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- PDB-4v8p: T.thermophila 60S ribosomal subunit in complex with initiation fa... -

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Basic information

Entry
Database: PDB / ID: 4v8p
TitleT.thermophila 60S ribosomal subunit in complex with initiation factor 6.
Components
  • (60S RIBOSOMAL PROTEIN ...) x 12
  • (RIBOSOMAL PROTEIN ...) x 4
  • (RPL19) x 2
  • 26S RRNA
  • 5.8S RRNA
  • 5S RRNA
  • RPL13
  • RPL14
  • RPL17
  • RPL18
  • RPL18A
  • RPL23
  • RPL23A
  • RPL24
  • RPL26
  • RPL27
  • RPL28
  • RPL29
  • RPL30
  • RPL34
  • RPL35
  • RPL35A
  • RPL37A
  • RPL38
  • RPL39
  • RPL4
  • RPL6
  • RPL7A
  • RPL8
  • RPLP0
  • TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsRIBOSOME / EUKARYOTIC INITIATION FACTOR 6 / EIF6 / 60S / TRANSLATION / LARGE RIBOSOMAL SUBUNIT / RRNA / RIBOSOMAL PROTEIN
Function / homology
Function and homology information


ribosomal large subunit binding / protein-RNA complex assembly / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly ...ribosomal large subunit binding / protein-RNA complex assembly / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family ...Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L30e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8 / 60S ribosomal protein L6E / 60S ribosomal protein L35 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal protein L35A superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L14 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL13 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL37 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL21 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesTETRAHYMENA THERMOPHILA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsKlinge, S. / Voigts-Hoffmann, F. / Leibundgut, M. / Arpagaus, S. / Ban, N.
CitationJournal: Science / Year: 2011
Title: Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6.
Authors: Klinge, S. / Voigts-Hoffmann, F. / Leibundgut, M. / Arpagaus, S. / Ban, N.
History
DepositionSep 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4A18, 4A1E, 4A17, 4A19, 4A1A, 4A1B, 4A1C, 4A1D
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jan 10, 2024Group: 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_sheet
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.pdbx_dist_value / _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_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: 26S RRNA
AA: RIBOSOMAL PROTEIN L37
AB: RPL39
AC: 60S RIBOSOMAL PROTEIN L36A
AE: RPL6
AF: RPL14
AG: RPL30
AH: RPL35A
AJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
AK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
AL: RPL34
AM: RIBOSOMAL PROTEIN L22
AN: RPL27
AO: RPL28
AP: RPL38
AQ: 60S RIBOSOMAL PROTEIN L36
AT: RPL29
AU: RPL13
AX: RPL18A
B2: 5.8S RRNA
B3: 5S RRNA
BA: RPL8
BB: RIBOSOMAL PROTEIN L3
BC: RPL4
BD: 60S RIBOSOMAL PROTEIN L11
BE: 60S RIBOSOMAL PROTEIN L9
BF: RPL7A
BG: RPLP0
BH: 60S RIBOSOMAL PROTEIN L10
BI: 60S RIBOSOMAL PROTEIN L13A
BJ: RPL23
BK: 60S RIBOSOMAL PROTEIN L27A
BL: RIBOSOMAL PROTEIN L15
BM: 60S RIBOSOMAL PROTEIN L5
BN: RPL18
BO: RPL19
BP: 60S RIBOSOMAL PROTEIN L21
BQ: RPL17
BR: RPL23A
BS: RPL26
BT: RPL24
BU: RPL35
BV: 60S RIBOSOMAL PROTEIN L7
BW: 60S RIBOSOMAL PROTEIN L31
BX: 60S RIBOSOMAL PROTEIN L32
BY: RPL37A
C2: 5.8S RRNA
C3: 5S RRNA
CA: RPL8
CB: RIBOSOMAL PROTEIN L3
CC: RPL4
CD: 60S RIBOSOMAL PROTEIN L11
CE: 60S RIBOSOMAL PROTEIN L9
CF: RPL7A
CG: RPLP0
CH: 60S RIBOSOMAL PROTEIN L10
CI: 60S RIBOSOMAL PROTEIN L13A
CJ: RPL23
CK: 60S RIBOSOMAL PROTEIN L27A
CL: RIBOSOMAL PROTEIN L15
CM: 60S RIBOSOMAL PROTEIN L5
CN: RPL18
CO: RPL19
CP: 60S RIBOSOMAL PROTEIN L21
CQ: RPL17
CR: RPL23A
CS: RPL26
CT: RPL24
CU: RPL35
CV: 60S RIBOSOMAL PROTEIN L7
CW: 60S RIBOSOMAL PROTEIN L31
CX: 60S RIBOSOMAL PROTEIN L32
CY: RPL37A
D1: 26S RRNA
DA: RIBOSOMAL PROTEIN L37
DB: RPL39
DC: 60S RIBOSOMAL PROTEIN L36A
DE: RPL6
DF: RPL14
DG: RPL30
DH: RPL35A
DJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
DK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
DL: RPL34
DM: RIBOSOMAL PROTEIN L22
DN: RPL27
DO: RPL28
DP: RPL38
DQ: 60S RIBOSOMAL PROTEIN L36
DT: RPL29
DU: RPL13
DX: RPL18A
E2: 5.8S RRNA
E3: 5S RRNA
EA: RPL8
EB: RIBOSOMAL PROTEIN L3
EC: RPL4
ED: 60S RIBOSOMAL PROTEIN L11
EE: 60S RIBOSOMAL PROTEIN L9
EF: RPL7A
EG: RPLP0
EH: 60S RIBOSOMAL PROTEIN L10
EI: 60S RIBOSOMAL PROTEIN L13A
EJ: RPL23
EK: 60S RIBOSOMAL PROTEIN L27A
EL: RIBOSOMAL PROTEIN L15
EM: 60S RIBOSOMAL PROTEIN L5
EN: RPL18
EO: RPL19
EP: 60S RIBOSOMAL PROTEIN L21
EQ: RPL17
ER: RPL23A
ES: RPL26
ET: RPL24
EU: RPL35
EV: 60S RIBOSOMAL PROTEIN L7
EW: 60S RIBOSOMAL PROTEIN L31
EX: 60S RIBOSOMAL PROTEIN L32
EY: RPL37A
F1: 26S RRNA
FA: RIBOSOMAL PROTEIN L37
FB: RPL39
FC: 60S RIBOSOMAL PROTEIN L36A
FE: RPL6
FF: RPL14
FG: RPL30
FH: RPL35A
FJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
FK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
FL: RPL34
FM: RIBOSOMAL PROTEIN L22
FN: RPL27
FO: RPL28
FP: RPL38
FQ: 60S RIBOSOMAL PROTEIN L36
FT: RPL29
FU: RPL13
FX: RPL18A
G2: 5.8S RRNA
G3: 5S RRNA
GA: RPL8
GB: RIBOSOMAL PROTEIN L3
GC: RPL4
GD: 60S RIBOSOMAL PROTEIN L11
GE: 60S RIBOSOMAL PROTEIN L9
GF: RPL7A
GG: RPLP0
GH: 60S RIBOSOMAL PROTEIN L10
GI: 60S RIBOSOMAL PROTEIN L13A
GJ: RPL23
GK: 60S RIBOSOMAL PROTEIN L27A
GL: RIBOSOMAL PROTEIN L15
GM: 60S RIBOSOMAL PROTEIN L5
GN: RPL18
GO: RPL19
GP: 60S RIBOSOMAL PROTEIN L21
GQ: RPL17
GR: RPL23A
GS: RPL26
GT: RPL24
GU: RPL35
GV: 60S RIBOSOMAL PROTEIN L7
GW: 60S RIBOSOMAL PROTEIN L31
GX: 60S RIBOSOMAL PROTEIN L32
GY: RPL37A
H1: 26S RRNA
HA: RIBOSOMAL PROTEIN L37
HB: RPL39
HC: 60S RIBOSOMAL PROTEIN L36A
HE: RPL6
HF: RPL14
HG: RPL30
HH: RPL35A
HJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
HK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
HL: RPL34
HM: RIBOSOMAL PROTEIN L22
HN: RPL27
HO: RPL28
HP: RPL38
HQ: 60S RIBOSOMAL PROTEIN L36
HT: RPL29
HU: RPL13
HX: RPL18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,975,7951069
Polymers7,953,463184
Non-polymers22,332885
Water93,4985190
1
A1: 26S RRNA
AA: RIBOSOMAL PROTEIN L37
AB: RPL39
AC: 60S RIBOSOMAL PROTEIN L36A
AE: RPL6
AF: RPL14
AG: RPL30
AH: RPL35A
AJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
AK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
AL: RPL34
AM: RIBOSOMAL PROTEIN L22
AN: RPL27
AO: RPL28
AP: RPL38
AQ: 60S RIBOSOMAL PROTEIN L36
AT: RPL29
AU: RPL13
AX: RPL18A
B2: 5.8S RRNA
B3: 5S RRNA
BA: RPL8
BB: RIBOSOMAL PROTEIN L3
BC: RPL4
BD: 60S RIBOSOMAL PROTEIN L11
BE: 60S RIBOSOMAL PROTEIN L9
BF: RPL7A
BG: RPLP0
BH: 60S RIBOSOMAL PROTEIN L10
BI: 60S RIBOSOMAL PROTEIN L13A
BJ: RPL23
BK: 60S RIBOSOMAL PROTEIN L27A
BL: RIBOSOMAL PROTEIN L15
BM: 60S RIBOSOMAL PROTEIN L5
BN: RPL18
BO: RPL19
BP: 60S RIBOSOMAL PROTEIN L21
BQ: RPL17
BR: RPL23A
BS: RPL26
BT: RPL24
BU: RPL35
BV: 60S RIBOSOMAL PROTEIN L7
BW: 60S RIBOSOMAL PROTEIN L31
BX: 60S RIBOSOMAL PROTEIN L32
BY: RPL37A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,994,325272
Polymers1,988,62646
Non-polymers5,698226
Water52229
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C2: 5.8S RRNA
C3: 5S RRNA
CA: RPL8
CB: RIBOSOMAL PROTEIN L3
CC: RPL4
CD: 60S RIBOSOMAL PROTEIN L11
CE: 60S RIBOSOMAL PROTEIN L9
CF: RPL7A
CG: RPLP0
CH: 60S RIBOSOMAL PROTEIN L10
CI: 60S RIBOSOMAL PROTEIN L13A
CJ: RPL23
CK: 60S RIBOSOMAL PROTEIN L27A
CL: RIBOSOMAL PROTEIN L15
CM: 60S RIBOSOMAL PROTEIN L5
CN: RPL18
CO: RPL19
CP: 60S RIBOSOMAL PROTEIN L21
CQ: RPL17
CR: RPL23A
CS: RPL26
CT: RPL24
CU: RPL35
CV: 60S RIBOSOMAL PROTEIN L7
CW: 60S RIBOSOMAL PROTEIN L31
CX: 60S RIBOSOMAL PROTEIN L32
CY: RPL37A
D1: 26S RRNA
DA: RIBOSOMAL PROTEIN L37
DB: RPL39
DC: 60S RIBOSOMAL PROTEIN L36A
DE: RPL6
DF: RPL14
DG: RPL30
DH: RPL35A
DJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
DK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
DL: RPL34
DM: RIBOSOMAL PROTEIN L22
DN: RPL27
DO: RPL28
DP: RPL38
DQ: 60S RIBOSOMAL PROTEIN L36
DT: RPL29
DU: RPL13
DX: RPL18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,994,206310
Polymers1,987,58446
Non-polymers6,622264
Water57632
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E2: 5.8S RRNA
E3: 5S RRNA
EA: RPL8
EB: RIBOSOMAL PROTEIN L3
EC: RPL4
ED: 60S RIBOSOMAL PROTEIN L11
EE: 60S RIBOSOMAL PROTEIN L9
EF: RPL7A
EG: RPLP0
EH: 60S RIBOSOMAL PROTEIN L10
EI: 60S RIBOSOMAL PROTEIN L13A
EJ: RPL23
EK: 60S RIBOSOMAL PROTEIN L27A
EL: RIBOSOMAL PROTEIN L15
EM: 60S RIBOSOMAL PROTEIN L5
EN: RPL18
EO: RPL19
EP: 60S RIBOSOMAL PROTEIN L21
EQ: RPL17
ER: RPL23A
ES: RPL26
ET: RPL24
EU: RPL35
EV: 60S RIBOSOMAL PROTEIN L7
EW: 60S RIBOSOMAL PROTEIN L31
EX: 60S RIBOSOMAL PROTEIN L32
EY: RPL37A
F1: 26S RRNA
FA: RIBOSOMAL PROTEIN L37
FB: RPL39
FC: 60S RIBOSOMAL PROTEIN L36A
FE: RPL6
FF: RPL14
FG: RPL30
FH: RPL35A
FJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
FK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
FL: RPL34
FM: RIBOSOMAL PROTEIN L22
FN: RPL27
FO: RPL28
FP: RPL38
FQ: 60S RIBOSOMAL PROTEIN L36
FT: RPL29
FU: RPL13
FX: RPL18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,994,033260
Polymers1,988,62646
Non-polymers5,407214
Water48627
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G2: 5.8S RRNA
G3: 5S RRNA
GA: RPL8
GB: RIBOSOMAL PROTEIN L3
GC: RPL4
GD: 60S RIBOSOMAL PROTEIN L11
GE: 60S RIBOSOMAL PROTEIN L9
GF: RPL7A
GG: RPLP0
GH: 60S RIBOSOMAL PROTEIN L10
GI: 60S RIBOSOMAL PROTEIN L13A
GJ: RPL23
GK: 60S RIBOSOMAL PROTEIN L27A
GL: RIBOSOMAL PROTEIN L15
GM: 60S RIBOSOMAL PROTEIN L5
GN: RPL18
GO: RPL19
GP: 60S RIBOSOMAL PROTEIN L21
GQ: RPL17
GR: RPL23A
GS: RPL26
GT: RPL24
GU: RPL35
GV: 60S RIBOSOMAL PROTEIN L7
GW: 60S RIBOSOMAL PROTEIN L31
GX: 60S RIBOSOMAL PROTEIN L32
GY: RPL37A
H1: 26S RRNA
HA: RIBOSOMAL PROTEIN L37
HB: RPL39
HC: 60S RIBOSOMAL PROTEIN L36A
HE: RPL6
HF: RPL14
HG: RPL30
HH: RPL35A
HJ: TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
HK: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
HL: RPL34
HM: RIBOSOMAL PROTEIN L22
HN: RPL27
HO: RPL28
HP: RPL38
HQ: 60S RIBOSOMAL PROTEIN L36
HT: RPL29
HU: RPL13
HX: RPL18A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,993,231227
Polymers1,988,62646
Non-polymers4,605181
Water48627
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)320.190, 289.250, 535.040
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 3 types, 12 molecules A1D1F1H1B2C2E2G2B3C3E3G3

#1: RNA chain
26S RRNA


Mass: 1084310.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: JN547815
#20: RNA chain
5.8S RRNA


Mass: 49800.582 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: JN547815
#21: RNA chain
5S RRNA


Mass: 38740.992 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: J01893

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RIBOSOMAL PROTEIN ... , 4 types, 16 molecules AADAFAHAAMDMFMHMBBCBEBGBBLCLELGL

#2: Protein
RIBOSOMAL PROTEIN L37 / RPL37


Mass: 10703.564 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ24
#12: Protein
RIBOSOMAL PROTEIN L22 / RPL22


Mass: 13804.006 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23BV5
#23: Protein
RIBOSOMAL PROTEIN L3 / RPL3


Mass: 44348.539 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: O96774
#33: Protein
RIBOSOMAL PROTEIN L15 / RPL15


Mass: 24134.201 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22A30

+
Protein , 28 types, 108 molecules ABDBFBHBAEDEFEHEAFDFFFHFAGDGFGHGAHDHFHHHAJDJFJHJAKDKFKHKALDL...

#3: Protein
RPL39


Mass: 6607.818 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ61
#5: Protein
RPL6


Mass: 21777.270 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ56
#6: Protein
RPL14


Mass: 14629.494 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q24C27
#7: Protein
RPL30


Mass: 11368.177 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ59
#8: Protein
RPL35A


Mass: 12650.589 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ22
#9: Protein
TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN / EIF6


Mass: 27188.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q245F2
#10: Protein
UBIQUITIN-60S RIBOSOMAL PROTEIN L40 / UBIQUITIN / 60S RIBOSOMAL PROTEIN L40 / CEP52 / CEP53 RPL40


Mass: 14599.096 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ25
#11: Protein
RPL34


Mass: 14071.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ23
#13: Protein
RPL27


Mass: 16767.939 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ19
#14: Protein
RPL28


Mass: 14695.092 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ20
#15: Protein
RPL38


Mass: 10219.279 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22SV3
#17: Protein
RPL29


Mass: 7742.058 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ21
#18: Protein
RPL13


Mass: 23390.307 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ58
#19: Protein
RPL18A


Mass: 22018.760 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ18
#22: Protein
RPL8


Mass: 28706.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ52
#24: Protein
RPL4


Mass: 45190.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ55
#27: Protein
RPL7A


Mass: 29129.400 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ14
#28: Protein
RPLP0


Mass: 10485.917 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#31: Protein
RPL23


Mass: 14903.538 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ53
#35: Protein
RPL18


Mass: 20632.193 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ17
#36: Protein RPL19


Mass: 21429.377 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ60
#38: Protein
RPL17


Mass: 20417.725 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ16
#39: Protein
RPL23A


Mass: 16897.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ57
#40: Protein
RPL26


Mass: 15421.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23F79
#41: Protein
RPL24


Mass: 18104.650 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ54
#42: Protein
RPL35


Mass: 14231.148 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ51
#46: Protein
RPL37A


Mass: 11375.646 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23G98
#47: Protein RPL19


Mass: 20387.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ60

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60S RIBOSOMAL PROTEIN ... , 12 types, 48 molecules ACDCFCHCAQDQFQHQBDCDEDGDBECEEEGEBHCHEHGHBICIEIGIBKCKEKGKBMCM...

#4: Protein
60S RIBOSOMAL PROTEIN L36A / 60S RIBOSOMAL PROTEIN L44


Mass: 12786.319 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22X38
#16: Protein
60S RIBOSOMAL PROTEIN L36 / RPL36


Mass: 11703.105 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q24F59
#25: Protein
60S RIBOSOMAL PROTEIN L11 / L21 / RPL11


Mass: 19754.959 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P24119
#26: Protein
60S RIBOSOMAL PROTEIN L9 / RPL9


Mass: 21373.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22AX5
#29: Protein
60S RIBOSOMAL PROTEIN L10 / RPL10


Mass: 24511.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q235M8
#30: Protein
60S RIBOSOMAL PROTEIN L13A / RPL13A


Mass: 22641.775 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ15
#32: Protein
60S RIBOSOMAL PROTEIN L27A / L29 / RPL27A


Mass: 16662.867 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q00454
#34: Protein
60S RIBOSOMAL PROTEIN L5 / RPL5


Mass: 34525.941 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q231U7
#37: Protein
60S RIBOSOMAL PROTEIN L21 / RPL21


Mass: 18164.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23TC8
#43: Protein
60S RIBOSOMAL PROTEIN L7 / RPL7


Mass: 27670.322 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0DJ13
#44: Protein
60S RIBOSOMAL PROTEIN L31 / RPL31


Mass: 12990.064 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22DH9
#45: Protein
60S RIBOSOMAL PROTEIN L32 / RPL32


Mass: 15347.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q236T0

-
Non-polymers , 3 types, 6075 molecules

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


Mass: 24.305 Da / Num. of mol.: 865 / Source method: obtained synthetically / Formula: Mg
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
#50: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5190 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsUBIQUITIN FUSION, UBIQUITIN NOT VISIBLE IN STRUCTURE FOR CHAIN K. THE ENTRY 4A18 CONTAINS THE ...UBIQUITIN FUSION, UBIQUITIN NOT VISIBLE IN STRUCTURE FOR CHAIN K. THE ENTRY 4A18 CONTAINS THE PROTEINS THAT ARE DESCRIBED WITH LOWER CASE CHAIN IDS IN THE CITATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 55 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.52→40 Å / Num. obs: 1192534 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 96.88 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.8
Reflection shellResolution: 3.52→3.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHASERmodel building
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JJ2

1jj2


Resolution: 3.52→19.998 Å / SU ML: 0.89 / σ(F): 1.99 / Phase error: 24.46 / Stereochemistry target values: ML / Details: CHAIN G IS MODELLED AS UNK OF PDB ENTRY 1ZAX
RfactorNum. reflection% reflection
Rfree0.2445 9951 0.8 %
Rwork0.2161 --
obs0.2163 1186656 99.42 %
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.324 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 108.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.7797 Å2-0 Å2-13.5499 Å2
2--13.16 Å20 Å2
3---6.6885 Å2
Refinement stepCycle: LAST / Resolution: 3.52→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17189 66769 4 0 83962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.144
X-RAY DIFFRACTIONf_dihedral_angle_d19.426
X-RAY DIFFRACTIONf_chiral_restr0.07599993
X-RAY DIFFRACTIONf_plane_restr0.00650698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.52-3.55980.35233310.331439236X-RAY DIFFRACTION100
3.5598-3.60140.32833320.32339222X-RAY DIFFRACTION100
3.6014-3.64510.35933320.320639184X-RAY DIFFRACTION100
3.6451-3.69090.30763300.308939012X-RAY DIFFRACTION99
3.6909-3.73920.32153320.289439235X-RAY DIFFRACTION100
3.7392-3.79010.3263310.287739308X-RAY DIFFRACTION100
3.7901-3.84380.3063330.278939247X-RAY DIFFRACTION100
3.8438-3.90080.27443320.271839259X-RAY DIFFRACTION100
3.9008-3.96130.30493320.265139273X-RAY DIFFRACTION100
3.9613-4.02570.29583310.253439201X-RAY DIFFRACTION100
4.0257-4.09460.26113310.245639182X-RAY DIFFRACTION100
4.0946-4.16840.26213340.237339371X-RAY DIFFRACTION100
4.1684-4.24780.23193320.225839289X-RAY DIFFRACTION100
4.2478-4.33360.23333320.224439304X-RAY DIFFRACTION100
4.3336-4.42690.26123320.226539225X-RAY DIFFRACTION100
4.4269-4.52870.24923320.219939335X-RAY DIFFRACTION100
4.5287-4.64060.21573320.211739234X-RAY DIFFRACTION100
4.6406-4.76440.24723320.207239145X-RAY DIFFRACTION100
4.7644-4.90260.23493310.199739301X-RAY DIFFRACTION99
4.9026-5.05840.21343310.191538934X-RAY DIFFRACTION99
5.0584-5.23610.21983290.188838944X-RAY DIFFRACTION99
5.2361-5.44160.21463320.1839325X-RAY DIFFRACTION100
5.4416-5.68390.22133330.185939381X-RAY DIFFRACTION100
5.6839-5.9760.23743310.189539192X-RAY DIFFRACTION99
5.976-6.33910.24823330.191439340X-RAY DIFFRACTION99
6.3391-6.81060.20973330.184739354X-RAY DIFFRACTION100
6.8106-7.46340.21273330.174839409X-RAY DIFFRACTION100
7.4634-8.47070.18873330.169439278X-RAY DIFFRACTION99
8.4707-10.4150.20263290.173738920X-RAY DIFFRACTION98
10.415-19.9980.22933300.198239065X-RAY DIFFRACTION98

+
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