[English] 日本語
Yorodumi
- PDB-5a9z: Complex of Thermous thermophilus ribosome bound to BipA-GDPCP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a9z
TitleComplex of Thermous thermophilus ribosome bound to BipA-GDPCP
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • BipA
  • Unknown peptide
KeywordsRIBOSOME / BIPA / TRANSLATIONAL GTPASE FACTORS / X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / large ribosomal subunit rRNA binding / regulation of translation / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / transferase activity ...guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / large ribosomal subunit rRNA binding / regulation of translation / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / TypA/BipA C-terminal domain / GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx ...: / : / : / : / TypA/BipA C-terminal domain / GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / 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 L11, bacterial-type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 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 L10-like domain superfamily / Ribosomal protein L11 signature. / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal L25p family / Ribosomal protein L25 / 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, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / NEOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / NEOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / 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 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / 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 bS18 / 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 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 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
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 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 1.1Feb 3, 2016Group: Database references / Other
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_imaging / Item: _em_imaging.nominal_defocus_max
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_radiation ...atom_site / diffrn_radiation / diffrn_radiation_wavelength / em_software / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _em_software.image_processing_id / _em_software.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _struct_asym.entity_id
Revision 2.1Dec 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]
Remark 700SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ...SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6396
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
AI: 50S ribosomal protein L10
AJ: 50S ribosomal protein L11
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
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
CA: BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,236,38858
Polymers2,234,63755
Non-polymers1,7503
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1
MethodPISA

-
Components

-
RNA chain , 3 types, 3 molecules AAABBA

#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: 55771382
#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

+
50S ribosomal protein ... , 30 types, 30 molecules ACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAeAf

#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 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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

-
Protein , 2 types, 2 molecules AgCA

#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)
#55: Protein BipA


Mass: 65979.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P0DTT0*PLUS

-
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: P62662, UniProt: P80371*PLUS
#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: P62663, UniProt: P80372*PLUS
#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: P62664, UniProt: P80373*PLUS
#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: P62665, UniProt: Q5SHQ5*PLUS
#39: Protein 30S ribosomal protein S6 /


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62666, UniProt: Q5SLP8*PLUS
#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: P62667, UniProt: P17291*PLUS
#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: P62668, 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: P62653, UniProt: Q5SHN7*PLUS
#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: P62654, UniProt: P80376*PLUS
#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: P61941, UniProt: Q5SHN3*PLUS
#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: P62655, UniProt: P80377*PLUS
#47: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62656, 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: P62657, UniProt: Q5SJ76*PLUS
#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: P62238, UniProt: Q5SJH3*PLUS
#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: P62658, UniProt: P0DOY7*PLUS
#51: Protein 30S ribosomal protein S18 /


Mass: 8483.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS
#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: P62660, UniProt: Q5SHP2*PLUS
#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 / Ribosome


Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: F6DII0, UniProt: Q5SIH3*PLUS

-
Non-polymers , 2 types, 3 molecules

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


Mass: 614.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM
#57: 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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RIBOSOME / Type: RIBOSOME / Details: RIBOSOME AND BIPA
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.: 0.17 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

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 5, 2015
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal magnification: 53000 X / Nominal defocus max: 2700 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: 658

-
Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: CTFFIND3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.7 Å / Num. of particles: 61165 / Symmetry type: POINT
RefinementHighest resolution: 4.7 Å
Refinement stepCycle: LAST / Highest resolution: 4.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29342 64859 42 0 94243

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more