5CZP: 70S termination complex containing E. coli RF2
70S termination complex containing E. coli RF2. Determined by X-ray diffraction at 3.3 Å resolution. Released 12 Oct 2016.
- Method
- X-ray diffraction
- Resolution
- 3.3 Å
- Organisms
- Thermus thermophilus HB8, Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Escherichia coli str. K-12 substr. MG1655
- Chains
- 110
- Atoms
- 296,497
- Mol. weight
- 4552.32 kDa
- Ligands
- MG, ZN, SF4
- Released
- 12 Oct 2016
Explore 5CZP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5CZP contains 549 α-helices and 673 β-strands across 100 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 QB: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-31 | 6 | |
| β-strand | 32-35 | 4 | 7 |
| β-strand | 40-42 | 3 | 7 |
| α-helix | 44-62 | 19 | |
| β-strand | 68-71 | 4 | 8 |
| α-helix | 78-87 | 10 | |
| β-strand | 92-93 | 2 | 8 |
| α-helix | 105-121 | 17 | |
| α-helix | 132-149 | 18 | |
| α-helix | 152-154 | 3 | |
| β-strand | 161-164 | 4 | 8 |
| α-helix | 171-179 | 9 | |
| β-strand | 184-188 | 5 | 8 |
| α-helix | 194-196 | 3 | |
| β-strand | 199-202 | 4 | 8 |
| α-helix | 208-225 | 18 | |
Chain QC: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12 | 1 | 24 |
| β-strand | 16 | 1 | 24 |
| β-strand | 20-21 | 2 | 25 |
| α-helix | 29-46 | 18 | |
| α-helix | 48-50 | 3 | |
| β-strand | 52-59 | 8 | 25 |
| β-strand | 63-70 | 8 | 25 |
| α-helix | 73-77 | 5 | |
| α-helix | 82-95 | 14 | |
| β-strand | 98-105 | 8 | 25 |
| α-helix | 109-111 | 3 | |
| α-helix | 113-125 | 13 | |
| α-helix | 130-143 | 14 | |
| β-strand | 148-155 | 8 | 26 |
| α-helix | 157-159 | 3 | |
| β-strand | 164-171 | 8 | 26 |
| β-strand | 180-190 | 11 | 26 |
| β-strand | 195-206 | 12 | 26 |
Chain QD: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| α-helix | 24-27 | 4 | |
| α-helix | 32-35 | 4 | |
| α-helix | 47-52 | 6 | |
| α-helix | 53-68 | 16 | |
| α-helix | 72-84 | 13 | |
| α-helix | 89-98 | 10 | |
| β-strand | 100 | 1 | 38 |
| α-helix | 101-107 | 7 | |
| α-helix | 114-122 | 9 | |
| β-strand | 126-128 | 3 | 39 |
| β-strand | 131-132 | 2 | 39 |
| β-strand | 139 | 1 | 38 |
| β-strand | 144-148 | 5 | 39 |
| α-helix | 156-163 | 8 | |
| β-strand | 174-177 | 4 | 39 |
| β-strand | 182-185 | 4 | 39 |
| α-helix | 188-190 | 3 | |
| α-helix | 201-206 | 6 | |
Chains QE and XE: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-20 | 14 | 45 |
| β-strand | 23-35 | 13 | 45 |
| β-strand | 40-48 | 9 | 45 |
| α-helix | 51-64 | 14 | |
| β-strand | 66-68 | 3 | 45 |
| β-strand | 72 | 1 | 46 |
| β-strand | 75 | 1 | 46 |
| β-strand | 80-84 | 5 | 47 |
| β-strand | 87-93 | 7 | 47 |
| β-strand | 100-101 | 2 | 47 |
| α-helix | 104-111 | 8 | |
| β-strand | 118-124 | 7 | 47 |
| α-helix | 128-139 | 12 | |
| α-helix | 145-151 | 7 | |
Chain QF: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-10 | 9 | 58 |
| α-helix | 16-32 | 17 | |
| β-strand | 36-40 | 5 | 58 |
| β-strand | 44-52 | 9 | 58 |
| β-strand | 55-67 | 13 | 58 |
| α-helix | 69-71 | 3 | |
| α-helix | 72-80 | 9 | |
| β-strand | 85-92 | 8 | 58 |
| β-strand | 98-99 | 2 | 59 |
Chain QG: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-15 | 9 | |
| α-helix | 21-30 | 10 | |
| α-helix | 36-53 | 18 | |
| α-helix | 58-69 | 12 | |
| β-strand | 73-80 | 8 | 68 |
| β-strand | 83-90 | 8 | 68 |
| α-helix | 91-92 | 2 | |
| α-helix | 93-108 | 16 | |
| α-helix | 116-129 | 14 | |
| α-helix | 132-147 | 16 | |
| α-helix | 149-154 | 6 | |
Chain QH: 6 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-18 | 14 | |
| β-strand | 23-27 | 5 | 81 |
| α-helix | 30-41 | 12 | |
| β-strand | 47-53 | 7 | 81 |
| β-strand | 56-62 | 7 | 81 |
| β-strand | 65 | 1 | 82 |
| α-helix | 75-77 | 3 | |
| β-strand | 78 | 1 | 82 |
| β-strand | 83-85 | 3 | 83 |
| β-strand | 94-95 | 2 | 83 |
| α-helix | 97-99 | 3 | |
| α-helix | 103-106 | 4 | |
| β-strand | 109-114 | 6 | 83 |
| β-strand | 117-120 | 4 | 83 |
| α-helix | 121-127 | 7 | |
| β-strand | 131-137 | 7 | 83 |
Chain QI: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-10 | 7 | 90 |
| β-strand | 13-21 | 9 | 90 |
| β-strand | 26-28 | 3 | 90 |
| β-strand | 31-32 | 2 | 90 |
| α-helix | 33-36 | 4 | |
| α-helix | 43-45 | 3 | |
| α-helix | 48-52 | 5 | |
| β-strand | 59-66 | 8 | 90 |
| α-helix | 70-88 | 19 | |
| α-helix | 90-92 | 3 | |
| α-helix | 109-113 | 5 | |
| α-helix | 122-124 | 3 | |
77 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 |
|---|
| 23S rRNA | RA, YA | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S rRNA | RB, YB | RNA | 122 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L2 | RD, YD | protein | 276 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | RE, YE | protein | 206 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | RF, YF | protein | 210 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | RG, YG | protein | 182 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ0 (AlphaFold model) |
| 50S ribosomal protein L6 | RH, YH | protein | 180 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P0DOY8 |
| 50S ribosomal protein L9 | RI, YI | protein | 148 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SLQ1 |
| 50S ribosomal protein L13 | RN, YN | protein | 140 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60488 |
| 50S ribosomal protein L14 | RO, YO | protein | 122 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHP8 |
| 50S ribosomal protein L15 | RP, YP | protein | 150 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ7 |
| 50S ribosomal protein L16 | RQ, YQ | protein | 141 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60489 |
43 more molecules are not listed.
Sequence of entity 1 (RA, YA), FASTA
>5CZP_1 23S rRNA (chains RA, YA)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC
Sequence of entity 2 (RB, YB), FASTA
>5CZP_2 5S rRNA (chains RB, YB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
UU
Sequence of entity 3 (RD, YD), FASTA
>5CZP_3 50S ribosomal protein L2 (chains RD, YD)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 4 (RE, YE), FASTA
>5CZP_4 50S ribosomal protein L3 (chains RE, YE)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 5 (RF, YF), FASTA
>5CZP_5 50S ribosomal protein L4 (chains RF, YF)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 6 (RG, YG), FASTA
>5CZP_6 50S ribosomal protein L5 (chains RG, YG)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 7 (RH, YH), FASTA
>5CZP_7 50S ribosomal protein L6 (chains RH, YH)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 8 (RI, YI), FASTA
>5CZP_8 50S ribosomal protein L9 (chains RI, YI)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 9 (RN, YN), FASTA
>5CZP_9 50S ribosomal protein L13 (chains RN, YN)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 10 (RO, YO), FASTA
>5CZP_10 50S ribosomal protein L14 (chains RO, YO)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Sequence of entity 11 (RP, YP), FASTA
>5CZP_11 50S ribosomal protein L15 (chains RP, YP)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA
Sequence of entity 12 (RQ, YQ), FASTA
>5CZP_12 50S ribosomal protein L16 (chains RQ, YQ)
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAARVAMVRHFRR
GGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRI
AGHKLPIKTKIVRRDAYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2520 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
Primary citation
Uniformity of Peptide Release Is Maintained by Methylation of Release Factors. Pierson, W.E., Hoffer, E.D., Keedy, H.E. et al. Cell Rep (2016) 17:11-18. DOI 10.1016/j.celrep.2016.08.085 · PubMed
Other PDB entries of the same protein (UniProt P60405 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
- 8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
- 8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
- 6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
- 7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
Browse structure collections
About this viewer
MolViewer shows 5CZP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.