[English] 日本語
Yorodumi
- PDB-4v6f: Elongation complex of the 70S ribosome with three tRNAs and mRNA. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v6f
TitleElongation complex of the 70S ribosome with three tRNAs and mRNA.
Components
  • (16S ribosomal ...) x 2
  • (30S ribosomal protein ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • 23S RIBOSOMAL RNA
  • 23S RRNA
  • 5S RIBOSOMAL RNA
  • MRNA
  • TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
KeywordsRIBOSOME / tRNA / mRNA
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein ...Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 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 L10 / : / : / Ribosomal protein S14, type Z / 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 L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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 protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein 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 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein uL10 / 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
AuthorsJenner, L.B. / Yusupova, G. / Yusupov, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural aspects of messenger RNA reading frame maintenance by the ribosome.
Authors: Jenner, L.B. / Demeshkina, N. / Yusupova, G. / Yusupov, M.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3I8F, 3I8G, 3I8H, 3I8I
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2May 31, 2017Group: Other
Revision 2.0Jul 3, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / struct_conn / struct_ref_seq
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.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_ref_seq_dif.details
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 23S RIBOSOMAL RNA
AB: 5S RIBOSOMAL RNA
AD: 50S RIBOSOMAL PROTEIN L2
AE: 50S RIBOSOMAL PROTEIN L3
AF: 50S RIBOSOMAL PROTEIN L4
AG: 50S RIBOSOMAL PROTEIN L5
AH: 50S RIBOSOMAL PROTEIN L6
AK: 50S RIBOSOMAL PROTEIN L9
AM: 50S RIBOSOMAL PROTEIN L13
AN: 50S RIBOSOMAL PROTEIN L14
AO: 50S RIBOSOMAL PROTEIN L15
AP: 50S RIBOSOMAL PROTEIN L16
A0: 50S RIBOSOMAL PROTEIN L17
AQ: 50S RIBOSOMAL PROTEIN L18
AR: 50S RIBOSOMAL PROTEIN L19
A1: 50S RIBOSOMAL PROTEIN L20
A2: 50S RIBOSOMAL PROTEIN L21
AS: 50S RIBOSOMAL PROTEIN L22
AT: 50S RIBOSOMAL PROTEIN L23
AU: 50S RIBOSOMAL PROTEIN L24
AV: 50S RIBOSOMAL PROTEIN L25
A3: 50S RIBOSOMAL PROTEIN L27
AZ: 50S RIBOSOMAL PROTEIN L28
AW: 50S RIBOSOMAL PROTEIN L29
AX: 50S RIBOSOMAL PROTEIN L30
A4: 50S RIBOSOMAL PROTEIN L31
A5: 50S RIBOSOMAL PROTEIN L32
A6: 50S RIBOSOMAL PROTEIN L33
A7: 50S RIBOSOMAL PROTEIN L34
A8: 50S RIBOSOMAL PROTEIN L35
BA: 16S ribosomal RNA
BE: 30S ribosomal protein S2
BF: 30S ribosomal protein S3
BG: 30S ribosomal protein S4
BH: 30S ribosomal protein S5
BI: 30S ribosomal protein S6
BJ: 30S ribosomal protein S7
BK: 30S ribosomal protein S8
BL: 30S ribosomal protein S9
BM: 30S ribosomal protein S10
BN: 30S ribosomal protein S11
BO: 30S ribosomal protein S12
BP: 30S ribosomal protein S13
BQ: 30S ribosomal protein S14 type Z
BR: 30S ribosomal protein S15
BS: 30S ribosomal protein S16
BT: 30S ribosomal protein S17
BU: 30S ribosomal protein S18
BV: 30S ribosomal protein S19
BW: 30S ribosomal protein S20
BX: 30S ribosomal protein Thx
BD: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
BB: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
BC: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
B1: MRNA
CA: 16S ribosomal RNA
CE: 30S ribosomal protein S2
CF: 30S ribosomal protein S3
CG: 30S ribosomal protein S4
CH: 30S ribosomal protein S5
CI: 30S ribosomal protein S6
CJ: 30S ribosomal protein S7
CK: 30S ribosomal protein S8
CL: 30S ribosomal protein S9
CM: 30S ribosomal protein S10
CN: 30S ribosomal protein S11
CO: 30S ribosomal protein S12
CP: 30S ribosomal protein S13
CQ: 30S ribosomal protein S14 type Z
CR: 30S ribosomal protein S15
CS: 30S ribosomal protein S16
CT: 30S ribosomal protein S17
CU: 30S ribosomal protein S18
CV: 30S ribosomal protein S19
CW: 30S ribosomal protein S20
CX: 30S ribosomal protein Thx
CD: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
CB: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
CC: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
C1: MRNA
DA: 23S RRNA
DB: 5S RIBOSOMAL RNA
DD: 50S RIBOSOMAL PROTEIN L2
DE: 50S RIBOSOMAL PROTEIN L3
DF: 50S RIBOSOMAL PROTEIN L4
DG: 50S RIBOSOMAL PROTEIN L5
DH: 50S RIBOSOMAL PROTEIN L6
DI: 50S ribosomal protein L7/L12
DK: 50S RIBOSOMAL PROTEIN L9
DY: 50S ribosomal protein L10
DL: 50S ribosomal protein L11
DJ: 50S ribosomal protein L7/L12
DM: 50S RIBOSOMAL PROTEIN L13
DN: 50S RIBOSOMAL PROTEIN L14
DO: 50S RIBOSOMAL PROTEIN L15
DP: 50S RIBOSOMAL PROTEIN L16
D0: 50S RIBOSOMAL PROTEIN L17
DQ: 50S RIBOSOMAL PROTEIN L18
DR: 50S RIBOSOMAL PROTEIN L19
D1: 50S RIBOSOMAL PROTEIN L20
D2: 50S RIBOSOMAL PROTEIN L21
DS: 50S RIBOSOMAL PROTEIN L22
DT: 50S RIBOSOMAL PROTEIN L23
DU: 50S RIBOSOMAL PROTEIN L24
DV: 50S RIBOSOMAL PROTEIN L25
D3: 50S RIBOSOMAL PROTEIN L27
DZ: 50S RIBOSOMAL PROTEIN L28
DW: 50S RIBOSOMAL PROTEIN L29
DX: 50S RIBOSOMAL PROTEIN L30
D4: 50S RIBOSOMAL PROTEIN L31
D5: 50S RIBOSOMAL PROTEIN L32
D6: 50S RIBOSOMAL PROTEIN L33
D7: 50S RIBOSOMAL PROTEIN L34
D8: 50S RIBOSOMAL PROTEIN L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,678,9695465
Polymers4,548,666114
Non-polymers130,3035351
Water1086
1
AA: 23S RIBOSOMAL RNA
AB: 5S RIBOSOMAL RNA
AD: 50S RIBOSOMAL PROTEIN L2
AE: 50S RIBOSOMAL PROTEIN L3
AF: 50S RIBOSOMAL PROTEIN L4
AG: 50S RIBOSOMAL PROTEIN L5
AH: 50S RIBOSOMAL PROTEIN L6
AK: 50S RIBOSOMAL PROTEIN L9
AM: 50S RIBOSOMAL PROTEIN L13
AN: 50S RIBOSOMAL PROTEIN L14
AO: 50S RIBOSOMAL PROTEIN L15
AP: 50S RIBOSOMAL PROTEIN L16
A0: 50S RIBOSOMAL PROTEIN L17
AQ: 50S RIBOSOMAL PROTEIN L18
AR: 50S RIBOSOMAL PROTEIN L19
A1: 50S RIBOSOMAL PROTEIN L20
A2: 50S RIBOSOMAL PROTEIN L21
AS: 50S RIBOSOMAL PROTEIN L22
AT: 50S RIBOSOMAL PROTEIN L23
AU: 50S RIBOSOMAL PROTEIN L24
AV: 50S RIBOSOMAL PROTEIN L25
A3: 50S RIBOSOMAL PROTEIN L27
AZ: 50S RIBOSOMAL PROTEIN L28
AW: 50S RIBOSOMAL PROTEIN L29
AX: 50S RIBOSOMAL PROTEIN L30
A4: 50S RIBOSOMAL PROTEIN L31
A5: 50S RIBOSOMAL PROTEIN L32
A6: 50S RIBOSOMAL PROTEIN L33
A7: 50S RIBOSOMAL PROTEIN L34
A8: 50S RIBOSOMAL PROTEIN L35
BA: 16S ribosomal RNA
BE: 30S ribosomal protein S2
BF: 30S ribosomal protein S3
BG: 30S ribosomal protein S4
BH: 30S ribosomal protein S5
BI: 30S ribosomal protein S6
BJ: 30S ribosomal protein S7
BK: 30S ribosomal protein S8
BL: 30S ribosomal protein S9
BM: 30S ribosomal protein S10
BN: 30S ribosomal protein S11
BO: 30S ribosomal protein S12
BP: 30S ribosomal protein S13
BQ: 30S ribosomal protein S14 type Z
BR: 30S ribosomal protein S15
BS: 30S ribosomal protein S16
BT: 30S ribosomal protein S17
BU: 30S ribosomal protein S18
BV: 30S ribosomal protein S19
BW: 30S ribosomal protein S20
BX: 30S ribosomal protein Thx
BD: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
BB: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
BC: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
B1: MRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,294,8542147
Polymers2,243,88455
Non-polymers50,9692092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S ribosomal RNA
CE: 30S ribosomal protein S2
CF: 30S ribosomal protein S3
CG: 30S ribosomal protein S4
CH: 30S ribosomal protein S5
CI: 30S ribosomal protein S6
CJ: 30S ribosomal protein S7
CK: 30S ribosomal protein S8
CL: 30S ribosomal protein S9
CM: 30S ribosomal protein S10
CN: 30S ribosomal protein S11
CO: 30S ribosomal protein S12
CP: 30S ribosomal protein S13
CQ: 30S ribosomal protein S14 type Z
CR: 30S ribosomal protein S15
CS: 30S ribosomal protein S16
CT: 30S ribosomal protein S17
CU: 30S ribosomal protein S18
CV: 30S ribosomal protein S19
CW: 30S ribosomal protein S20
CX: 30S ribosomal protein Thx
CD: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
CB: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
CC: TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
C1: MRNA
DA: 23S RRNA
DB: 5S RIBOSOMAL RNA
DD: 50S RIBOSOMAL PROTEIN L2
DE: 50S RIBOSOMAL PROTEIN L3
DF: 50S RIBOSOMAL PROTEIN L4
DG: 50S RIBOSOMAL PROTEIN L5
DH: 50S RIBOSOMAL PROTEIN L6
DI: 50S ribosomal protein L7/L12
DK: 50S RIBOSOMAL PROTEIN L9
DY: 50S ribosomal protein L10
DL: 50S ribosomal protein L11
DJ: 50S ribosomal protein L7/L12
DM: 50S RIBOSOMAL PROTEIN L13
DN: 50S RIBOSOMAL PROTEIN L14
DO: 50S RIBOSOMAL PROTEIN L15
DP: 50S RIBOSOMAL PROTEIN L16
D0: 50S RIBOSOMAL PROTEIN L17
DQ: 50S RIBOSOMAL PROTEIN L18
DR: 50S RIBOSOMAL PROTEIN L19
D1: 50S RIBOSOMAL PROTEIN L20
D2: 50S RIBOSOMAL PROTEIN L21
DS: 50S RIBOSOMAL PROTEIN L22
DT: 50S RIBOSOMAL PROTEIN L23
DU: 50S RIBOSOMAL PROTEIN L24
DV: 50S RIBOSOMAL PROTEIN L25
D3: 50S RIBOSOMAL PROTEIN L27
DZ: 50S RIBOSOMAL PROTEIN L28
DW: 50S RIBOSOMAL PROTEIN L29
DX: 50S RIBOSOMAL PROTEIN L30
D4: 50S RIBOSOMAL PROTEIN L31
D5: 50S RIBOSOMAL PROTEIN L32
D6: 50S RIBOSOMAL PROTEIN L33
D7: 50S RIBOSOMAL PROTEIN L34
D8: 50S RIBOSOMAL PROTEIN L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,384,1153318
Polymers2,304,78259
Non-polymers79,3333259
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.460, 446.200, 623.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
RNA chain , 5 types, 12 molecules AAABDBBDBBBCCDCBCCB1C1DA

#1: RNA chain 23S RIBOSOMAL RNA


Mass: 946094.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#2: RNA chain 5S RIBOSOMAL RNA


Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: X01554.1
#52: RNA chain
TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37


Mass: 24599.748 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#53: RNA chain MRNA


Mass: 9442.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Dharmacon
#55: RNA chain 23S RRNA


Mass: 947013.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1

+
50S RIBOSOMAL PROTEIN ... , 31 types, 60 molecules ADDDAEDEAFDFAGDGAHDHAKDKAMDMANDNAODOAPDPA0D0AQDQARDRA1D1A2D2...

#3: Protein 50S RIBOSOMAL PROTEIN L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60405
#4: Protein 50S RIBOSOMAL PROTEIN L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN8
#5: Protein 50S RIBOSOMAL PROTEIN L4


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#6: Protein 50S RIBOSOMAL PROTEIN L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ0
#7: Protein 50S RIBOSOMAL PROTEIN L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#8: Protein 50S RIBOSOMAL PROTEIN L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ1
#9: Protein 50S RIBOSOMAL PROTEIN L13


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


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


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ7
#12: Protein 50S RIBOSOMAL PROTEIN L16


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


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


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ4
#15: Protein 50S RIBOSOMAL PROTEIN L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60490
#16: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60491
#17: Protein 50S RIBOSOMAL PROTEIN L21


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


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP3
#19: Protein 50S RIBOSOMAL PROTEIN L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP0
#20: Protein 50S RIBOSOMAL PROTEIN L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP9
#21: Protein 50S RIBOSOMAL PROTEIN L25


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHZ1
#22: Protein 50S RIBOSOMAL PROTEIN L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60493
#23: Protein 50S RIBOSOMAL PROTEIN L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60494
#24: Protein 50S RIBOSOMAL PROTEIN L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP6
#25: Protein 50S RIBOSOMAL PROTEIN L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ6
#26: Protein 50S RIBOSOMAL PROTEIN L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJE1
#27: Protein 50S RIBOSOMAL PROTEIN L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80339
#28: Protein 50S RIBOSOMAL PROTEIN L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P35871
#29: Protein/peptide 50S RIBOSOMAL PROTEIN L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80340
#30: Protein 50S RIBOSOMAL PROTEIN L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKU1
#56: Protein 50S ribosomal protein L7/L12


Mass: 13086.210 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q8VVE2
#57: Protein 50S ribosomal protein L10


Mass: 18586.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q8VVE3
#58: 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: Q5SLP6

-
16S ribosomal ... , 2 types, 2 molecules BACA

#31: RNA chain 16S ribosomal RNA


Mass: 492083.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: M26923.1
#54: RNA chain 16S ribosomal RNA


Mass: 491777.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: M26923.1

-
30S ribosomal protein ... , 20 types, 40 molecules BECEBFCFBGCGBHCHBICIBJCJBKCKBLCLBMCMBNCNBOCOBPCPBQCQBRCRBSCS...

#32: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#33: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#34: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#35: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#36: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#37: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#38: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#39: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#40: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#41: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#42: Protein 30S ribosomal protein S12


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#43: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#44: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: P24320, UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#45: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#46: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#47: Protein 30S ribosomal protein S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#48: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#49: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#50: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#51: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

-
Non-polymers , 3 types, 5357 molecules

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


Mass: 24.305 Da / Num. of mol.: 5345 / Source method: obtained synthetically / Formula: Mg
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→300 Å / Num. all: 1043872 / Num. obs: 1041156 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 69.143 Å2 / Rmerge(I) obs: 0.191 / Rsym value: 0.266 / Net I/σ(I): 6.94
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 8.86 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / Num. unique all: 94202 / Rsym value: 0.6 / % possible all: 88.4

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J00, 2J01, 2J02, 2J03

2j00
PDB Unreleased entry

2j01
PDB Unreleased entry

2j02
PDB Unreleased entry

2j03
PDB Unreleased entry


Resolution: 3.1→300 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 31119 -RANDOM
Rwork0.215 ---
all0.266 1043872 --
obs-1041126 96.5 %-
Displacement parametersBiso max: 200.53 Å2 / Biso mean: 79.448 Å2 / Biso min: 20.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27007 65264 0 0 92271
LS refinement shellResolution: 3.1→3.12 Å
RfactorNum. reflection
Rfree0.3485 595
Rwork0.324 -
obs-20166

+
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