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- PDB-4v5a: Structure of the Ribosome Recycling Factor bound to the Thermus t... -

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Basic information

Entry
Database: PDB / ID: 4v5a
TitleStructure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMet
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • MRNAMessenger RNA
  • P-SITE RNA ASL-PHE
  • RIBOSOME RECYCLING FACTOR
  • TRNA-FMET
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / TRNA-BINDING / RRNA-BINDING / METAL-BINDING / RRF / TRNA / MRNA / RECYCLING / PROTEIN BIOSYNTHESIS / RNA-BINDING / ZINC-FINGER / TRANSLATION
Function / homology
Function and homology information


translational termination / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...translational termination / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L1, 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 L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 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 S14/S29 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
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 ...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 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Ribosome-recycling factor / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus HB8 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWeixlbaumer, A. / Petry, S. / Dunham, C.M. / Selmer, M. / Kelley, A.C. / Ramakrishnan, V.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2007
Title: Crystal structure of the ribosome recycling factor bound to the ribosome.
Authors: Weixlbaumer, A. / Petry, S. / Dunham, C.M. / Selmer, M. / Kelley, A.C. / Ramakrishnan, V.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2V46, 2V47, 2V48, 2V49
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 7, 2018Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_entity_src_syn / software
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _software.name
Revision 1.4Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: entity_src_nat / struct_conn / struct_ref_seq
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.5Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S RIBOSOMAL PROTEIN S2
AC: 30S RIBOSOMAL PROTEIN S3
AD: 30S RIBOSOMAL PROTEIN S4
AE: 30S RIBOSOMAL PROTEIN S5
AF: 30S RIBOSOMAL PROTEIN S6
AG: 30S RIBOSOMAL PROTEIN S7
AH: 30S RIBOSOMAL PROTEIN S8
AI: 30S RIBOSOMAL PROTEIN S9
AJ: 30S RIBOSOMAL PROTEIN S10
AK: 30S RIBOSOMAL PROTEIN S11
AL: 30S RIBOSOMAL PROTEIN S12
AM: 30S RIBOSOMAL PROTEIN S13
AN: 30S RIBOSOMAL PROTEIN S14
AO: 30S RIBOSOMAL PROTEIN S15
AP: 30S RIBOSOMAL PROTEIN S16
AQ: 30S RIBOSOMAL PROTEIN S17
AR: 30S RIBOSOMAL PROTEIN S18
AS: 30S RIBOSOMAL PROTEIN S19
AT: 30S RIBOSOMAL PROTEIN S20
AU: 30S RIBOSOMAL PROTEIN THX
AV: P-SITE RNA ASL-PHE
AW: TRNA-FMET
AX: MRNA
AY: RIBOSOME RECYCLING FACTOR
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
B4: 50S RIBOSOMAL PROTEIN L31
B5: 50S RIBOSOMAL PROTEIN L32
B6: 50S RIBOSOMAL PROTEIN L33
B7: 50S RIBOSOMAL PROTEIN L34
B8: 50S RIBOSOMAL PROTEIN L35
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S RIBOSOMAL PROTEIN L1
BD: 50S RIBOSOMAL PROTEIN L2
BE: 50S RIBOSOMAL PROTEIN L3
BF: 50S RIBOSOMAL PROTEIN L4
BG: 50S RIBOSOMAL PROTEIN L5
BH: 50S RIBOSOMAL PROTEIN L6
BI: 50S RIBOSOMAL PROTEIN L9
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
CA: 16S ribosomal RNA
CB: 30S RIBOSOMAL PROTEIN S2
CC: 30S RIBOSOMAL PROTEIN S3
CD: 30S RIBOSOMAL PROTEIN S4
CE: 30S RIBOSOMAL PROTEIN S5
CF: 30S RIBOSOMAL PROTEIN S6
CG: 30S RIBOSOMAL PROTEIN S7
CH: 30S RIBOSOMAL PROTEIN S8
CI: 30S RIBOSOMAL PROTEIN S9
CJ: 30S RIBOSOMAL PROTEIN S10
CK: 30S RIBOSOMAL PROTEIN S11
CL: 30S RIBOSOMAL PROTEIN S12
CM: 30S RIBOSOMAL PROTEIN S13
CN: 30S RIBOSOMAL PROTEIN S14
CO: 30S RIBOSOMAL PROTEIN S15
CP: 30S RIBOSOMAL PROTEIN S16
CQ: 30S RIBOSOMAL PROTEIN S17
CR: 30S RIBOSOMAL PROTEIN S18
CS: 30S RIBOSOMAL PROTEIN S19
CT: 30S RIBOSOMAL PROTEIN S20
CU: 30S RIBOSOMAL PROTEIN THX
CV: P-SITE RNA ASL-PHE
CW: TRNA-FMET
CX: MRNA
CY: RIBOSOME RECYCLING FACTOR
D0: 50S RIBOSOMAL PROTEIN L27
D1: 50S RIBOSOMAL PROTEIN L28
D2: 50S RIBOSOMAL PROTEIN L29
D3: 50S RIBOSOMAL PROTEIN L30
D4: 50S RIBOSOMAL PROTEIN L31
D5: 50S RIBOSOMAL PROTEIN L32
D6: 50S RIBOSOMAL PROTEIN L33
D7: 50S RIBOSOMAL PROTEIN L34
D8: 50S RIBOSOMAL PROTEIN L35
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DC: 50S RIBOSOMAL PROTEIN L1
DD: 50S RIBOSOMAL PROTEIN L2
DE: 50S RIBOSOMAL PROTEIN L3
DF: 50S RIBOSOMAL PROTEIN L4
DG: 50S RIBOSOMAL PROTEIN L5
DH: 50S RIBOSOMAL PROTEIN L6
DI: 50S RIBOSOMAL PROTEIN L9
DN: 50S RIBOSOMAL PROTEIN L13
DO: 50S RIBOSOMAL PROTEIN L14
DP: 50S RIBOSOMAL PROTEIN L15
DQ: 50S RIBOSOMAL PROTEIN L16
DR: 50S RIBOSOMAL PROTEIN L17
DS: 50S RIBOSOMAL PROTEIN L18
DT: 50S RIBOSOMAL PROTEIN L19
DU: 50S RIBOSOMAL PROTEIN L20
DV: 50S RIBOSOMAL PROTEIN L21
DW: 50S RIBOSOMAL PROTEIN L22
DX: 50S RIBOSOMAL PROTEIN L23
DY: 50S RIBOSOMAL PROTEIN L24
DZ: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,489,9851598
Polymers4,453,703112
Non-polymers36,2821486
Water0
1
AA: 16S ribosomal RNA
AB: 30S RIBOSOMAL PROTEIN S2
AC: 30S RIBOSOMAL PROTEIN S3
AD: 30S RIBOSOMAL PROTEIN S4
AE: 30S RIBOSOMAL PROTEIN S5
AF: 30S RIBOSOMAL PROTEIN S6
AG: 30S RIBOSOMAL PROTEIN S7
AH: 30S RIBOSOMAL PROTEIN S8
AI: 30S RIBOSOMAL PROTEIN S9
AJ: 30S RIBOSOMAL PROTEIN S10
AK: 30S RIBOSOMAL PROTEIN S11
AL: 30S RIBOSOMAL PROTEIN S12
AM: 30S RIBOSOMAL PROTEIN S13
AN: 30S RIBOSOMAL PROTEIN S14
AO: 30S RIBOSOMAL PROTEIN S15
AP: 30S RIBOSOMAL PROTEIN S16
AQ: 30S RIBOSOMAL PROTEIN S17
AR: 30S RIBOSOMAL PROTEIN S18
AS: 30S RIBOSOMAL PROTEIN S19
AT: 30S RIBOSOMAL PROTEIN S20
AU: 30S RIBOSOMAL PROTEIN THX
AV: P-SITE RNA ASL-PHE
AW: TRNA-FMET
AX: MRNA
AY: RIBOSOME RECYCLING FACTOR
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
B4: 50S RIBOSOMAL PROTEIN L31
B5: 50S RIBOSOMAL PROTEIN L32
B6: 50S RIBOSOMAL PROTEIN L33
B7: 50S RIBOSOMAL PROTEIN L34
B8: 50S RIBOSOMAL PROTEIN L35
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S RIBOSOMAL PROTEIN L1
BD: 50S RIBOSOMAL PROTEIN L2
BE: 50S RIBOSOMAL PROTEIN L3
BF: 50S RIBOSOMAL PROTEIN L4
BG: 50S RIBOSOMAL PROTEIN L5
BH: 50S RIBOSOMAL PROTEIN L6
BI: 50S RIBOSOMAL PROTEIN L9
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,244,992799
Polymers2,226,85256
Non-polymers18,141743
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area278800 Å2
ΔGint-161.9 kcal/mol
Surface area983160 Å2
MethodPQS
2
CA: 16S ribosomal RNA
CB: 30S RIBOSOMAL PROTEIN S2
CC: 30S RIBOSOMAL PROTEIN S3
CD: 30S RIBOSOMAL PROTEIN S4
CE: 30S RIBOSOMAL PROTEIN S5
CF: 30S RIBOSOMAL PROTEIN S6
CG: 30S RIBOSOMAL PROTEIN S7
CH: 30S RIBOSOMAL PROTEIN S8
CI: 30S RIBOSOMAL PROTEIN S9
CJ: 30S RIBOSOMAL PROTEIN S10
CK: 30S RIBOSOMAL PROTEIN S11
CL: 30S RIBOSOMAL PROTEIN S12
CM: 30S RIBOSOMAL PROTEIN S13
CN: 30S RIBOSOMAL PROTEIN S14
CO: 30S RIBOSOMAL PROTEIN S15
CP: 30S RIBOSOMAL PROTEIN S16
CQ: 30S RIBOSOMAL PROTEIN S17
CR: 30S RIBOSOMAL PROTEIN S18
CS: 30S RIBOSOMAL PROTEIN S19
CT: 30S RIBOSOMAL PROTEIN S20
CU: 30S RIBOSOMAL PROTEIN THX
CV: P-SITE RNA ASL-PHE
CW: TRNA-FMET
CX: MRNA
CY: RIBOSOME RECYCLING FACTOR
D0: 50S RIBOSOMAL PROTEIN L27
D1: 50S RIBOSOMAL PROTEIN L28
D2: 50S RIBOSOMAL PROTEIN L29
D3: 50S RIBOSOMAL PROTEIN L30
D4: 50S RIBOSOMAL PROTEIN L31
D5: 50S RIBOSOMAL PROTEIN L32
D6: 50S RIBOSOMAL PROTEIN L33
D7: 50S RIBOSOMAL PROTEIN L34
D8: 50S RIBOSOMAL PROTEIN L35
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DC: 50S RIBOSOMAL PROTEIN L1
DD: 50S RIBOSOMAL PROTEIN L2
DE: 50S RIBOSOMAL PROTEIN L3
DF: 50S RIBOSOMAL PROTEIN L4
DG: 50S RIBOSOMAL PROTEIN L5
DH: 50S RIBOSOMAL PROTEIN L6
DI: 50S RIBOSOMAL PROTEIN L9
DN: 50S RIBOSOMAL PROTEIN L13
DO: 50S RIBOSOMAL PROTEIN L14
DP: 50S RIBOSOMAL PROTEIN L15
DQ: 50S RIBOSOMAL PROTEIN L16
DR: 50S RIBOSOMAL PROTEIN L17
DS: 50S RIBOSOMAL PROTEIN L18
DT: 50S RIBOSOMAL PROTEIN L19
DU: 50S RIBOSOMAL PROTEIN L20
DV: 50S RIBOSOMAL PROTEIN L21
DW: 50S RIBOSOMAL PROTEIN L22
DX: 50S RIBOSOMAL PROTEIN L23
DY: 50S RIBOSOMAL PROTEIN L24
DZ: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,244,992799
Polymers2,226,85256
Non-polymers18,141743
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area279290 Å2
ΔGint-161.6 kcal/mol
Surface area991970 Å2
MethodPQS
Unit cell
Length a, b, c (Å)212.414, 450.107, 630.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 6 types, 12 molecules AACAAVCVAWCWAXCXBADABBDB

#1: RNA chain 16S ribosomal RNA /


Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY.
Source: (natural) Thermus thermophilus HB8 (bacteria)
#22: RNA chain P-SITE RNA ASL-PHE


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: RNA chain TRNA-FMET


Mass: 24816.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#24: RNA chain MRNA / Messenger RNA


Mass: 10087.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: RNA chain 23S ribosomal RNA /


Mass: 904824.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source: (natural) Thermus thermophilus HB8 (bacteria)
#36: RNA chain 5S ribosomal RNA /


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria)

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30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...

#2: Protein 30S RIBOSOMAL PROTEIN S2 /


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


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


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


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


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


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


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P62669
#10: Protein 30S RIBOSOMAL PROTEIN S10 /


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


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


Mass: 14920.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHN3
#13: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80377
#14: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15 /


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


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


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18 /


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


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


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80380
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome


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

-
Protein , 1 types, 2 molecules AYCY

#25: Protein RIBOSOME RECYCLING FACTOR / / RRF


Mass: 21029.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q9WX76

+
50S RIBOSOMAL PROTEIN ... , 29 types, 58 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8BCDCBDDDBEDEBFDFBGDGBHDH...

#26: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9557.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P60493
#27: Protein 50S RIBOSOMAL PROTEIN L28 /


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


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


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


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


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


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P35871
#33: 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 HB8 (bacteria) / References: UniProt: P80340
#34: Protein 50S RIBOSOMAL PROTEIN L35 /


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: P80341, UniProt: Q5SKU1*PLUS
#37: Protein 50S RIBOSOMAL PROTEIN L1 /


Mass: 24900.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SLP7
#38: Protein 50S RIBOSOMAL PROTEIN L2 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHZ1

-
Non-polymers , 2 types, 1486 molecules

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


Mass: 24.305 Da / Num. of mol.: 1482 / Source method: obtained synthetically / Formula: Mg
#58: Chemical
ChemComp-ZN / ZINC ION


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.65 % / Description: NONE
Crystal growpH: 7 / Details: COMPARE SELMER ET AL SCIENCE 2006, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97943
DetectorType: ADSC / Detector: CCD / Date: Nov 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 727953 / % possible obs: 96.7 % / Observed criterion σ(I): 1.6 / Redundancy: 6.2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 3.8
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.6 / % possible all: 88.8

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Processing

Software
NameVersionClassification
Cootmodel building
CNS1.2refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2J00, 2J01, 2J02, 2J03

2j00
PDB Unreleased entry

2j01
PDB Unreleased entry

2j02
PDB Unreleased entry

2j03
PDB Unreleased entry


Resolution: 3.5→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 19903003.23 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.326 33920 4.6 %RANDOM
Rwork0.265 ---
obs0.265 740306 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 2.47921 Å2 / ksol: 0.15 e/Å3
Displacement parametersBiso mean: 89.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å20 Å20 Å2
2---7.84 Å20 Å2
3---11.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a1.37 Å1.25 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20635 34562 743 0 55940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.48
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 5854 4.9 %
Rwork0.41 112508 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1APROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO.PARAMWATER.TOP
X-RAY DIFFRACTION4PROTEIN_REP.PARAMA
X-RAY DIFFRACTION5ION.PARAMION.TOP

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