[English] 日本語
Yorodumi
- PDB-4v5l: The structure of EF-Tu and aminoacyl-tRNA bound to the 70S riboso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v5l
TitleThe structure of EF-Tu and aminoacyl-tRNA bound to the 70S ribosome with a GTP analog
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • 16S RRNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • A-SITE TRNA G24A TRP-TRNA TRP
  • E-SITE TRNA PHE OR P-SITE TRNA PHE
  • ELONGATION FACTOR TUEF-Tu
  • MRNAMessenger RNA
KeywordsRIBOSOME / EF-TU / TRNA / GDPCP / GTPASE
Function / homology
Function and homology information


translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / GTPase activity / GTP binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Ribosomal protein L1, bacterial-type / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Ribosomal protein L1, bacterial-type / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / 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 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Elongation factor Tu domain 2 / 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 L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / 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 L28 / 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 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 S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 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 S4, bacterial-type / Ribosomal protein L14P, 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 / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL6 ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein bL33 / Elongation factor Tu-B / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / 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 uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / 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 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVoorhees, R.M. / Schmeing, T.M. / Ramakrishnan, V.
CitationJournal: Science / Year: 2010
Title: The Mechanism for Activation of GTP Hydrolysis on the Ribosome.
Authors: Voorhees, R.M. / Schmeing, T.M. / Kelley, A.C. / Ramakrishnan, V.
History
DepositionSep 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2XQD, 2XQE
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Category: pdbx_validate_polymer_linkage
Revision 2.0Jun 26, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_seq_map_depositor_info / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 16S RRNA
AB: 30S RIBOSOMAL PROTEIN S2
AC: 30S RIBOSOMAL PROTEIN S3
AD: 30S RIBOSOMAL PROTEIN S4
AE: 30S RIBOSOMAL PROTEIN S5
AF: 30S RIBOSOMAL PROTEIN S6
AG: 30S RIBOSOMAL PROTEIN S7
AH: 30S RIBOSOMAL PROTEIN S8
AI: 30S RIBOSOMAL PROTEIN S9
AJ: 30S RIBOSOMAL PROTEIN S10
AK: 30S RIBOSOMAL PROTEIN S11
AL: 30S RIBOSOMAL PROTEIN S12
AM: 30S RIBOSOMAL PROTEIN S13
AN: 30S RIBOSOMAL PROTEIN S14
AO: 30S RIBOSOMAL PROTEIN S15
AP: 30S RIBOSOMAL PROTEIN S16
AQ: 30S RIBOSOMAL PROTEIN S17
AR: 30S RIBOSOMAL PROTEIN S18
AS: 30S RIBOSOMAL PROTEIN S19
AT: 30S RIBOSOMAL PROTEIN S20
AU: 30S RIBOSOMAL PROTEIN THX
AV: E-SITE TRNA PHE OR P-SITE TRNA PHE
AW: E-SITE TRNA PHE OR P-SITE TRNA PHE
AX: MRNA
AY: A-SITE TRNA G24A TRP-TRNA TRP
AZ: ELONGATION FACTOR TU
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
B4: 50S RIBOSOMAL PROTEIN L31
B5: 50S RIBOSOMAL PROTEIN L32
B6: 50S RIBOSOMAL PROTEIN L33
B7: 50S RIBOSOMAL PROTEIN L34
B8: 50S RIBOSOMAL PROTEIN L35
B9: 50S RIBOSOMAL PROTEIN L36
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
BJ: 50S RIBOSOMAL PROTEIN L10
BK: 50S RIBOSOMAL PROTEIN L11
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,325,01466
Polymers2,323,59159
Non-polymers1,4237
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.598, 274.932, 282.459
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
RNA chain , 6 types, 7 molecules AAAVAWAXAYBABB

#1: RNA chain 16S RRNA /


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AVY.
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: GenBank: 55979969
#22: RNA chain E-SITE TRNA PHE OR P-SITE TRNA PHE


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12
#23: RNA chain MRNA / Messenger RNA


Mass: 4495.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#24: RNA chain A-SITE TRNA G24A TRP-TRNA TRP


Mass: 24813.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12
#36: RNA chain 23S RIBOSOMAL RNA /


Mass: 947975.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: GenBank: 55979969
#37: RNA chain 5S RIBOSOMAL RNA /


Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: GenBank: 55979969

-
30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU

#2: 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-MRC-MSAW1 / References: UniProt: P80371
#3: 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-MRC-MSAW1 / References: UniProt: P80372
#4: 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-MRC-MSAW1 / References: UniProt: P80373
#5: 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-MRC-MSAW1 / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#6: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#7: 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-MRC-MSAW1 / References: UniProt: P62667, UniProt: P17291*PLUS
#8: 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-MRC-MSAW1 / References: UniProt: P24319, UniProt: P0DOY9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P62669
#10: 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-MRC-MSAW1 / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#11: 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-MRC-MSAW1 / References: UniProt: P80376
#12: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P17293, UniProt: Q5SHN3*PLUS
#13: 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-MRC-MSAW1 / References: UniProt: P80377
#14: 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-MRC-MSAW1 / References: UniProt: P24320, UniProt: P0DOY6*PLUS
#15: 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-MRC-MSAW1 / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-17 AND 21-91 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P80379, UniProt: Q5SJH3*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P62659, UniProt: Q5SLQ0*PLUS
#19: 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-MRC-MSAW1 / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#20: 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-MRC-MSAW1 / References: UniProt: P80380
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P62612, UniProt: Q5SIH3*PLUS

-
Protein , 1 types, 1 molecules AZ

#25: Protein ELONGATION FACTOR TU / EF-Tu / EF-TU-B


Mass: 44709.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED USING RECOMBINANT TECHNIQUES / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P60339

+
50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules B0B1B2B3B4B5B6B7B8B9BCBDBEBFBGBHBJBKBNBOBPBQBRBSBTBUBVBWBXBYBZ

#26: 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-MRC-MSAW1 / References: UniProt: P60493
#27: Protein 50S RIBOSOMAL PROTEIN L28 /


Mass: 11004.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: P60494
#28: Protein 50S RIBOSOMAL PROTEIN L29 /


Mass: 8670.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHP6
#29: 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-MRC-MSAW1 / References: UniProt: Q5SHQ6
#30: 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-MRC-MSAW1 / References: UniProt: Q5SJE1
#31: 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-MRC-MSAW1 / References: UniProt: P80339
#32: 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-MRC-MSAW1 / References: UniProt: P35871
#33: 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-MRC-MSAW1 / References: UniProt: P80340
#34: 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-MRC-MSAW1 / References: UniProt: Q5SKU1
#35: 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 (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHR2
#38: Protein 50S RIBOSOMAL PROTEIN L1 /


Mass: 24872.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SLP7
#39: 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-MRC-MSAW1 / References: UniProt: P60405
#40: 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-MRC-MSAW1 / References: UniProt: Q5SHN8
#41: 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-MRC-MSAW1 / References: UniProt: Q5SHN9
#42: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 21061.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHQ0
#43: 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-MRC-MSAW1 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#44: Protein 50S RIBOSOMAL PROTEIN L10 /


Mass: 11081.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1
#45: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 11932.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BUILT AS POLY-ALA / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1
#46: 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-MRC-MSAW1 / References: UniProt: P60488
#47: Protein 50S RIBOSOMAL PROTEIN L14 /


Mass: 13323.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHP8
#48: 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-MRC-MSAW1 / References: UniProt: Q5SHQ7
#49: 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-MRC-MSAW1 / References: UniProt: P60489
#50: 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-MRC-MSAW1 / References: UniProt: Q9Z9H5
#51: Protein 50S RIBOSOMAL PROTEIN L18 /


Mass: 12639.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHQ4
#52: 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-MRC-MSAW1 / References: UniProt: P60490
#53: 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-MRC-MSAW1 / References: UniProt: P60491
#54: 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-MRC-MSAW1 / References: UniProt: P60492
#55: 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-MRC-MSAW1 / References: UniProt: Q5SHP3
#56: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 10759.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHP0
#57: 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-MRC-MSAW1 / References: UniProt: Q5SHP9
#58: Protein 50S RIBOSOMAL PROTEIN L25 /


Mass: 23238.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8-MRC-MSAW1 / References: UniProt: Q5SHZ1

-
Non-polymers , 5 types, 8 molecules

#59: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#61: 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
#62: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#63: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.73 % / Description: NONE
Crystal growpH: 6.3
Details: 100 MM MES PH 6.3, 60-100 MM KCL, 50 MM SUCROSE, 1% GLYCEROL, AND 5.3% (W/V) PEG20K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC / Detector: CCD / Date: Jun 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 537024 / % possible obs: 98.8 % / Observed criterion σ(I): 1.16 / Redundancy: 5.2 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 6.98
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.16 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
CNSmodel building
CNS1.2refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WRO

2wro
PDB Unreleased entry


Resolution: 3.1→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 9936247 / Data cutoff low absF: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 26914 5 %INHERITED FROM 2WRN
Rwork0.2312 ---
obs0.2312 537024 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6038 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 85.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.94 Å20 Å2-0.51 Å2
2---4.04 Å20 Å2
3----4.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22289 37509 79 1 59878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 4236 5 %
Rwork0.316 80731 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1GCP.PARGCP.TOP
X-RAY DIFFRACTION2DNS-RNA_TRP_MODS.PARAMDNA-RNA_TRP_MODS.TOP
X-RAY DIFFRACTION3PROTEIN_REP_TRP.PARAMPROTEIN_REP_TRP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PAR_LIGAND.PARPAR_LIGAND.TOP

+
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