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- PDB-5fdv: Crystal structure of the Pyrrhocoricin antimicrobial peptide boun... -

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Basic information

Entry
Database: PDB / ID: 5fdv
TitleCrystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus thermophilus 70S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Pyrrhocoricin
  • Ribosome-associated inhibitor A
KeywordsRIBOSOME / bacterial ribosome / proline-rich antimicrobial peptide / antibiotics / protein biosynthesis
Function / homology
Function and homology information


dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / defense response to bacterium / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / innate immune response / mRNA binding / extracellular region / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal ...: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein
Similarity search - Domain/homology
ADENOSINE-5'-MONOPHOSPHATE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...ADENOSINE-5'-MONOPHOSPHATE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Ribosome-associated inhibitor A / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Pyrrhocoricin / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Escherichia coli K-12 (bacteria)
Pyrrhocoris apterus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / Wilson, D.N. / Innis, C.A.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
Authors: Seefeldt, A.C. / Graf, M. / Perebaskine, N. / Nguyen, F. / Arenz, S. / Mardirossian, M. / Scocchi, M. / Wilson, D.N. / Innis, C.A.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Structure summary
Revision 1.3Mar 30, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order
Revision 1.6Mar 12, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: 23S ribosomal RNA
1B: 5S ribosomal RNA
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1I: 50S ribosomal protein L9
1N: 50S ribosomal protein L13
1O: 50S ribosomal protein L14
1P: 50S ribosomal protein L15
1Q: 50S ribosomal protein L16
1R: 50S ribosomal protein L17
1S: 50S ribosomal protein L18
1T: 50S ribosomal protein L19
1U: 50S ribosomal protein L20
1V: 50S ribosomal protein L21
1W: 50S ribosomal protein L22
1X: 50S ribosomal protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S ribosomal protein L35
19: 50S ribosomal protein L36
1a: 16S ribosomal RNA
2x: Ribosome-associated inhibitor A
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1x: Ribosome-associated inhibitor A
1y: Pyrrhocoricin
2A: 23S ribosomal RNA
2B: 5S ribosomal RNA
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2I: 50S ribosomal protein L9
2N: 50S ribosomal protein L13
2O: 50S ribosomal protein L14
2P: 50S ribosomal protein L15
2Q: 50S ribosomal protein L16
2R: 50S ribosomal protein L17
2S: 50S ribosomal protein L18
2T: 50S ribosomal protein L19
2U: 50S ribosomal protein L20
2V: 50S ribosomal protein L21
2W: 50S ribosomal protein L22
2X: 50S ribosomal protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S ribosomal protein L35
29: 50S ribosomal protein L36
2a: 16S ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2y: Pyrrhocoricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,369,0592543
Polymers4,308,405108
Non-polymers60,6542435
Water81,8964546
1
1A: 23S ribosomal RNA
1B: 5S ribosomal RNA
1D: 50S ribosomal protein L2
1E: 50S ribosomal protein L3
1F: 50S ribosomal protein L4
1G: 50S ribosomal protein L5
1H: 50S ribosomal protein L6
1I: 50S ribosomal protein L9
1N: 50S ribosomal protein L13
1O: 50S ribosomal protein L14
1P: 50S ribosomal protein L15
1Q: 50S ribosomal protein L16
1R: 50S ribosomal protein L17
1S: 50S ribosomal protein L18
1T: 50S ribosomal protein L19
1U: 50S ribosomal protein L20
1V: 50S ribosomal protein L21
1W: 50S ribosomal protein L22
1X: 50S ribosomal protein L23
1Y: 50S ribosomal protein L24
1Z: 50S ribosomal protein L25
10: 50S ribosomal protein L27
11: 50S ribosomal protein L28
12: 50S ribosomal protein L29
13: 50S ribosomal protein L30
14: 50S ribosomal protein L31
15: 50S ribosomal protein L32
16: 50S ribosomal protein L33
17: 50S ribosomal protein L34
18: 50S ribosomal protein L35
19: 50S ribosomal protein L36
1a: 16S ribosomal RNA
1b: 30S ribosomal protein S2
1c: 30S ribosomal protein S3
1d: 30S ribosomal protein S4
1e: 30S ribosomal protein S5
1f: 30S ribosomal protein S6
1g: 30S ribosomal protein S7
1h: 30S ribosomal protein S8
1i: 30S ribosomal protein S9
1j: 30S ribosomal protein S10
1k: 30S ribosomal protein S11
1l: 30S ribosomal protein S12
1m: 30S ribosomal protein S13
1n: 30S ribosomal protein S14 type Z
1o: 30S ribosomal protein S15
1p: 30S ribosomal protein S16
1q: 30S ribosomal protein S17
1r: 30S ribosomal protein S18
1s: 30S ribosomal protein S19
1t: 30S ribosomal protein S20
1u: 30S ribosomal protein Thx
1x: Ribosome-associated inhibitor A
1y: Pyrrhocoricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,186,3491353
Polymers2,154,20354
Non-polymers32,1461299
Water68538
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
2x: Ribosome-associated inhibitor A
2A: 23S ribosomal RNA
2B: 5S ribosomal RNA
2D: 50S ribosomal protein L2
2E: 50S ribosomal protein L3
2F: 50S ribosomal protein L4
2G: 50S ribosomal protein L5
2H: 50S ribosomal protein L6
2I: 50S ribosomal protein L9
2N: 50S ribosomal protein L13
2O: 50S ribosomal protein L14
2P: 50S ribosomal protein L15
2Q: 50S ribosomal protein L16
2R: 50S ribosomal protein L17
2S: 50S ribosomal protein L18
2T: 50S ribosomal protein L19
2U: 50S ribosomal protein L20
2V: 50S ribosomal protein L21
2W: 50S ribosomal protein L22
2X: 50S ribosomal protein L23
2Y: 50S ribosomal protein L24
2Z: 50S ribosomal protein L25
20: 50S ribosomal protein L27
21: 50S ribosomal protein L28
22: 50S ribosomal protein L29
23: 50S ribosomal protein L30
24: 50S ribosomal protein L31
25: 50S ribosomal protein L32
26: 50S ribosomal protein L33
27: 50S ribosomal protein L34
28: 50S ribosomal protein L35
29: 50S ribosomal protein L36
2a: 16S ribosomal RNA
2b: 30S ribosomal protein S2
2c: 30S ribosomal protein S3
2d: 30S ribosomal protein S4
2e: 30S ribosomal protein S5
2f: 30S ribosomal protein S6
2g: 30S ribosomal protein S7
2h: 30S ribosomal protein S8
2i: 30S ribosomal protein S9
2j: 30S ribosomal protein S10
2k: 30S ribosomal protein S11
2l: 30S ribosomal protein S12
2m: 30S ribosomal protein S13
2n: 30S ribosomal protein S14 type Z
2o: 30S ribosomal protein S15
2p: 30S ribosomal protein S16
2q: 30S ribosomal protein S17
2r: 30S ribosomal protein S18
2s: 30S ribosomal protein S19
2t: 30S ribosomal protein S20
2u: 30S ribosomal protein Thx
2y: Pyrrhocoricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,182,7101190
Polymers2,154,20354
Non-polymers28,5071136
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)209.940, 450.100, 622.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 3 types, 6 molecules 1A2A1B2B1a2a

#1: RNA chain 23S ribosomal RNA


Mass: 948007.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#2: RNA chain 5S ribosomal RNA


Mass: 38882.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#32: RNA chain 16S ribosomal RNA


Mass: 493863.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382

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50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...

#3: Protein 50S ribosomal protein L2


Mass: 30401.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60405
#4: Protein 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN8
#5: Protein 50S ribosomal protein L4 / L1e


Mass: 22512.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN9
#6: Protein 50S ribosomal protein L5


Mass: 20930.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ0
#7: Protein 50S ribosomal protein L6


Mass: 18980.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#8: Protein 50S ribosomal protein L9


Mass: 16293.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ1
#9: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60488
#10: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP8
#11: Protein 50S ribosomal protein L15


Mass: 16248.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ7
#12: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60489
#13: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q9Z9H5
#14: Protein 50S ribosomal protein L18 / TL24


Mass: 12437.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ4
#15: Protein 50S ribosomal protein L19


Mass: 15503.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60490
#16: Protein 50S ribosomal protein L20


Mass: 13591.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60491
#17: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60492
#18: Protein 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP3
#19: Protein 50S ribosomal protein L23


Mass: 10646.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP0
#20: Protein 50S ribosomal protein L24


Mass: 11726.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP9
#21: Protein 50S ribosomal protein L25 / TL5


Mass: 22851.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHZ1
#22: Protein 50S ribosomal protein L27


Mass: 8689.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60493
#23: Protein 50S ribosomal protein L28


Mass: 10872.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60494
#24: Protein 50S ribosomal protein L29


Mass: 8485.077 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP6
#25: Protein 50S ribosomal protein L30


Mass: 6667.931 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ6
#26: Protein 50S ribosomal protein L31


Mass: 8086.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJE1
#27: Protein 50S ribosomal protein L32


Mass: 6590.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80339
#28: Protein 50S ribosomal protein L33


Mass: 6501.700 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P35871
#29: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80340
#30: Protein 50S ribosomal protein L35


Mass: 7374.981 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SKU1
#31: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHR2

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30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...

#34: Protein 30S ribosomal protein S2


Mass: 26646.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371
#35: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372
#36: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373
#37: Protein 30S ribosomal protein S5


Mass: 16144.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5
#38: Protein 30S ribosomal protein S6 / TS9


Mass: 11917.675 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP8
#39: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P17291
#40: Protein 30S ribosomal protein S8


Mass: 15737.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#41: Protein 30S ribosomal protein S9


Mass: 14279.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374
#42: Protein 30S ribosomal protein S10


Mass: 11169.997 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7
#43: Protein 30S ribosomal protein S11


Mass: 12032.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376
#44: Protein 30S ribosomal protein S12


Mass: 13650.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3
#45: Protein 30S ribosomal protein S13


Mass: 13237.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377
#46: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#47: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76
#48: Protein 30S ribosomal protein S16


Mass: 9795.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3
#49: Protein 30S ribosomal protein S17


Mass: 11722.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#50: Protein 30S ribosomal protein S18


Mass: 7897.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0
#51: Protein 30S ribosomal protein S19


Mass: 9455.995 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2
#52: Protein 30S ribosomal protein S20


Mass: 10876.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380
#53: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 2831.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpsU, TTHA1396 / Plasmid: pGS21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SIH3

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Protein / Protein/peptide , 2 types, 4 molecules 2x1x1y2y

#33: Protein Ribosome-associated inhibitor A / Protein Y / SpotY / pY


Mass: 10964.620 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AD49
#54: Protein/peptide Pyrrhocoricin


Mass: 1796.098 Da / Num. of mol.: 2 / Fragment: UNP residues 1-16 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Pyrrhocoris apterus (insect) / References: UniProt: P37362

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Non-polymers , 5 types, 6981 molecules

#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2420 / Source method: obtained synthetically / Formula: Mg
#56: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#57: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#58: Chemical ChemComp-A / ADENOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#59: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4546 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Tris-HCl, PEG 20000, MPD, Arginine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 1428776 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 64.57 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.178 / Χ2: 0.967 / Net I/σ(I): 15.99 / Num. measured all: 19712065
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.870.4112.211.2914060771052321052222.297100
2.87-2.950.5991.5861.8714545051024951024861.645100
2.95-3.040.7551.132.7140188699730997251.172100
3.04-3.130.8660.7963.87134077096954969530.827100
3.13-3.230.9220.5875.19124346493958939540.61100
3.23-3.350.9550.4566.89127747690881908790.473100
3.35-3.470.970.3748.29121347087760877590.388100
3.47-3.610.9790.3059.98114091084529845270.317100
3.61-3.780.9880.23713.03115518781106811060.245100
3.78-3.960.9920.18816108821377559775590.195100
3.96-4.170.9940.15418.6698760673821738210.16100
4.17-4.430.9960.12622.898947969872698720.13100
4.43-4.730.9970.10426.1889556665757657570.108100
4.73-5.110.9980.0930.1486889861300613000.093100
5.11-5.60.9980.07833.7679303856402564020.081100
5.6-6.260.9980.07334.6968685951214512130.075100
6.26-7.230.9990.06438.6461971845305453050.066100
7.23-8.850.9990.0547.7653256638382383820.052100
8.85-12.520.9990.03660.5539870029977299770.038100
12.520.9990.02576.4421767716927165770.02697.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y4O

4y4o


Resolution: 2.8→49.812 Å / FOM work R set: 0.8317 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 70495 4.93 %
Rwork0.1885 1358125 -
obs0.191 1428620 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.28 Å2 / Biso mean: 60.09 Å2 / Biso min: 8.77 Å2
Refinement stepCycle: final / Resolution: 2.8→49.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms93252 193336 6980 15 293583
Biso mean--55.09 37.34 -
Num. residues----20846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.029324631
X-RAY DIFFRACTIONf_angle_d1.942472068
X-RAY DIFFRACTIONf_chiral_restr0.08358935
X-RAY DIFFRACTIONf_plane_restr0.0125484
X-RAY DIFFRACTIONf_dihedral_angle_d15.503144386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.83180.38323650.32744493147296
2.8318-2.86510.365223690.31064502547394
2.8651-2.90010.342223660.28884494847314
2.9001-2.93680.337823660.27794494147307
2.9368-2.97540.332723710.27164505847429
2.9754-3.01620.32423700.26214503047400
3.0162-3.05920.308823700.24654503047400
3.0592-3.10490.281619240.22354548047404
3.1049-3.15340.281723090.21624507547384
3.1534-3.20510.274923510.21394509347444
3.2051-3.26040.269123560.20814507147427
3.2604-3.31960.257423630.1964511947482
3.3196-3.38350.2523860.19214511347499
3.3835-3.45250.256423480.19444507547423
3.4525-3.52760.251123570.19294516947526
3.5276-3.60960.249123430.19114514347486
3.6096-3.69980.247423510.18584517147522
3.6998-3.79980.231923660.17864519047556
3.7998-3.91160.226423540.17394524147595
3.9116-4.03780.228623590.17734528847647
4.0378-4.18210.228723770.17634513747514
4.1821-4.34940.224523390.1734529147630
4.3494-4.54720.220523890.17254535147740
4.5472-4.78680.220723640.16784535747721
4.7868-5.08640.220223500.16574539847748
5.0864-5.47870.206623820.15694545047832
5.4787-6.02920.207923790.15844558047959
6.0292-6.89970.214323930.16184570548098
6.8997-8.68540.212223730.16714593448307
8.6854-49.81990.220824050.19824673149136

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