7O5B: Signal recognition particle protein
Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound. Determined by electron microscopy at 3.33 Å resolution. Released 2 Feb 2022.
- Method
- Electron microscopy
- Resolution
- 3.33 Å
- Organism
- Bacillus subtilis subsp. subtilis str. 168
- Chains
- 56
- Atoms
- 150,422
- Mol. weight
- 2295.48 kDa
- Ligands
- G4P
- Released
- 2 Feb 2022
Explore 7O5B in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7O5B contains 226 α-helices and 302 β-strands across 50 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 0: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-17 | 8 | |
| α-helix | 23-25 | 3 | |
| β-strand | 27-29 | 3 | 14 |
| β-strand | 36-38 | 3 | 14 |
| β-strand | 48 | 1 | 15 |
| β-strand | 53 | 1 | 15 |
Chain 1: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 18 |
| β-strand | 7-9 | 3 | 19 |
| β-strand | 18-22 | 5 | 18 |
| β-strand | 31-36 | 6 | 19 |
| β-strand | 41-47 | 7 | 19 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-23 | 6 | |
| α-helix | 25-36 | 12 | |
Chain 3: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 8-13 | 6 | |
| β-strand | 15-16 | 2 | 22 |
| α-helix | 18-20 | 3 | |
| β-strand | 22-25 | 4 | 22 |
| α-helix | 38-44 | 7 | |
| β-strand | 47-49 | 3 | 22 |
| α-helix | 52-58 | 7 | |
| α-helix | 60-62 | 3 | |
Chain 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 23 |
| β-strand | 15-19 | 5 | 23 |
| β-strand | 22-26 | 5 | 23 |
| α-helix | 30-32 | 3 | |
| β-strand | 35 | 1 | 23 |
Chain 6: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-16 | 7 | 31 |
| β-strand | 21-26 | 6 | 31 |
| β-strand | 30-33 | 4 | 31 |
| α-helix | 49-53 | 5 | |
Chain a: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 32 |
| β-strand | 22-29 | 8 | 32 |
| α-helix | 31-32 | 2 | |
| β-strand | 33-39 | 7 | 33 |
| β-strand | 48-53 | 6 | 33 |
| α-helix | 63-69 | 7 | |
| β-strand | 79-84 | 6 | 33 |
| β-strand | 96-97 | 2 | 33 |
| α-helix | 99-101 | 3 | |
| β-strand | 107-113 | 7 | 32 |
| β-strand | 116-120 | 5 | 34 |
| α-helix | 122-126 | 5 | |
| α-helix | 154-155 | 2 | |
| β-strand | 162-165 | 4 | 34 |
| β-strand | 168-180 | 13 | 32 |
| β-strand | 185-189 | 5 | 32 |
| β-strand | 199-204 | 6 | 32 |
Chain b: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 35 |
| β-strand | 6-7 | 2 | 36 |
| β-strand | 13 | 1 | 36 |
| β-strand | 17-18 | 2 | 35 |
| α-helix | 27-28 | 2 | |
| α-helix | 30-44 | 15 | |
| α-helix | 54-56 | 3 | |
| α-helix | 103-119 | 17 | |
| β-strand | 123-126 | 4 | 36 |
| α-helix | 137-145 | 9 | |
| β-strand | 152-155 | 4 | 36 |
| α-helix | 161-165 | 5 | |
| β-strand | 173-176 | 4 | 36 |
| α-helix | 184-188 | 5 | |
| β-strand | 192-194 | 3 | 36 |
| α-helix | 196-205 | 10 | |
42 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 |
|---|
| tRNA | U | RNA | 77 | Bacillus subtilis subsp. subtilis str. 168 | |
| mRNA | V | RNA | 8 | Bacillus subtilis subsp. subtilis str. 168 | |
| Srp RNA (266-mer) | W | RNA | 266 | Bacillus subtilis subsp. subtilis str. 168 | |
| Signal recognition particle protein | g | protein | 447 | Bacillus subtilis subsp. subtilis str. 168 | P37105 (AlphaFold model) |
| MifM-stalling construct | h | protein | 96 | Bacillus subtilis subsp. subtilis str. 168 | |
| 50S ribosomal protein L10 | p | protein | 166 | Bacillus subtilis subsp. subtilis str. 168 | P42923 (AlphaFold model) |
| 50S ribosomal protein L11 | q | protein | 141 | Bacillus subtilis subsp. subtilis str. 168 | Q06796 (AlphaFold model) |
| 23S rRNA (2887-mer) | X | RNA | 2887 | Bacillus subtilis subsp. subtilis str. 168 | |
| 5S rRNA (112-mer) | Y | RNA | 112 | Bacillus subtilis subsp. subtilis str. 168 | |
| 50S ribosomal protein L2 | Z | protein | 277 | Bacillus subtilis subsp. subtilis str. 168 | P42919 (AlphaFold model) |
| 50S ribosomal protein L3 | a | protein | 208 | Bacillus subtilis subsp. subtilis str. 168 | P42920 |
| 50S ribosomal protein L4 | b | protein | 207 | Bacillus subtilis subsp. subtilis str. 168 | P42921 |
44 more molecules are not listed.
Sequence of entity 1 (U), FASTA
>7O5B_1 tRNA (chains U)
GGUCCGGUAGUUCAGUUGGUUAGAAUGCCUGCCUGUCACGCAGGAGGUCGCGGGUUCGAG
UCCCGUCCGGACCGCCA
Sequence of entity 2 (V), FASTA
>7O5B_2 mRNA (chains V)
AGGAAGAC
Sequence of entity 3 (W), FASTA
>7O5B_3 SRP RNA (266-MER) (chains W)
GCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGA
AUCCCUUCUCGAGGUUCGUUUACUUUAAGGCCUGCCUUAAGUAAGUGGUGUUGACGUUUG
GGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUG
AAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGCUAACUGCUUAAGUAACGCUAGGG
UAGCGAAUCGACAGAAGGUGCACGGU
Sequence of entity 4 (g), FASTA
>7O5B_4 Signal recognition particle protein (chains g)
HMGFEGLADRLQQTISKIRGKGKVSEQDVKEMMREVRLALLEADVNFKVVKDFVKKVSER
AVGQDVMKSLTPGQQVIKVVQEELTELMGGEESKIAVAKRPPTVIMMVGLQGAGKTTTSG
KLANLLRKKHNRKPMLVAADIYRPAAIKQLETLGKQLDMPVFSLGDQVSPVEIAKQAIEK
AKEEHYDYVILDTAGRLHIDHELMDELTNVKEIANPEEIFLVVDSMTGQDAVNVAKSFNE
QLGLTGVVLTKLDGDTRGGAALSIRAVTNTPIKFAGLGEKLDALEPFHPERMASRILGMG
DVLTLIEKAQASVDEDKAKELEQKMRTMSFTLDDFLEQLGQVRNMGPLDELLQMMPGAGK
MKGLKNIQVDEKQLNHVEAIIKSMTVLEKEQPDIINASRRKRIAKGSGTSVQEVNRLLKQ
FDEMKKMMKQMTNMSKGKKKGFKLPFM
Sequence of entity 5 (h), FASTA
>7O5B_5 MifM-stalling construct (chains h)
GPGTMFVESINDVLFLVDFFTIILPALTAIGIAFLLRECRAGEQWKSKRTDGPGKPIPNP
LLGLDSTDFLIIIYHRITTWIRKVFRMNSPVNDEED
Sequence of entity 6 (p), FASTA
>7O5B_6 50S ribosomal protein L10 (chains p)
MSSAIETKKVVVEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVEFKVYKNTMT
RRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVSTV
EEVKALAELPSREGLLSMLLSVLQAPVRNLALATKAVAEQKEEQGA
Sequence of entity 7 (q), FASTA
>7O5B_7 50S ribosomal protein L11 (chains q)
MAKKVVKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTADQAGLIIPVEISV
YEDRSFTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATVKRDKVREIAETKMPDLNAAD
VEAAMRMVEGTARSMGIVIED
Sequence of entity 8 (X), FASTA
>7O5B_8 23S rRNA (2887-MER) (chains X)
GUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGGA
CGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUGG
GGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAGG
CAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCCC
UGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUGU
AGGACACUCGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCCGCCAUAGGAGGUAACAGC
CCUGUAGUCAAAACUUCGUUCGAGUGGAUCCUGAGUACGGCGGAACACGUGAAAUUCCGU
CGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUACUCCCUAGUGACCGAUAGUGAACCA
GUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAGAGAUCCUGAAACCG
UGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGAUGGCGUGCCUUUUGUAGAAUGAAC
CGGCGAGUUACGAUCUCGUGCAAGGUUAAGCAGAAGAUGCGGAGCCGCAGCGAAAGCGAG
UCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCCGAAACCAGGUGAUCUACCCAUGUC
CAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCGAACCCACGCACGUUGAAAAGUGCG
GGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCC
GAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCUUGGAGGUAGAGCACUGAUUGGACU
AGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACUCCGAAUGCCAAUGACUUAUCCUUG
GGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAAAGGGAAACAGCCCAGACCGCCAGC
UAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUGUGGAGUUGCUUAGACAACCAGGAU
GUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACUC
UGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCGAAGCUGCGGACUGUUCGAACAGUG
GUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGACCGGAAGGACUGGUGGAGCGCUUAGAA
GUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGGUGAGAAUCCCCUCCACCGAAUGCCUAA
GGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUUAGUCGGGACCUAAGCCGAGGCCGAAAG
GCGUAGGCGAUGGACAACAGGUUGAUAUUCCUGUACCACCUCCUCACCAUUUGAGCAAUG
GGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAUUGGAUAUCCGCGUCCAAGCAGUUAGGC
UGGGAAAUAGGCAAAUCCGUUUCCCAAAGGCUGAGCUGUGAUGGCGAGCGCGAAGUUCCU
GAUUCCACACUGCCAAGAAAAGCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGA
CACAGGUAGGCGAGGAGAGAAUCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGG
CAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAG
CCGCAGUGAAUAGGCCCAGGCGACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAA
GGCGAAGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGU
AAGCGAAGGUGCGAAUUGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGG
UAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCAC
UGUCUCAACGAGAGACUCGGUGAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGAC
AGGACGGAAAGACCCCGUGGAGCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUG
UACAGGAUAGGUAGGAGCCUUGGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGG
AUACUACCCUGGCUGUAUUGACCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUG
UCAGGUGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGG
UUCCCUCAGAAUGGUUGGAAAUCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGC
GAGACCUACAAGUCGAGCAGGGACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGG
AAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAG
AGUCCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGU
AGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAA
CGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUC
CUUAGUACGAGAGGACCGGGAUGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGC
AUCGCUGGGUAGCUAUGUGCGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCC
CCUCAAGAUGAGAUUUCCCAUUCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUG
AUAGGUCUGAGGUGGAAGUGUGGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGA
CUUAACC
Sequence of entity 9 (Y), FASTA
>7O5B_9 5S rRNA (112-MER) (chains Y)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA
Sequence of entity 10 (Z), FASTA
>7O5B_10 50S ribosomal protein L2 (chains Z)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 11 (a), FASTA
>7O5B_11 50S ribosomal protein L3 (chains a)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKS
Sequence of entity 12 (b), FASTA
>7O5B_12 50S ribosomal protein L4 (chains b)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| G4P | Guanosine-5',3'-tetraphosphate | C10 H17 N5 O17 P4 | 1 |
Primary citation
Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Czech, L., Mais, C.N., Kratzat, H. et al. Nat Commun (2022) 13:1069-1069. DOI 10.1038/s41467-022-28675-0 · PubMed
Other PDB entries of the same protein (UniProt P37105 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7O9F 2.51 Å, Bacillus subtilis Ffh in complex with ppGpp
- 4UE4 7.0 Å, Structural basis for targeting and elongation arrest of Bacillus signal recognition…
Browse structure collections
About this viewer
MolViewer shows 7O5B 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.