains
86
Atoms
224,970
Mol. weight
3325.22 kDa
Ligands
ZN, SPD, SPM, MG
Released
24 Dec 2025

Explore 9P7O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P7O contains 576 α-helices and 600 β-strands across 79 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 CF: 14 helices, 32 β-strands

ElementResiduesLengthSheet
β-strand7-13715
α-helix20-3112
α-helix36-4914
α-helix52-543
α-helix57-593
α-helix64-696
β-strand77-81515
β-strand86-90515
α-helix99-1079
β-strand111-117715
α-helix123-1264
α-helix132-14312
β-strand147-153715
α-helix164-18118
β-strand190-192315
β-strand194116
β-strand199116
β-strand214-217417
β-strand222-225417
α-helix228-2325
α-helix235-2395
α-helix245-2462
β-strand247118
β-strand248-249219
β-strand252-256520
β-strand260-266720
β-strand269118
β-strand272121
β-strand277-280419
β-strand285-288419
β-strand289-294620
β-strand297-298220
β-strand302121
β-strand307-312620
β-strand325-328419
α-helix332-3343
β-strand340-346722
β-strand353123
β-strand360-363422
β-strand366-3791422
β-strand386-389422
β-strand394123
β-strand398-406922
α-helix419-4224
β-strand423-428622
β-strand431-4411122
Chain CI: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix52-6211
α-helix70-723
Chain La: 8 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix3-53
α-helix7-93
α-helix42-487
α-helix65-684
β-strand72-74342
α-helix78-814
α-helix84-929
β-strand97-982138
β-strand100-102343
α-helix103-1064
β-strand110-112342
β-strand123-126443
β-strand128-129242
α-helix131-1399
β-strand143-146443
Chain LA: 10 helices, 20 β-strands
ElementResiduesLengthSheet
α-helix4-52
α-helix29-324
α-helix34-385
β-strand40-501149
α-helix511
β-strand57-64849
β-strand71-77749
β-strand79150
β-strand83151
β-strand87-91549
β-strand101-103349
α-helix104-1063
β-strand112-113252
β-strand116153
β-strand120154
β-strand122154
β-strand126153
β-strand134-140752
α-helix142-1443
β-strand145-149552
β-strand155-159552
β-strand163-165349
β-strand166152
β-strand169150
α-helix174-1763
α-helix182-1909
α-helix201-2033
β-strand224-225255
α-helix229-2302
β-strand237-238255
Chain Lb: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix12-187
α-helix22-243
α-helix37-4812
α-helix49-513
α-helix54-7320
α-helix92-1009
α-helix106-11712
Chain LB: 19 helices, 20 β-strands
ElementResiduesLengthSheet
α-helix9-102
α-helix14-163
α-helix32-354
α-helix40-412
β-strand42-43259
β-strand45-591560
β-strand71-801060
α-helix82-832
β-strand84-951261
β-strand98-106961
α-helix1071
α-helix112-1165
α-helix134-1374
α-helix140-15617
β-strand159-165761
α-helix168-1703
β-strand180-184561
β-strand185-186259
α-helix190-19910
β-strand204-205261
α-helix207-2093
β-strand216-222760
β-strand225-229562
α-helix231-2344
α-helix237-2415
β-strand270-273462
β-strand276-2881360
β-strand292-293263
β-strand297-298263
α-helix300-3034
α-helix3161
β-strand320164
β-strand324164
β-strand330-334560
β-strand344-349660
α-helix361-3633
β-strand365-368460
α-helix382-3898
α-helix393-4019
Chain Lc: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix10-2112
β-strand26-29465
α-helix31-4010
β-strand45-49565
α-helix54-6714
β-strand70-74565
α-helix78-858
β-strand93-98665
Chain LC: 25 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand7-11568
α-helix121
β-strand17-23768
α-helix24-252
α-helix26-294
α-helix31-322
α-helix34-4411
β-strand65-66269
β-strand77-78269
β-strand90169
α-helix100-1012
α-helix117-13014
α-helix134-1396
β-strand152-154368
α-helix156-1605
α-helix164-17310
α-helix177-18610
β-strand188-189270
α-helix190-1912
α-helix193-1975
β-strand201-202270
β-strand208-211468
α-helix217-2204
β-strand228-231468
α-helix232-2343
α-helix237-2404
β-strand250-253468
α-helix254-2585
α-helix260-2645
α-helix279-2824
α-helix289-2946
α-helix296-3016
α-helix302-3054
α-helix316-3172
α-helix322-3287
α-helix331-36535

71 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Transcription factor BTF3CIprotein31Homo sapiensP20290 (AlphaFold model)
P site tRNAPtRNA74Homo sapiens
Elongation factor 1-alpha 1CFprotein441Homo sapiensP68104 (AlphaFold model)
A/T site tRNAATRNA76Homo sapiens
28S rRNAL5RNA3655Homo sapiens
5S rRNAL7RNA120Homo sapiens
5.8S rRNAL8RNA156Homo sapiens
60S ribosomal protein L8LAprotein248Homo sapiensP62917 (AlphaFold model)
Large ribosomal subunit protein uL3LBprotein402Homo sapiensP39023 (AlphaFold model)
60S ribosomal protein L4LCprotein368Homo sapiensP36578
Large ribosomal subunit protein uL18LDprotein293Homo sapiensP46777
Large ribosomal subunit protein eL6LEprotein250Homo sapiensQ02878

74 more molecules are not listed.

Sequence of entity 1 (CI), FASTA
>9P7O_1 Transcription factor BTF3 (chains CI)
IMNQEKLAKLQAQVRIGGKGTARRKKKVVHR
Sequence of entity 2 (Pt), FASTA
>9P7O_2 P site tRNA (chains Pt)
GUCUCCGUAGUGUAGGGUAUCACGUUCGCCUAACACGCGAAAGGUCCUCGGUUCGAAACC
GGGCGGAAACACCA
Sequence of entity 3 (CF), FASTA
>9P7O_3 Elongation factor 1-alpha 1 (chains CF)
EKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKL
KAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEF
EAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGY
NPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTD
KPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEAL
PGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDC
HTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGR
FAVRDMRQTVAVGVIKAVDKK
Sequence of entity 4 (AT), FASTA
>9P7O_4 A/T site tRNA (chains AT)
GUCUCCGUAGUGUAGCGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCUCGGUUCGAAA
CCGGGCGGAAACACCA
Sequence of entity 5 (L5), FASTA
>9P7O_5 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 6 (L7), FASTA
>9P7O_6 5S rRNA (chains L7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
Sequence of entity 7 (L8), FASTA
>9P7O_7 5.8S rRNA (chains L8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Sequence of entity 8 (LA), FASTA
>9P7O_8 60S ribosomal protein L8 (chains LA)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT
Sequence of entity 9 (LB), FASTA
>9P7O_9 Large ribosomal subunit protein uL3 (chains LB)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 10 (LC), FASTA
>9P7O_10 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEK
Sequence of entity 11 (LD), FASTA
>9P7O_11 Large ribosomal subunit protein uL18 (chains LD)
GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDII
CQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEG
QVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFP
GYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYK
KAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA
Sequence of entity 12 (LE), FASTA
>9P7O_12 Large ribosomal subunit protein eL6 (chains LE)
KGKPHCSRNPVLVRGIGRYSRSAMYSRKAMYKRKYSAAKSKVEKKKKEKVLATVTKPVGG
DKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHR
GKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDISNVKIPKHLTDAYFK
KKKLRKPRHQEGEIFDTEKEKYEITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALT
NGIYPHKLVF

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn6
SPDSpermidineC7 H19 N310
SPMSpermineC10 H26 N47
MGMagnesium ionMg219

Primary citation

Visualizing the translation landscape in human cells at high resolution. Zheng, W., Zhang, Y., Wang, J. et al. Nat Commun (2025) 16:10757-10757. DOI 10.1038/s41467-025-65795-9 · PubMed

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

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