[English] 日本語
Yorodumi
- PDB-4xej: IRES bound to bacterial Ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xej
TitleIRES bound to bacterial Ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • IRES RNA
KeywordsRIBOSOME / Internal Ribosome Entry Site / IRES / 70S / bacterial initiation
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 / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small 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 / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / 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 S14/S29 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein bTHX ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
Similarity search - Component
Biological speciesPlautia stali intestine virus
Thermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsZhu, J. / Korostelev, A. / Noller, H.F. / Donohue, J.P.
CitationJournal: Nature / Year: 2015
Title: Initiation of translation in bacteria by a structured eukaryotic IRES RNA.
Authors: Colussi, T.M. / Costantino, D.A. / Zhu, J. / Donohue, J.P. / Korostelev, A.A. / Jaafar, Z.A. / Plank, T.D. / Noller, H.F. / Kieft, J.S.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Data collection
Revision 1.3Jul 6, 2016Group: Data collection
Revision 1.4Sep 28, 2016Group: Data collection
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AL02: 50S ribosomal protein L2
AL03: 50S ribosomal protein L3
AL04: 50S ribosomal protein L4
AL05: 50S ribosomal protein L5
AL06: 50S ribosomal protein L6
AL09: 50S ribosomal protein L9
AL11: 50S ribosomal protein L11
AL13: 50S ribosomal protein L13
AL14: 50S ribosomal protein L14
AL15: 50S ribosomal protein L15
AL16: 50S ribosomal protein L16
AL17: 50S ribosomal protein L17
AL18: 50S ribosomal protein L18
AL19: 50S ribosomal protein L19
AL20: 50S ribosomal protein L20
AL21: 50S ribosomal protein L21
AL22: 50S ribosomal protein L22
AL23: 50S ribosomal protein L23
AL24: 50S ribosomal protein L24
AL25: 50S ribosomal protein L25
AL27: 50S ribosomal protein L27
AL28: 50S ribosomal protein L28
AL29: 50S ribosomal protein L29
AL30: 50S ribosomal protein L30
AL32: 50S ribosomal protein L32
AL33: 50S ribosomal protein L33
AL34: 50S ribosomal protein L34
AL35: 50S ribosomal protein L35
AS02: 30S ribosomal protein S2
AS03: 30S ribosomal protein S3
AS04: 30S ribosomal protein S4
AS05: 30S ribosomal protein S5
AS06: 30S ribosomal protein S6
AS07: 30S ribosomal protein S7
AS08: 30S ribosomal protein S8
AS09: 30S ribosomal protein S9
AS10: 30S ribosomal protein S10
AS11: 30S ribosomal protein S11
AS12: 30S ribosomal protein S12
AS13: 30S ribosomal protein S13
AS14: 30S ribosomal protein S14
AS15: 30S ribosomal protein S15
AS16: 30S ribosomal protein S16
AS17: 30S ribosomal protein S17
AS18: 30S ribosomal protein S18
AS19: 30S ribosomal protein S19
AS20: 30S ribosomal protein S20
ATHX: 30S ribosomal protein Thx
BL02: 50S ribosomal protein L2
BL03: 50S ribosomal protein L3
BL04: 50S ribosomal protein L4
BL05: 50S ribosomal protein L5
BL06: 50S ribosomal protein L6
BL09: 50S ribosomal protein L9
BL11: 50S ribosomal protein L11
BL13: 50S ribosomal protein L13
BL14: 50S ribosomal protein L14
BL15: 50S ribosomal protein L15
BL16: 50S ribosomal protein L16
BL17: 50S ribosomal protein L17
BL18: 50S ribosomal protein L18
BL19: 50S ribosomal protein L19
BL20: 50S ribosomal protein L20
BL21: 50S ribosomal protein L21
BL22: 50S ribosomal protein L22
BL23: 50S ribosomal protein L23
BL24: 50S ribosomal protein L24
BL25: 50S ribosomal protein L25
BL27: 50S ribosomal protein L27
BL28: 50S ribosomal protein L28
BL29: 50S ribosomal protein L29
BL30: 50S ribosomal protein L30
BL32: 50S ribosomal protein L32
BL33: 50S ribosomal protein L33
BL34: 50S ribosomal protein L34
BL35: 50S ribosomal protein L35
BS02: 30S ribosomal protein S2
BS03: 30S ribosomal protein S3
BS04: 30S ribosomal protein S4
BS05: 30S ribosomal protein S5
BS06: 30S ribosomal protein S6
BS07: 30S ribosomal protein S7
BS08: 30S ribosomal protein S8
BS09: 30S ribosomal protein S9
BS10: 30S ribosomal protein S10
BS11: 30S ribosomal protein S11
BS12: 30S ribosomal protein S12
BS13: 30S ribosomal protein S13
BS14: 30S ribosomal protein S14
BS15: 30S ribosomal protein S15
BS16: 30S ribosomal protein S16
BS17: 30S ribosomal protein S17
BS18: 30S ribosomal protein S18
BS19: 30S ribosomal protein S19
BS20: 30S ribosomal protein S20
BTHX: 30S ribosomal protein Thx
AL31: 50S ribosomal protein L31
BL31: 50S ribosomal protein L31
A16S: 16S ribosomal RNA
A23S: 23S ribosomal RNA
A5S: 5S ribosomal RNA
B16S: 16S ribosomal RNA
B23S: 23S ribosomal RNA
B5S: 5S ribosomal RNA
AIRE: IRES RNA
BIRE: IRES RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,366,159110
Polymers4,365,898106
Non-polymers2624
Water00
1
AL02: 50S ribosomal protein L2
AL03: 50S ribosomal protein L3
AL04: 50S ribosomal protein L4
AL05: 50S ribosomal protein L5
AL06: 50S ribosomal protein L6
AL09: 50S ribosomal protein L9
AL11: 50S ribosomal protein L11
AL13: 50S ribosomal protein L13
AL14: 50S ribosomal protein L14
AL15: 50S ribosomal protein L15
AL16: 50S ribosomal protein L16
AL17: 50S ribosomal protein L17
AL18: 50S ribosomal protein L18
AL19: 50S ribosomal protein L19
AL20: 50S ribosomal protein L20
AL21: 50S ribosomal protein L21
AL22: 50S ribosomal protein L22
AL23: 50S ribosomal protein L23
AL24: 50S ribosomal protein L24
AL25: 50S ribosomal protein L25
AL27: 50S ribosomal protein L27
AL28: 50S ribosomal protein L28
AL29: 50S ribosomal protein L29
AL30: 50S ribosomal protein L30
AL32: 50S ribosomal protein L32
AL33: 50S ribosomal protein L33
AL34: 50S ribosomal protein L34
AL35: 50S ribosomal protein L35
AS02: 30S ribosomal protein S2
AS03: 30S ribosomal protein S3
AS04: 30S ribosomal protein S4
AS05: 30S ribosomal protein S5
AS06: 30S ribosomal protein S6
AS07: 30S ribosomal protein S7
AS08: 30S ribosomal protein S8
AS09: 30S ribosomal protein S9
AS10: 30S ribosomal protein S10
AS11: 30S ribosomal protein S11
AS12: 30S ribosomal protein S12
AS13: 30S ribosomal protein S13
AS14: 30S ribosomal protein S14
AS15: 30S ribosomal protein S15
AS16: 30S ribosomal protein S16
AS17: 30S ribosomal protein S17
AS18: 30S ribosomal protein S18
AS19: 30S ribosomal protein S19
AS20: 30S ribosomal protein S20
ATHX: 30S ribosomal protein Thx
AL31: 50S ribosomal protein L31
A16S: 16S ribosomal RNA
A23S: 23S ribosomal RNA
A5S: 5S ribosomal RNA
AIRE: IRES RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,183,08055
Polymers2,182,94953
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BL02: 50S ribosomal protein L2
BL03: 50S ribosomal protein L3
BL04: 50S ribosomal protein L4
BL05: 50S ribosomal protein L5
BL06: 50S ribosomal protein L6
BL09: 50S ribosomal protein L9
BL11: 50S ribosomal protein L11
BL13: 50S ribosomal protein L13
BL14: 50S ribosomal protein L14
BL15: 50S ribosomal protein L15
BL16: 50S ribosomal protein L16
BL17: 50S ribosomal protein L17
BL18: 50S ribosomal protein L18
BL19: 50S ribosomal protein L19
BL20: 50S ribosomal protein L20
BL21: 50S ribosomal protein L21
BL22: 50S ribosomal protein L22
BL23: 50S ribosomal protein L23
BL24: 50S ribosomal protein L24
BL25: 50S ribosomal protein L25
BL27: 50S ribosomal protein L27
BL28: 50S ribosomal protein L28
BL29: 50S ribosomal protein L29
BL30: 50S ribosomal protein L30
BL32: 50S ribosomal protein L32
BL33: 50S ribosomal protein L33
BL34: 50S ribosomal protein L34
BL35: 50S ribosomal protein L35
BS02: 30S ribosomal protein S2
BS03: 30S ribosomal protein S3
BS04: 30S ribosomal protein S4
BS05: 30S ribosomal protein S5
BS06: 30S ribosomal protein S6
BS07: 30S ribosomal protein S7
BS08: 30S ribosomal protein S8
BS09: 30S ribosomal protein S9
BS10: 30S ribosomal protein S10
BS11: 30S ribosomal protein S11
BS12: 30S ribosomal protein S12
BS13: 30S ribosomal protein S13
BS14: 30S ribosomal protein S14
BS15: 30S ribosomal protein S15
BS16: 30S ribosomal protein S16
BS17: 30S ribosomal protein S17
BS18: 30S ribosomal protein S18
BS19: 30S ribosomal protein S19
BS20: 30S ribosomal protein S20
BTHX: 30S ribosomal protein Thx
BL31: 50S ribosomal protein L31
B16S: 16S ribosomal RNA
B23S: 23S ribosomal RNA
B5S: 5S ribosomal RNA
BIRE: IRES RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,183,08055
Polymers2,182,94953
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.050, 447.220, 608.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

+
50S ribosomal protein ... , 29 types, 58 molecules AL02BL02AL03BL03AL04BL04AL05BL05AL06BL06AL09BL09AL11BL11AL13BL13AL14BL14AL15BL15AL16BL16AL17BL17AL18BL18AL19BL19AL20BL20...

#1: Protein 50S ribosomal protein L2


Mass: 29828.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I07
#2: Protein 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I04
#3: Protein 50S ribosomal protein L4


Mass: 22487.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I05
#4: Protein 50S ribosomal protein L5


Mass: 20944.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I16
#5: Protein 50S ribosomal protein L6


Mass: 17363.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I19
#6: Protein 50S ribosomal protein L9


Mass: 16107.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GV5
#7: Protein 50S ribosomal protein L11


Mass: 15526.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62442
#8: Protein 50S ribosomal protein L13


Mass: 15568.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72IN1
#9: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I14
#10: Protein 50S ribosomal protein L15


Mass: 15858.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I23
#11: Protein 50S ribosomal protein L16


Mass: 15148.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I11
#12: Protein 50S ribosomal protein L17


Mass: 13618.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I33
#13: Protein 50S ribosomal protein L18


Mass: 10941.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I20
#14: Protein 50S ribosomal protein L19


Mass: 16247.915 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72JU9
#15: Protein 50S ribosomal protein L20


Mass: 13648.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72L76
#16: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72HR2
#17: Protein 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I09
#18: Protein 50S ribosomal protein L23


Mass: 10273.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I06
#19: Protein 50S ribosomal protein L24


Mass: 11078.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I15
#20: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 21021.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72IA7
#21: Protein 50S ribosomal protein L27


Mass: 8587.940 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72HR3
#22: Protein 50S ribosomal protein L28


Mass: 9884.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72G84
#23: Protein 50S ribosomal protein L29


Mass: 7457.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I12
#24: Protein 50S ribosomal protein L30


Mass: 6670.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72I22
#25: Protein 50S ribosomal protein L32


Mass: 5818.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62652
#26: Protein/peptide 50S ribosomal protein L33


Mass: 5473.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GW3
#27: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P80340
#28: Protein 50S ribosomal protein L35


Mass: 7245.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72L77
#49: Protein/peptide 50S ribosomal protein L31


Mass: 3278.860 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72JR0

-
30S ribosomal protein ... , 20 types, 40 molecules AS02BS02AS03BS03AS04BS04AS05BS05AS06BS06AS07BS07AS08BS08AS09BS09AS10BS10AS11BS11AS12BS12AS13BS13AS14BS14AS15BS15AS16BS16...

#29: Protein 30S ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62662
#30: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62663
#31: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62664
#32: Protein 30S ribosomal protein S5


Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62665
#33: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62666
#34: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62667
#35: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62668
#36: Protein 30S ribosomal protein S9


Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62669
#37: Protein 30S ribosomal protein S10


Mass: 11299.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62653
#38: Protein 30S ribosomal protein S11


Mass: 12014.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62654
#39: Protein 30S ribosomal protein S12


Mass: 13604.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P61941
#40: Protein 30S ribosomal protein S13


Mass: 13308.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62655
#41: Protein 30S ribosomal protein S14


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62656
#42: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62657
#43: Protein 30S ribosomal protein S16


Mass: 9924.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62238
#44: Protein 30S ribosomal protein S17


Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62658
#45: Protein 30S ribosomal protein S18


Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62659
#46: Protein 30S ribosomal protein S19


Mass: 8949.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62660
#47: Protein 30S ribosomal protein S20


Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62661
#48: Protein/peptide 30S ribosomal protein Thx


Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: P62613

-
RNA chain , 4 types, 8 molecules A16SB16SA23SB23SA5SB5SAIREBIRE

#50: RNA chain 16S ribosomal RNA


Mass: 489042.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#51: RNA chain 23S ribosomal RNA


Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#52: RNA chain 5S ribosomal RNA


Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#53: RNA chain IRES RNA


Mass: 62739.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plautia stali intestine virus / Production host: Escherichia coli (E. coli) / References: GenBank: 2344756

-
Non-polymers , 1 types, 4 molecules

#54: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Details

Has protein modificationY
Sequence detailsTHE AUTHORS BELIEVE THAT THE C1161U CONFLICT IS AN ERROR IN THE SEQUENCE DATABASE. G2808U CHANGE IS ...THE AUTHORS BELIEVE THAT THE C1161U CONFLICT IS AN ERROR IN THE SEQUENCE DATABASE. G2808U CHANGE IS A SUBSTITUTION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art ...Details: Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art Robbins) on 96-well plates. Once optimal crystallization conditions were determined, crystals were grown by the sitting-drop vapor-diffusion method using drops dispensed by the Phoenix with 1- to 2-mL ribosome complexes mixed with 1-2 mL of reservoir solution [100 mM Tris-OAc, pH 7.0, 200 mM potassium thiocyanate (KSCN), 3.6-5% PEG 20,000, 6-14% 2-methyl-2,4-pentanediol (MPD)] at 22.5C. Crystals emerged after 5-7 d and matured between 2-3 wk. Crystals were then subjected to cryoprotection by gradually replacing the mother liquor with cryoprotection buffer I (100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 5% PEG 20,000, 25% MPD, 14% PEG 200, and 10 mM Mg(OAc)2). The crystals then were flash-frozen by plunging into liquid nitrogen.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.8→60 Å / Num. obs: 555726 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.995 / Rrim(I) all: 0.2 / Net I/σ(I): 8.28
Reflection shellResolution: 3.8→4 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.998 / Rrim(I) all: 1.6 / % possible all: 99.8

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4V83

4v83


Resolution: 3.8→60 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.284 2000 -
Rwork0.246 553726 -
obs-555726 99.9 %
Refinement stepCycle: LAST / Resolution: 3.8→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms92320 194969 4 0 287293

+
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