[English] 日本語
Yorodumi
- PDB-4v8e: Crystal structure analysis of ribosomal decoding (near-cognate tR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v8e
TitleCrystal structure analysis of ribosomal decoding (near-cognate tRNA-tyr complex).
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 5S RIBOSOMAL RNA
  • MRNA
  • RNA (2912-MER)
  • TRNA-FMET
  • TRNA-TYR
KeywordsRIBOSOME / RNA / tRNA / translation / mRNA
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 L31 type A ...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 L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / 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 S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily
Similarity search - Domain/homology
osmium (III) hexammine / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...osmium (III) hexammine / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / 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 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJenner, L. / Demeshkina, N. / Yusupov, M. / Yusupova, G.
CitationJournal: Nature / Year: 2012
Title: A new understanding of the decoding principle on the ribosome.
Authors: Demeshkina, N. / Jenner, L. / Westhof, E. / Yusupov, M. / Yusupova, G.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3UZF, 3UZG, 3UZH, 3UZI
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
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 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: RNA (2912-MER)
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
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
BB: TRNA-TYR
BC: TRNA-FMET
BD: TRNA-TYR
B1: MRNA
CA: RNA (2912-MER)
CB: 5S RIBOSOMAL RNA
CD: 50S ribosomal protein L2
CE: 50S ribosomal protein L3
CF: 50S ribosomal protein L4
CG: 50S ribosomal protein L5
CH: 50S ribosomal protein L6
CK: 50S ribosomal protein L9
CM: 50S ribosomal protein L13
CN: 50S ribosomal protein L14
CO: 50S ribosomal protein L15
CP: 50S ribosomal protein L16
C0: 50S ribosomal protein L17
CQ: 50S ribosomal protein L18
CR: 50S ribosomal protein L19
C1: 50S ribosomal protein L20
C2: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
C3: 50S ribosomal protein L27
CZ: 50S ribosomal protein L28
CW: 50S ribosomal protein L29
CX: 50S ribosomal protein L30
C4: 50S ribosomal protein L31
C5: 50S ribosomal protein L32
C6: 50S ribosomal protein L33
C7: 50S ribosomal protein L34
C8: 50S ribosomal protein L35
DA: 16S ribosomal RNA
DE: 30S RIBOSOMAL PROTEIN S2
DF: 30S RIBOSOMAL PROTEIN S3
DG: 30S RIBOSOMAL PROTEIN S4
DH: 30S RIBOSOMAL PROTEIN S5
DI: 30S RIBOSOMAL PROTEIN S6
DJ: 30S RIBOSOMAL PROTEIN S7
DK: 30S RIBOSOMAL PROTEIN S8
DL: 30S RIBOSOMAL PROTEIN S9
DM: 30S RIBOSOMAL PROTEIN S10
DN: 30S RIBOSOMAL PROTEIN S11
DO: 30S RIBOSOMAL PROTEIN S12
DP: 30S RIBOSOMAL PROTEIN S13
DQ: 30S RIBOSOMAL PROTEIN S14
DR: 30S RIBOSOMAL PROTEIN S15
DS: 30S RIBOSOMAL PROTEIN S16
DT: 30S RIBOSOMAL PROTEIN S17
DU: 30S RIBOSOMAL PROTEIN S18
DV: 30S RIBOSOMAL PROTEIN S19
DW: 30S RIBOSOMAL PROTEIN S20
DX: 30S RIBOSOMAL PROTEIN THX
DB: TRNA-TYR
DC: TRNA-FMET
DD: TRNA-TYR
D1: MRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,712,1491720
Polymers4,486,266110
Non-polymers225,8821610
Water00
1
AA: RNA (2912-MER)
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
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
BB: TRNA-TYR
BC: TRNA-FMET
BD: TRNA-TYR
B1: MRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,360,861906
Polymers2,243,13355
Non-polymers117,728851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: RNA (2912-MER)
CB: 5S RIBOSOMAL RNA
CD: 50S ribosomal protein L2
CE: 50S ribosomal protein L3
CF: 50S ribosomal protein L4
CG: 50S ribosomal protein L5
CH: 50S ribosomal protein L6
CK: 50S ribosomal protein L9
CM: 50S ribosomal protein L13
CN: 50S ribosomal protein L14
CO: 50S ribosomal protein L15
CP: 50S ribosomal protein L16
C0: 50S ribosomal protein L17
CQ: 50S ribosomal protein L18
CR: 50S ribosomal protein L19
C1: 50S ribosomal protein L20
C2: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
C3: 50S ribosomal protein L27
CZ: 50S ribosomal protein L28
CW: 50S ribosomal protein L29
CX: 50S ribosomal protein L30
C4: 50S ribosomal protein L31
C5: 50S ribosomal protein L32
C6: 50S ribosomal protein L33
C7: 50S ribosomal protein L34
C8: 50S ribosomal protein L35
DA: 16S ribosomal RNA
DE: 30S RIBOSOMAL PROTEIN S2
DF: 30S RIBOSOMAL PROTEIN S3
DG: 30S RIBOSOMAL PROTEIN S4
DH: 30S RIBOSOMAL PROTEIN S5
DI: 30S RIBOSOMAL PROTEIN S6
DJ: 30S RIBOSOMAL PROTEIN S7
DK: 30S RIBOSOMAL PROTEIN S8
DL: 30S RIBOSOMAL PROTEIN S9
DM: 30S RIBOSOMAL PROTEIN S10
DN: 30S RIBOSOMAL PROTEIN S11
DO: 30S RIBOSOMAL PROTEIN S12
DP: 30S RIBOSOMAL PROTEIN S13
DQ: 30S RIBOSOMAL PROTEIN S14
DR: 30S RIBOSOMAL PROTEIN S15
DS: 30S RIBOSOMAL PROTEIN S16
DT: 30S RIBOSOMAL PROTEIN S17
DU: 30S RIBOSOMAL PROTEIN S18
DV: 30S RIBOSOMAL PROTEIN S19
DW: 30S RIBOSOMAL PROTEIN S20
DX: 30S RIBOSOMAL PROTEIN THX
DB: TRNA-TYR
DC: TRNA-FMET
DD: TRNA-TYR
D1: MRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,351,287814
Polymers2,243,13355
Non-polymers108,154759
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.250, 450.870, 622.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
RNA chain , 6 types, 14 molecules AACAABCBBADABBBDDBDDBCDCB1D1

#1: RNA chain RNA (2912-MER)


Mass: 947013.000 Da / Num. of mol.: 2 / 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: AP008226.1
#31: RNA chain 16S ribosomal RNA


Mass: 489002.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#52: RNA chain
TRNA-TYR


Mass: 27402.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: GenBank: AP012306.1
#53: RNA chain TRNA-FMET


Mass: 24801.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: GenBank: AP012306.1
#54: RNA chain MRNA


Mass: 5177.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct

+
50S ribosomal protein ... , 28 types, 56 molecules ADCDAECEAFCFAGCGAHCHAKCKAMCMANCNAOCOAPCPA0C0AQCQARCRA1C1A2C2...

#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

-
30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules BEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQBRDRBSDS...

#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: 24242.254 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


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: A0A0M9AFS9*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


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*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: A0A0N0BLS5*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


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: Q5SIH3

-
Non-polymers , 3 types, 1610 molecules

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


Mass: 24.305 Da / Num. of mol.: 894 / Source method: obtained synthetically / Formula: Mg
#56: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 712 / Source method: obtained synthetically / Formula: H12N6Os
#57: Chemical
ChemComp-ZN / ZINC ION


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 11, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→300 Å / Num. all: 962504 / Num. obs: 962434 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 95.831 Å2 / Rmerge(I) obs: 0.299 / Net I/σ(I): 8.53
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.2-3.31.171549319842961100
3.3-3.41.61384863747511100
3.4-3.51.931241346664931100
3.5-3.62.431168250592191100
3.6-3.73.041047225531361100
3.7-44.2925011231293031100
4-4.256.11523492817341100
4.25-4.57.921235379646671100
4.5-4.759.681011767517471100
4.75-511.27812464419741100
5-614.2719869731066121100
6-7181051067544291100
7-821.21543168306651100
8-923.57326045185941100
9-1026.77441278119801100
10-5033.481150794325281100
50-20075.474662305197.8
200-30047.2231133.3
1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_810refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
PHENIXmodel building
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→256.189 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8272 / SU ML: 0.97 / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1825 0.21 %Random
Rwork0.206 ---
obs0.2061 878027 99.98 %-
all-962504 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.746 Å2 / ksol: 0.234 e/Å3
Displacement parametersBiso max: 254.47 Å2 / Biso mean: 91.1434 Å2 / Biso min: 18.31 Å2
Baniso -1Baniso -2Baniso -3
1--23.3825 Å20 Å20 Å2
2--3.4306 Å20 Å2
3---19.9519 Å2
Refinement stepCycle: LAST / Resolution: 3.3→256.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26679 65324 0 0 92003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014340109
X-RAY DIFFRACTIONf_angle_d0.694500297
X-RAY DIFFRACTIONf_chiral_restr0.07262114
X-RAY DIFFRACTIONf_plane_restr0.00426270
X-RAY DIFFRACTIONf_dihedral_angle_d18.943153261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.38920.30981390.28356703767176
3.3892-3.4890.31961400.26926688667026
3.489-3.60160.28991400.2436703567175
3.6016-3.73030.25891400.21766703567175
3.7303-3.87970.26271390.20476710267241
3.8797-4.05630.27041400.20036714667286
4.0563-4.27020.27581400.1916714467284
4.2702-4.53770.24371400.18316726667406
4.5377-4.88810.24121400.17326736267502
4.8881-5.38010.24331410.17186746067601
5.3801-6.15860.23721400.17656762967769
6.1586-7.75930.22631410.1986794968090
7.7593-256.96390.27811450.23886915169296

+
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