[English] 日本語
Yorodumi
- PDB-4v4x: Crystal structure of the 70S Thermus thermophilus ribosome showin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v4x
TitleCrystal structure of the 70S Thermus thermophilus ribosome showing how the 16S 3'-end mimicks mRNA E and P codons.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • tRNA PHE (unmodified bases)
  • tRNA fMET (unmodified bases)
KeywordsRIBOSOME / NO-TEMPLATE / CODON-MIMICRY
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / 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 L1, conserved site ...Ribosomal protein L1, bacterial-type / 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 L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / 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 / 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 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 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 L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL6 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL3 / 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 uL14 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / 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 / Large ribosomal subunit protein uL24 / 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 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 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsJenner, L. / Yusupova, G. / Rees, B. / Moras, D. / Yusupov, M.
CitationJournal: Nature / Year: 2006
Title: Structural basis for messenger RNA movement on the ribosome.
Authors: Yusupova, G. / Jenner, L. / Rees, B. / Moras, D. / Yusupov, M.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2HGI, 2HGJ
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Remark 400COMPOUND THE COMPLETE ASYMMETRIC UNIT CONTAINS 30S AND 50S RIBOSOMAL SUBUNITS. THIS ENTRY 2HGI ...COMPOUND THE COMPLETE ASYMMETRIC UNIT CONTAINS 30S AND 50S RIBOSOMAL SUBUNITS. THIS ENTRY 2HGI CONTAINS 30S RIBOSOMAL SUBUNIT. THE 50S RIBOSOMAL SUBUNIT CAN BE FOUND IN PDB ENTRY 2HGJ.
Remark 999SEQUENCE THE TRNA SEQUENCES (MOL. C AND D) WERE TAKEN FROM SPRINZL : TRNA COMPILATION 2000 (HTTP: ...SEQUENCE THE TRNA SEQUENCES (MOL. C AND D) WERE TAKEN FROM SPRINZL : TRNA COMPILATION 2000 (HTTP://WWW.STAFF.UNI-BAYREUTH.DE/~BTC914/SEARCH/). Residue C C 17 and Residue C G 18 are linked together.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 16S rRNA
AC: tRNA fMET (unmodified bases)
AD: tRNA PHE (unmodified bases)
AE: 30S ribosomal protein S2
AF: 30S ribosomal protein S3
AG: 30S ribosomal protein S4
AH: 30S ribosomal protein S5
AI: 30S ribosomal protein S6
AJ: 30S ribosomal protein S7
AK: 30S ribosomal protein S8
AL: 30S ribosomal protein S9
AM: 30S ribosomal protein S10
AN: 30S ribosomal protein S11
AO: 30S ribosomal protein S12
AP: 30S ribosomal protein S13
AQ: 30S ribosomal protein S14
AR: 30S ribosomal protein S15
AS: 30S ribosomal protein S16
AT: 30S ribosomal protein S17
AU: 30S ribosomal protein S18
AV: 30S ribosomal protein S19
AW: 30S ribosomal protein S20
AX: 30S ribosomal protein Thx
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L1
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BK: 50S ribosomal protein L9
BL: 50S ribosomal protein L11
BM: 50S ribosomal protein L13
BN: 50S ribosomal protein L14
BO: 50S ribosomal protein L15
BP: 50S ribosomal protein L16
BQ: 50S ribosomal protein L17
BR: 50S ribosomal protein L18
BS: 50S ribosomal protein L19
BT: 50S ribosomal protein L20
BU: 50S ribosomal protein L21
BV: 50S ribosomal protein L22
BW: 50S ribosomal protein L23
BX: 50S ribosomal protein L24
BY: 50S ribosomal protein L25
BZ: 50S ribosomal protein L27
B1: 50S ribosomal protein L29
B2: 50S ribosomal protein L30
B3: 50S ribosomal protein L31
B4: 50S ribosomal protein L32
B5: 50S ribosomal protein L33
B6: 50S ribosomal protein L34
B7: 50S ribosomal protein L35
B8: 50S ribosomal protein L36


Theoretical massNumber of molelcules
Total (without water)2,247,53755
Polymers2,247,53755
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)509.520, 509.520, 804.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

-
RNA chain , 5 types, 5 molecules AAACADBABB

#1: RNA chain 16S rRNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 155076
#2: RNA chain tRNA fMET (unmodified bases)


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain tRNA PHE (unmodified bases)


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#24: RNA chain 23S ribosomal RNA


Mass: 948280.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48268
#25: RNA chain 5S ribosomal RNA


Mass: 39846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48271

-
30S ribosomal protein ... , 20 types, 20 molecules AEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAX

#4: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#5: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#6: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#7: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#8: 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 (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#9: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#10: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#11: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#12: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#13: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#14: Protein 30S ribosomal protein S12


Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#15: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#16: Protein 30S ribosomal protein S14


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#17: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#18: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#19: Protein 30S ribosomal protein S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24321
#20: Protein 30S ribosomal protein S18


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80382
#21: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#22: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#23: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

+
50S ribosomal protein ... , 30 types, 30 molecules BCBDBEBFBGBHBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB1B2B3B4B5B6B7B8

#26: Protein 50S ribosomal protein L1


Mass: 24867.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27150
#27: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60405
#28: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P52860, UniProt: Q5SHN8*PLUS
#29: Protein 50S ribosomal protein L4


Mass: 23271.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#30: Protein 50S ribosomal protein L5 / TthL5 / TL4


Mass: 21061.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P41201, UniProt: Q5SHQ0*PLUS
#31: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P24316, UniProt: P0DOY8*PLUS
#32: Protein 50S ribosomal protein L9


Mass: 16422.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27151
#33: Protein 50S ribosomal protein L11


Mass: 15526.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P36238, UniProt: Q5SLP6*PLUS
#34: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60488
#35: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60558
#36: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P74910, UniProt: Q5SHQ7*PLUS
#37: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60489
#38: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#39: Protein 50S ribosomal protein L18 / TL24


Mass: 12639.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80320, UniProt: Q5SHQ4*PLUS
#40: Protein 50S ribosomal protein L19


Mass: 17188.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60490
#41: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60491
#42: Protein 50S ribosomal protein L21


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


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P48286, UniProt: Q5SHP3*PLUS
#44: Protein 50S ribosomal protein L23 / L*23


Mass: 10759.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9RA57, UniProt: Q5SHP0*PLUS
#45: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56435, UniProt: Q5SHP9*PLUS
#46: Protein 50S ribosomal protein L25 / TL5


Mass: 23238.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHZ1
#47: Protein 50S ribosomal protein L27


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


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


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P74909, UniProt: Q5SHQ6*PLUS
#50: Protein 50S ribosomal protein L31


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


Mass: 6722.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80339
#52: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P35871
#53: 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 (bacteria) / Strain: HB8 / References: UniProt: P80340
#54: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80341, UniProt: Q5SKU1*PLUS
#55: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4435.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80256, UniProt: Q5SHR2*PLUS

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 12

-
Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 87.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2H2O11
3MPD12
4H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98014 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Apr 26, 2006 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98014 Å / Relative weight: 1
ReflectionResolution: 5→300 Å / Num. all: 225054 / Num. obs: 223223 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 184.3 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.054 / Net I/σ(I): 9.1
Reflection shellResolution: 5→5.09 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 11079 / Χ2: 1.023 / % possible all: 99.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5→300 Å / FOM work R set: 0.728 / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Residue AC C 17 and Residue AC G 18 are linked together. However there is residue AC U 17A between them present in the sequence that was not observed in the electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.323 10172 4.5 %RANDOM
Rwork0.263 ---
all0.274 219331 --
obs0.266 211622 93.9 %-
Solvent computationSolvent model: CNS / Bsol: 122 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 167.6 Å2
Refinement stepCycle: LAST / Resolution: 5→300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19231 35801 0 0 55032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0151.5
X-RAY DIFFRACTIONc_angle_deg2.0652
X-RAY DIFFRACTIONc_mcbond_it1.7382
X-RAY DIFFRACTIONc_mcangle_it2.8872.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
5-5.030.4381800.41235993779
5.03-5.070.421900.38637343924
5.07-5.10.432090.37537663975
5.1-5.140.4271970.3838394036
5.14-5.180.3961820.37238434025
5.18-5.220.4311930.37337663959
5.22-5.260.4241930.34537503943
5.26-5.30.4441890.34238144003
5.3-5.340.3762050.3438184023
5.34-5.390.382310.34437724003
5.39-5.430.42010.3438084009
5.43-5.480.3811900.32239634153
5.48-5.530.3952060.30739364142
5.53-5.580.3542140.31838484062
5.58-5.630.4112000.31739034103
5.63-5.690.3742180.29438834101
5.69-5.740.3721960.28939754171
5.74-5.80.3571950.28339714166
5.8-5.860.3541730.26139734146
5.86-5.930.3842040.26140064210
5.93-60.3441760.26140404216
6-6.070.3621890.26440044193
6.07-6.140.3392090.24940004209
6.14-6.220.3431990.26840224221
6.22-6.30.4152110.27840294240
6.3-6.390.381720.27440644236
6.39-6.480.3891950.27840414236
6.48-6.570.3371850.25640754260
6.57-6.680.3252090.23740774286
6.68-6.790.3012110.2340694280
6.79-6.90.332240.22840974321
6.9-7.030.3192010.21340774278
7.03-7.160.3192110.23440944305
7.16-7.310.3292030.23340834286
7.31-7.470.331880.2241084296
7.47-7.640.3082460.22540954341
7.64-7.830.3451890.23241884377
7.83-8.050.342070.24141374344
8.05-8.280.3051820.23842094391
8.28-8.550.3122050.24741484353
8.55-8.860.3362180.24641914409
8.86-9.210.2962280.24741644392
9.21-9.630.311950.25842384433
9.63-10.140.3362120.27742344446
10.14-10.770.2982360.24242134449
10.77-11.60.2752270.22642624489
11.6-12.770.2562380.21842434481
12.77-14.620.282410.20942934534
14.62-18.420.31830.22143754558
18.42-3000.2092160.24546134829
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_modif.param
X-RAY DIFFRACTION2dna-rna_ext.param

+
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