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- PDB-4v6f: Elongation complex of the 70S ribosome with three tRNAs and mRNA. -

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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 RRNA23S ribosomal RNA
  • 5S RIBOSOMAL RNA
  • MRNAMessenger RNA
  • TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
KeywordsRIBOSOME / tRNA / mRNA
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
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 L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / 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/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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L9/RNase H1, N-terminal / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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 / Messenger RNA


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


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

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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 / Ribosome


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 / Ribosome


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 / Ribosome / 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 / Water


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

-
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

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