› › Structure analysis

Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome

Electron Microscopy
3.14Å resolution
PDB entry 8hkx coloured by chain, front view.
PDB entry 8hkx coloured by chain, side view.
PDB entry 8hkx coloured by chain, top view.
Source organism: Sulfolobus acidocaldarius DSM 639
Assembly composition:
hetero 28-mer (preferred)
Entry contents: 27 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 28-mer
Accessible surface area: 327707.48 Å2
Buried surface area: 117796.73 Å2
Dissociation area: 580.17 Å2
Dissociation energy (ΔGdiss): -5.78 kcal/mol
Dissociation entropy (TΔSdiss): 9.95 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271495

Macromolecules

Small ribosomal subunit protein uS2
Chain: AS2P
Length: 196 amino acids
Theoretical weight: 22.47 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS2 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 8hkx, assembly 1, top view.
119620406080100120140160180
 
50100150ELLVPLDTYLSAGVHIGTHTCTRYMERFIYRVRPEGLYVLDVRKIDERLRVAAKFISRFRPEAVLTVASRPYAFTPVQKFSEVVRGKEISGRFPPGTLTNPYLDNYIEPEVLIVTDPRTDLQAIKEASKVGIPIVAFTDTDARVDFIDVIIPANNKGRKSLALLYWVLARQILRERKEIPLDGDIPLRVEDFETRL
UniProt
P39478
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Small ribosomal subunit protein eS4
Chain: AS4E
Length: 240 amino acids
Theoretical weight: 27.34 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS4 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS4 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS4 in PDB entry 8hkx, assembly 1, top view.
124020406080100120140160180200220240
 
100200VHITRFEAPWFLKVGKKEYKWIIRSRAGPHKIQESVPLAILLKYYLKAVDTTREAKRIIFDGKVLVDGKVRRDYKYPVGLMDVVEIPSADLRVRIIPDNVRYLTTINISREDAKYKFVRIMNKTTLKSGVLQLNLEDGRNILLKGEELSQYNLPTLTTLKIELPEQKITTAYTIKEGVYAMIIGGRNAGLHGKISKIQLAKYKRIKYSLVTLEGKDGSTFQTNLINVMAIGENEADSNLG
UniProt
O05634
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Small ribosomal subunit protein uS4
Chain: AS4P
Length: 166 amino acids
Theoretical weight: 19.44 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS4 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 8hkx, assembly 1, top view.
116620406080100120140160
 
50100150DPRKSKKKWMGPSHPWIKINLGKEQILIGKYGLRNKKEIWIAQTMIRNFRHQARSLLALPPAERNIREKQLIQKLYRMGILEKDNSTLDDILSLTEENYLERRLQTIVYKKGLARTIYQARQLITHGHIAISGRKVTSPGYVVLRGEEDLIDYYPTSPFKQNPPSQ
UniProt
P39467
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Small ribosomal subunit protein uS5
Chain: AS5P
Length: 204 amino acids
Theoretical weight: 22.78 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS5 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 8hkx, assembly 1, top view.
120420406080100120140160180200
 
50100150200EDWKPRTKVGQLIKEGKINSMKELFERNLPIVEPEIVDVLLPKLRYDIVDIGIVQKQTDAGELSRYKVLIVMGNMDGYISYGTGKAKQLRVAIQKAIRDAKMRIIPVRRGCGSWECTCGESHSLPFIVSGKAGSVEVTLLPAPKGTGLVVGSVLKTFLSLAGLKDVWSRTKGSTYTHENFIKAAYIALYNTYRFVTPVDWGRMK
UniProt
O05641
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Small ribosomal subunit protein eS6
Chain: AS6E
Length: 105 amino acids
Theoretical weight: 11.48 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS6 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS6 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS6 in PDB entry 8hkx, assembly 1, top view.
1105102030405060708090100
 
50100ALAYRTRAFQLSLDQSKLPNLVGTKIGDVIDINVSGVNLKLKITGGSDNSGFSMRFDVGGGAKRKILVSGPPGYYPKEDGLRRKRTVRGNMITPEIVQINTIMIR
UniProt
Q4JAI1
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Small ribosomal subunit protein eS8
Chain: AS8E
Length: 126 amino acids
Theoretical weight: 14.11 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS8 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS8 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS8 in PDB entry 8hkx, assembly 1, top view.
1126102030405060708090100110120
 
50100SYYQGNDSRKITGGQKGKNRDKRKYELGSPPTETKISDKDIKEKDRVAGGNFKLRLRYASYANVYDPQSKTAKKVKIISVLESPANREYARRGIIVKGTLIQTELGKAKVTSRPGQDGIINALLLR
UniProt
Q4JAP5
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Small ribosomal subunit protein uS8
Chain: AS8P
Length: 130 amino acids
Theoretical weight: 14.62 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS8 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 8hkx, assembly 1, top view.
1130102030405060708090100110120130
 
50100INPLANALATLYNNEMRRNKQALITPASKLIISVLRVMQKEGYIGEFEYIDDGRAGKIIVQLLGRINKCGPISPRYPLDYNGLLRLPDYIRKYLPSKEIGIIIISTPKGVMSHRDGIREKIGGVTLGYVY
UniProt
O05636
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Small ribosomal subunit protein uS11
Chain: S11P
Length: 128 amino acids
Theoretical weight: 13.65 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS11 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 8hkx, assembly 1, top view.
1128102030405060708090100110120
 
50100REIRWGNARIYASQNNTIITITDITGAEIISKASGGMVVKADREKPSPYAAMLAANKAANDAFDKGISAIHIKVRAQGGYGSKTPGPGAQPAIRALARAGFIIGRIEDVTPLPHDTIRRPGGRRGRRV
UniProt
P39469
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Small ribosomal subunit protein uS12
Chain: S12P
Length: 143 amino acids
Theoretical weight: 15.7 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS12 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 8hkx, assembly 1, top view.
114320406080100120140
 
50100GSKSPKGLFAARKLRLKRLKFSWSQRSFKRRMLALKEKFDPLEGAPMARGIVLEKVGIESRQPNSAVRKAVRVQLVKNGRIVTAFVPGDGGVNFIDEHDEVVIAGIGGTLGRSMGDLPGVRYKVVMVNGVSLDALYKGKKQKP
UniProt
P11524
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Small ribosomal subunit protein uS15
Chain: S15P
Length: 149 amino acids
Theoretical weight: 17.44 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS15 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 8hkx, assembly 1, top view.
114920406080100120140
 
50100150MNKKRAKGNSHSIRPVRSGPPKWVRFTREEVELLVEELAKRGYPPSMIGMVLRDQYGVPLVKQITGRKLTAILQDRNMKPKIPEDLFNLMRRAVNIRRHLFEYPKDKSAKRGLEEVESKIRRLASYYKETGKLPQEWSYDPAKAELLVT
UniProt
Q4JAI3
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Small ribosomal subunit protein uS17
Chain: S17P
Length: 111 amino acids
Theoretical weight: 12.6 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS17 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 8hkx, assembly 1, top view.
1111102030405060708090100110
 
50100KKGQLVKNVGIEGVSAPSKTCDDEYCPYHGSLKVRGIVLEGKLIRARANRTGTVEREYIFYDSKYKRYERRRSRIHVHIPSCLEVKEGDNVIIGESRPIAKSISFVILGVK
UniProt
Q4JB49
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Small ribosomal subunit protein eS24
Chain: S24E
Length: 96 amino acids
Theoretical weight: 10.77 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS24 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS24 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS24 in PDB entry 8hkx, assembly 1, top view.
196102030405060708090
 
50VSDKVEGIVERDIQNNVANRRELYIKLFHIGSGTPSRKELVKAIASTFSTAEDLVVVKKVFTNYGSGISYARVNVYKDKDSLQKLEPQYLIGRDTG
UniProt
Q4JAF9
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Small ribosomal subunit protein eS27
Chain: S27E
Length: 59 amino acids
Theoretical weight: 6.58 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS27 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS27 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS27 in PDB entry 8hkx, assembly 1, top view.
159510152025303540455055
 
204060MKAKFKILIPEPKSKFIRVKCRQCNNEQVIFSNATFPVRCLSCGAQIVIPKGGKAKIEG
UniProt
Q4J9B1
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Small ribosomal subunit protein eS1
Chain: S3AE
Length: 189 amino acids
Theoretical weight: 21.88 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS1 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 8hkx, assembly 1, top view.
118920406080100120140160180
 
50100150IRDKWKLKKWYVITAPKVFGEALLGSTPAYDINKALSRKIEVTLYDLTGDYNLVYIHLYFKILGNISGDKLSTIFYGHELSRDYIRSLVRRKSSKINAVVDVTTKDGYMLRVKGLVLTTYRAHISQKTAIRKVISDITRKKAEESDFDQFVQDVIFGKLSNDIFQEAKKIYPLRKVEIEKTKLLKAPKV
UniProt
Q4JB17
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Small ribosomal subunit protein uS3
Chain: AS3P
Length: 201 amino acids
Theoretical weight: 22.4 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS3 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 8hkx, assembly 1, top view.
120120406080100120140160180200
 
50100150200VLIKRHFLQKAAIKVMVDEYLAKQFYNAEYAGVEIVKTPIGTRVIIYAGRPPLIIGKGGKTIKQLAQVLEKFFGLENPQITVTAAENPELNARVMAFRLAIALEKGYHFRRAAFITIRRIMSSGAVGAEVIVSGKLTSERAKYEKLKEGTVYKSGQQLEKIIDRAIGIAMLKPGVYGVEVVITKPTRSIDKIELKEKVEKT
UniProt
Q4JB46
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Small ribosomal subunit protein uS7
Chain: AS7P
Length: 193 amino acids
Theoretical weight: 21.86 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS7 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 8hkx, assembly 1, top view.
119320406080100120140160180
 
50100150ENIEVSNLNVKVFGKWDTKVEVRDPSLKKYIDLMSIYLPHTGGRHEHRRFGKSRIPIVERLINNLMRPGRNKGKKMLAYNIVKTTFDIIAVKTGQNPIQVLVRAIENAAPREEVTRIMYGGIVYYVAVDVAPQRRVDLALRHLVTGASEASFNNPKPIEEALAEEIIAAANNDNKSVAIRKKEEIERIALSSR
UniProt
P17198
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Small ribosomal subunit protein uS9
Chain: AS9P
Length: 136 amino acids
Theoretical weight: 15.64 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS9 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 8hkx, assembly 1, top view.
1136102030405060708090100110120130
 
50100QAEQNFMITYARRKSARASCYIKPGNGKVFVNDIPIEIIPIEVVRYKIMEPLVLAGDKITSSIEARIYTQGGGIMGQADAARMALARALVKFTNSKELVEIYKSYDRTMLAGDPRQTESEKWMRYSARRWRQKAYR
UniProt
P39468
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Small ribosomal subunit protein uS10
Chain: S10P
Length: 100 amino acids
Theoretical weight: 11.78 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS10 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 8hkx, assembly 1, top view.
1100102030405060708090100
 
50100TKARIRLWSSNIDSLNFVVNQIRNMAQKTGIQVSGPIPLPTTRMEVPVMRLPHGEGKKKWEHWEMKVHKRIIDIAADERVMRQLMRVRVPDDVYIEIELI
UniProt
P17199
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Small ribosomal subunit protein uS13
Chain: S13P
Length: 147 amino acids
Theoretical weight: 17.14 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS13 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 8hkx, assembly 1, top view.
114720406080100120140
 
50100QQQFKYIVRLFGQDVDGTMKLPYALAMIKGIGYNTAMIIIRKLNLDKDKRLGEISDEDIKKIENLLNNKIIPESPNWIYNRQKDYESGADMHLVTSDLIFYVRNDIERERRSRSWRGVRHSLGLKVRGQRTRTTGRTGATIGVRRAK
UniProt
P39470
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Small ribosomal subunit protein uS14
Chain: S14P
Length: 52 amino acids
Theoretical weight: 6.19 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS14 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS14 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS14 in PDB entry 8hkx, assembly 1, top view.
1525101520253035404550
 
2040KYKPPAERRFGKGVQLCKRCGSRDSVIQKYGLYLCRQCFREVAYPMGFRKTR
UniProt
O05635
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Small ribosomal subunit protein eS17
Chain: S17E
Length: 62 amino acids
Theoretical weight: 7.34 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS17 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS17 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS17 in PDB entry 8hkx, assembly 1, top view.
16251015202530354045505560
 
204060GNVYTKDIKRVARELYDKFKDQASDKYDDNKKLVDEYVNVSSKKVKNRIAGYLTRYVKISKN
UniProt
Q4JAX5
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Small ribosomal subunit protein eS19
Chain: S19E
Length: 150 amino acids
Theoretical weight: 17.56 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS19 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS19 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS19 in PDB entry 8hkx, assembly 1, top view.
115020406080100120140
 
50100150TVQMVPADILIPKLAEYLKNNVKELNPPNWVYFAKTASFKERVPDDIENWWYIRAASLLRHLYIYKEPIGLQKTRKLYSGSKRRGTKPPRSVKAPTHSIRTILQQLEKAGLVTKTRRGRILSPKGRSLLDKLAYEMFKELAEKKQDLKKY
UniProt
Q4J8U1
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Small ribosomal subunit protein uS19
Chain: S19P
Length: 115 amino acids
Theoretical weight: 13.8 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein uS19 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 8hkx, assembly 1, top view.
1115102030405060708090100110
 
50100WKKFRYRGKSLEDLLNMPMDEFIKLLPSRQRRSLKRGFSDKQRRLLEKIRKISREGKQNKVIKTHVRNMVILPEMVGLRFAVYNGKEFVEFQVVPEMIGRYLGEYSITTKKVEHG
UniProt
Q4JB44
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Small ribosomal subunit protein eS28
Chain: S28E
Length: 63 amino acids
Theoretical weight: 7.09 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS28 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS28 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS28 in PDB entry 8hkx, assembly 1, top view.
16351015202530354045505560
 
204060GFPAEVIQILDRTGVTGEVTQVRVRVLEGRDKGRILTRNVKGPVRLGDILILRETEREARKLS
UniProt
Q4JAV1
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Large ribosomal subunit protein eL8
Chain: SL7A
Length: 123 amino acids
Theoretical weight: 13.35 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Large ribosomal subunit protein eL8 in PDB entry 8hkx, assembly 1, front view.
Large ribosomal subunit protein eL8 in PDB entry 8hkx, assembly 1, side view.
Large ribosomal subunit protein eL8 in PDB entry 8hkx, assembly 1, top view.
1123102030405060708090100110120
 
50100PSYVKFEVPQELADKVLEAVKKAKDSGKIKKGTNETTKAVERSQAKLVVIAEDVQPEEIVAHLPLLCEEKKIPYVYVPSKKSLGEACGLQVAAASVALMDPGEAKDLVDEIVKRVNEIKGKSS
UniProt
Q4J8P1
Chains
Sequence conservation
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Small ribosomal subunit protein eS31
Chain: S27A
Length: 54 amino acids
Theoretical weight: 6.26 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Small ribosomal subunit protein eS31 in PDB entry 8hkx, assembly 1, front view.
Small ribosomal subunit protein eS31 in PDB entry 8hkx, assembly 1, side view.
Small ribosomal subunit protein eS31 in PDB entry 8hkx, assembly 1, top view.
1545101520253035404550
 
2040QSKAVVRTYYEVEQDSIKLKNKKCPRCGSIMAHHMKPLERWACGKCGYTEFIGK
UniProt
Q4JAG0
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30S ribosomal protein
Chain: A
Length: 57 amino acids
Theoretical weight: 4.87 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
30S ribosomal protein in PDB entry 8hkx, assembly 1, front view.
30S ribosomal protein in PDB entry 8hkx, assembly 1, side view.
30S ribosomal protein in PDB entry 8hkx, assembly 1, top view.
157510152025303540455055
 
2040*********************************************************
Chains
Chain BA (auth A)
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RNA chain A16S
Name: 16s rRNA (1491-MER)
Representative chains: A16S
Source organism: Sulfolobus acidocaldarius DSM 639 [330779]
Length: 1501 nucleotides
Theoretical weight: 486.92 KDa
Rfam: Archaeal small subunit ribosomal RNA
16s rRNA (1491-MER) in PDB entry 8hkx, assembly 1, front view.
16s rRNA (1491-MER) in PDB entry 8hkx, assembly 1, side view.
16s rRNA (1491-MER) in PDB entry 8hkx, assembly 1, top view.
115012004006008001,0001,2001,400
 
50010001500
Chains
Chain A (auth A16S)
Rfam
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