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- PDB-5aa0: Complex of Thermous thermophilus ribosome (A-and P-site tRNA) bou... -

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Basic information

Entry
Database: PDB / ID: 5aa0
TitleComplex of Thermous thermophilus ribosome (A-and P-site tRNA) bound to BipA-GDPCP
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • GTP-binding protein
  • Unknown peptide
  • tRNA chain 1
  • tRNA chain 2
KeywordsRIBOSOME / BIPA / TRANSLATIONAL GTPASE FACTORS / PROTEIN / X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY
Function / homology
Function and homology information


guanosine tetraphosphate binding / protein folding chaperone / response to cold / large ribosomal subunit / regulation of translation / ribosome binding / transferase activity / response to heat / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...guanosine tetraphosphate binding / protein folding chaperone / response to cold / large ribosomal subunit / regulation of translation / ribosome binding / transferase activity / response to heat / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / : / : / : / : / TypA/BipA C-terminal domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / : / : / : / : / TypA/BipA C-terminal domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L1, bacterial-type / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Elongation factor Tu domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / 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
Similarity search - Domain/homology
Chem-8AN / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / NEOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...Chem-8AN / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / NEOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Large ribosomal subunit assembly factor BipA / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / 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 uL11 / 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 / 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 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsKumar, V. / Chen, Y. / Ahmed, T. / Tan, J. / Ero, R. / Bhushan, S. / Gao, Y.-G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structure of BipA in GTP form bound to the ratcheted ribosome.
Authors: Veerendra Kumar / Yun Chen / Rya Ero / Tofayel Ahmed / Jackie Tan / Zhe Li / Andrew See Weng Wong / Shashi Bhushan / Yong-Gui Gao /
Abstract: BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly ...BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Other
Revision 1.2Feb 3, 2016Group: Database references / Other
Revision 1.3Aug 30, 2017Group: Advisory / Data collection / Structure summary
Category: em_imaging / pdbx_validate_polymer_linkage / struct_keywords
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _struct_keywords.text
Revision 1.4Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / em_software / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _em_software.name
Revision 1.5Oct 3, 2018Group: Data collection / Derived calculations
Category: em_software / ndb_struct_na_base_pair ...em_software / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _em_software.image_processing_id
Revision 1.6Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Revision 1.7Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.8Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

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Assembly

Deposited unit
AA: 23S ribosomal RNA
AB: 5S ribosomal RNA
AC: 50S ribosomal protein L1
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AK: 50S ribosomal protein L13
AL: 50S ribosomal protein L14
AM: 50S ribosomal protein L15
AN: 50S ribosomal protein L16
AO: 50S ribosomal protein L17
AP: 50S ribosomal protein L18
AQ: 50S ribosomal protein L19
AR: 50S ribosomal protein L20
AS: 50S ribosomal protein L21
AT: 50S ribosomal protein L22
AU: 50S ribosomal protein L23
AV: 50S ribosomal protein L24
AW: 50S ribosomal protein L25
AX: 50S ribosomal protein L27
AY: 50S ribosomal protein L29
AZ: 50S ribosomal protein L30
Aa: 50S ribosomal protein L31
Ab: 50S ribosomal protein L32
Ac: 50S ribosomal protein L33
Ad: 50S ribosomal protein L34
Ae: 50S ribosomal protein L35
Af: 50S ribosomal protein L36
AI: 50S ribosomal protein L10
AJ: 50S ribosomal protein L11
Ag: Unknown peptide
BA: 16S ribosomal RNA
BF: 30S ribosomal protein S2
BG: 30S ribosomal protein S3
BH: 30S ribosomal protein S4
BI: 30S ribosomal protein S5
BJ: 30S ribosomal protein S6
BK: 30S ribosomal protein S7
BL: 30S ribosomal protein S8
BM: 30S ribosomal protein S9
BN: 30S ribosomal protein S10
BO: 30S ribosomal protein S11
BP: 30S ribosomal protein S12
BQ: 30S ribosomal protein S13
BR: 30S ribosomal protein S14 type Z
BS: 30S ribosomal protein S15
BT: 30S ribosomal protein S16
BU: 30S ribosomal protein S17
BV: 30S ribosomal protein S18
BW: 30S ribosomal protein S19
BX: 30S ribosomal protein S20
BY: 30S ribosomal protein Thx
BC: tRNA chain 1
BD: tRNA chain 2
BE: tRNA chain 2
BZ: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,311,02363
Polymers2,308,58058
Non-polymers2,4435
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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RNA chain , 5 types, 6 molecules AAABBABCBDBE

#1: RNA chain 23S ribosomal RNA


Mass: 939567.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 37223181
#2: RNA chain 5S ribosomal RNA


Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 46197919
#34: RNA chain 16S ribosomal RNA


Mass: 491777.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 155076
#55: RNA chain tRNA chain 1


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#56: RNA chain tRNA chain 2


Mass: 24156.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)

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50S ribosomal protein ... , 30 types, 30 molecules ACADAEAFAGAHAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAeAfAIAJ

#3: Protein 50S ribosomal protein L1


Mass: 24736.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72GV9, UniProt: Q5SLP7*PLUS
#4: Protein 50S ribosomal protein L2


Mass: 30101.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I07, UniProt: P60405*PLUS
#5: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I04, UniProt: Q5SHN8*PLUS
#6: Protein 50S ribosomal protein L4 / L1e


Mass: 23011.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN9
#7: Protein 50S ribosomal protein L5


Mass: 21061.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ0
#8: Protein 50S ribosomal protein L6


Mass: 18864.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I19, UniProt: P0DOY8*PLUS
#9: Protein 50S ribosomal protein L13


Mass: 15796.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72IN1, UniProt: P60488*PLUS
#10: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I14, UniProt: Q5SHP8*PLUS
#11: Protein 50S ribosomal protein L15


Mass: 15743.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I23, UniProt: Q5SHQ7*PLUS
#12: Protein 50S ribosomal protein L16


Mass: 15364.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60489
#13: Protein 50S ribosomal protein L17


Mass: 13618.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I33, UniProt: Q9Z9H5*PLUS
#14: Protein 50S ribosomal protein L18


Mass: 12437.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I20, UniProt: Q5SHQ4*PLUS
#15: Protein 50S ribosomal protein L19


Mass: 13860.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72JU9, UniProt: P60490*PLUS
#16: Protein 50S ribosomal protein L20


Mass: 13648.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72L76, UniProt: P60491*PLUS
#17: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72HR2, UniProt: P60492*PLUS
#18: Protein 50S ribosomal protein L22


Mass: 12483.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I09, UniProt: Q5SHP3*PLUS
#19: Protein 50S ribosomal protein L23


Mass: 10499.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I06, UniProt: Q5SHP0*PLUS
#20: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I15, UniProt: Q5SHP9*PLUS
#21: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 20367.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72IA7, UniProt: Q5SHZ1*PLUS
#22: Protein 50S ribosomal protein L27


Mass: 9529.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60493
#23: Protein 50S ribosomal protein L29


Mass: 8112.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q9LCY4, UniProt: Q5SHP6*PLUS
#24: Protein 50S ribosomal protein L30


Mass: 6667.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I22, UniProt: Q5SHQ6*PLUS
#25: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72JR0, UniProt: Q5SJE1*PLUS
#26: Protein 50S ribosomal protein L32


Mass: 6390.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80339
#27: Protein/peptide 50S ribosomal protein L33


Mass: 6115.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72GW3, UniProt: P35871*PLUS
#28: Protein/peptide 50S ribosomal protein L34


Mass: 6132.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80340
#29: Protein 50S ribosomal protein L35


Mass: 7377.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72L77, UniProt: Q5SKU1*PLUS
#30: Protein/peptide 50S ribosomal protein L36


Mass: 4435.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72I28, UniProt: Q5SHR2*PLUS
#31: Protein 50S ribosomal protein L10


Mass: 16427.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q72GS1, UniProt: Q8VVE3*PLUS
#32: Protein 50S ribosomal protein L11


Mass: 14169.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62442, UniProt: Q5SLP6*PLUS

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Protein , 2 types, 2 molecules AgBZ

#33: Protein Unknown peptide


Mass: 10911.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)
#57: Protein GTP-binding protein


Mass: 67110.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DTT0*PLUS

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30S ribosomal protein ... , 20 types, 20 molecules BFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBY

#35: Protein 30S ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80371
#36: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80372
#37: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80373
#38: Protein 30S ribosomal protein S5


Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ5
#39: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP8
#40: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P17291
#41: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#42: Protein 30S ribosomal protein S9


Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80374
#43: Protein 30S ribosomal protein S10


Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN7
#44: Protein 30S ribosomal protein S11


Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80376
#45: Protein 30S ribosomal protein S12


Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3
#46: Protein 30S ribosomal protein S13


Mass: 13037.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377
#47: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#48: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ76
#49: Protein 30S ribosomal protein S16


Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJH3
#50: Protein 30S ribosomal protein S17


Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#51: Protein 30S ribosomal protein S18


Mass: 8497.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLQ0
#52: Protein 30S ribosomal protein S19


Mass: 9203.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP2
#53: Protein 30S ribosomal protein S20


Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380
#54: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIH3

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Non-polymers , 3 types, 5 molecules

#58: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM
#59: Chemical ChemComp-8AN / 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 346.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N6O6P
#60: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: THERMUS THERMOPHILUS RIBOSOME / Type: RIBOSOME
Buffer solutionName: 5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL
pH: 7.5
Details: 5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: May 5, 2015
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Calibrated magnification: 73684 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1531

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: CTFFIND3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5 Å / Num. of particles: 77127 / Magnification calibration: FSC / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--XRAY
Atomic model buildingPDB-ID: 4V4Y

4v4y


Accession code: 4V4Y / Source name: PDB / Type: experimental model
RefinementHighest resolution: 5 Å
Refinement stepCycle: LAST / Highest resolution: 5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29342 64859 42 0 94243

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