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- PDB-4v4h: Crystal structure of the bacterial ribosome from Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 4v4h
TitleCrystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution.
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • 16S RIBOSOMAL RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
KeywordsRIBOSOME / KASUGAMYCIN
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / : / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / molecular adaptor activity / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 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/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / 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 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 L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, 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 protein L33 / Ribosomal protein L33 / 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.
Similarity search - Domain/homology
Chem-KSG / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 ...Chem-KSG / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 50S ribosomal protein L6 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / Large ribosomal subunit protein uL15 / 50S ribosomal protein L16 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L23 / 50S ribosomal protein L30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / 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 uS8 / Small ribosomal subunit protein uS9 / 50S ribosomal protein L13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsSchuwirth, B.S. / Vila-Sanjurjo, A. / Cate, J.H.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural analysis of kasugamycin inhibition of translation.
Authors: Schuwirth, B.S. / Day, J.M. / Hau, C.W. / Janssen, G.R. / Dahlberg, A.E. / Cate, J.H.D. / Vila-Sanjurjo, A.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1VS5, 1VS6, 1VS7, 1VS8
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL UNIT CONSISTS OF TWO SUBUNITS. THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT.
Remark 400COMPOUND THIS FILE, 1VS5, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 1VS5, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND ARE DEPOSITED UNDER: 70S RIBOSOME ONE: 1VS5 (30S SUBUNIT), 1VS6 (50S SUBUNIT) 70S RIBOSOME TWO: 1VS7 (30S SUBUNIT), 1VS8 (50S SUBUNIT)
Remark 600HETEROGEN MO4 38 HAS SQUARE-PLANAR HYDRATION OF MG2+ MO4 10,16,30,31,34,40,43,44,51 HAVE 2 VICINAL ...HETEROGEN MO4 38 HAS SQUARE-PLANAR HYDRATION OF MG2+ MO4 10,16,30,31,34,40,43,44,51 HAVE 2 VICINAL WATERS MISSING FROM HYDRATION OF MG2+ MO3 11,48 HAVE ALL WATER BONDS MUTUALLY ORTHOGONAL TO OTHER MG2+-WATER BONDS MO3 4,9 HAVE ALL WATERS AND MG2+ IN-PLANE MO2 35 HAS ALL WATERS AND MG2+ ORTHOGONAL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S RIBOSOMAL RNA
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
AB: 30S RIBOSOMAL PROTEIN S2
AU: 30S RIBOSOMAL PROTEIN S21
BA: 5S RIBOSOMAL RNA
BB: 23S RIBOSOMAL RNA
BV: 50S RIBOSOMAL PROTEIN L25
BC: 50S RIBOSOMAL PROTEIN L2
BD: 50S RIBOSOMAL PROTEIN L3
BE: 50S RIBOSOMAL PROTEIN L4
BF: 50S RIBOSOMAL PROTEIN L5
BG: 50S RIBOSOMAL PROTEIN L6
BH: 50S RIBOSOMAL PROTEIN L9
BJ: 50S RIBOSOMAL PROTEIN L13
BK: 50S RIBOSOMAL PROTEIN L14
BL: 50S RIBOSOMAL PROTEIN L15
BM: 50S RIBOSOMAL PROTEIN L16
BN: 50S RIBOSOMAL PROTEIN L17
BO: 50S RIBOSOMAL PROTEIN L18
BP: 50S RIBOSOMAL PROTEIN L19
BQ: 50S RIBOSOMAL PROTEIN L20
BR: 50S RIBOSOMAL PROTEIN L21
BS: 50S RIBOSOMAL PROTEIN L22
BT: 50S RIBOSOMAL PROTEIN L23
BU: 50S RIBOSOMAL PROTEIN L24
BW: 50S RIBOSOMAL PROTEIN L27
BX: 50S RIBOSOMAL PROTEIN L29
BY: 50S RIBOSOMAL PROTEIN L30
BZ: 50S RIBOSOMAL PROTEIN L31
B0: 50S RIBOSOMAL PROTEIN L32
B1: 50S RIBOSOMAL PROTEIN L33
B2: 50S RIBOSOMAL PROTEIN L34
B3: 50S RIBOSOMAL PROTEIN L35
B4: 50S RIBOSOMAL PROTEIN L36
BI: 50S RIBOSOMAL PROTEIN L11
CA: 16S RIBOSOMAL RNA
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
CB: 30S RIBOSOMAL PROTEIN S2
CU: 30S RIBOSOMAL PROTEIN S21
DA: 5S RIBOSOMAL RNA
DB: 23S RIBOSOMAL RNA
DV: 50S RIBOSOMAL PROTEIN L25
DC: 50S RIBOSOMAL PROTEIN L2
DD: 50S RIBOSOMAL PROTEIN L3
DE: 50S RIBOSOMAL PROTEIN L4
DF: 50S RIBOSOMAL PROTEIN L5
DG: 50S RIBOSOMAL PROTEIN L6
DH: 50S RIBOSOMAL PROTEIN L9
DJ: 50S RIBOSOMAL PROTEIN L13
DK: 50S RIBOSOMAL PROTEIN L14
DL: 50S RIBOSOMAL PROTEIN L15
DM: 50S RIBOSOMAL PROTEIN L16
DN: 50S RIBOSOMAL PROTEIN L17
DO: 50S RIBOSOMAL PROTEIN L18
DP: 50S RIBOSOMAL PROTEIN L19
DQ: 50S RIBOSOMAL PROTEIN L20
DR: 50S RIBOSOMAL PROTEIN L21
DS: 50S RIBOSOMAL PROTEIN L22
DT: 50S RIBOSOMAL PROTEIN L23
DU: 50S RIBOSOMAL PROTEIN L24
DW: 50S RIBOSOMAL PROTEIN L27
DX: 50S RIBOSOMAL PROTEIN L29
DY: 50S RIBOSOMAL PROTEIN L30
DZ: 50S RIBOSOMAL PROTEIN L31
D0: 50S RIBOSOMAL PROTEIN L32
D1: 50S RIBOSOMAL PROTEIN L33
D2: 50S RIBOSOMAL PROTEIN L34
D3: 50S RIBOSOMAL PROTEIN L35
D4: 50S RIBOSOMAL PROTEIN L36
DI: 50S RIBOSOMAL PROTEIN L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,301,003449
Polymers4,291,907104
Non-polymers9,095345
Water29,3101627
1
AA: 16S RIBOSOMAL RNA
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
AB: 30S RIBOSOMAL PROTEIN S2
AU: 30S RIBOSOMAL PROTEIN S21
BA: 5S RIBOSOMAL RNA
BB: 23S RIBOSOMAL RNA
BV: 50S RIBOSOMAL PROTEIN L25
BC: 50S RIBOSOMAL PROTEIN L2
BD: 50S RIBOSOMAL PROTEIN L3
BE: 50S RIBOSOMAL PROTEIN L4
BF: 50S RIBOSOMAL PROTEIN L5
BG: 50S RIBOSOMAL PROTEIN L6
BH: 50S RIBOSOMAL PROTEIN L9
BJ: 50S RIBOSOMAL PROTEIN L13
BK: 50S RIBOSOMAL PROTEIN L14
BL: 50S RIBOSOMAL PROTEIN L15
BM: 50S RIBOSOMAL PROTEIN L16
BN: 50S RIBOSOMAL PROTEIN L17
BO: 50S RIBOSOMAL PROTEIN L18
BP: 50S RIBOSOMAL PROTEIN L19
BQ: 50S RIBOSOMAL PROTEIN L20
BR: 50S RIBOSOMAL PROTEIN L21
BS: 50S RIBOSOMAL PROTEIN L22
BT: 50S RIBOSOMAL PROTEIN L23
BU: 50S RIBOSOMAL PROTEIN L24
BW: 50S RIBOSOMAL PROTEIN L27
BX: 50S RIBOSOMAL PROTEIN L29
BY: 50S RIBOSOMAL PROTEIN L30
BZ: 50S RIBOSOMAL PROTEIN L31
B0: 50S RIBOSOMAL PROTEIN L32
B1: 50S RIBOSOMAL PROTEIN L33
B2: 50S RIBOSOMAL PROTEIN L34
B3: 50S RIBOSOMAL PROTEIN L35
B4: 50S RIBOSOMAL PROTEIN L36
BI: 50S RIBOSOMAL PROTEIN L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,150,465223
Polymers2,145,95452
Non-polymers4,511171
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S RIBOSOMAL RNA
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
CB: 30S RIBOSOMAL PROTEIN S2
CU: 30S RIBOSOMAL PROTEIN S21
DA: 5S RIBOSOMAL RNA
DB: 23S RIBOSOMAL RNA
DV: 50S RIBOSOMAL PROTEIN L25
DC: 50S RIBOSOMAL PROTEIN L2
DD: 50S RIBOSOMAL PROTEIN L3
DE: 50S RIBOSOMAL PROTEIN L4
DF: 50S RIBOSOMAL PROTEIN L5
DG: 50S RIBOSOMAL PROTEIN L6
DH: 50S RIBOSOMAL PROTEIN L9
DJ: 50S RIBOSOMAL PROTEIN L13
DK: 50S RIBOSOMAL PROTEIN L14
DL: 50S RIBOSOMAL PROTEIN L15
DM: 50S RIBOSOMAL PROTEIN L16
DN: 50S RIBOSOMAL PROTEIN L17
DO: 50S RIBOSOMAL PROTEIN L18
DP: 50S RIBOSOMAL PROTEIN L19
DQ: 50S RIBOSOMAL PROTEIN L20
DR: 50S RIBOSOMAL PROTEIN L21
DS: 50S RIBOSOMAL PROTEIN L22
DT: 50S RIBOSOMAL PROTEIN L23
DU: 50S RIBOSOMAL PROTEIN L24
DW: 50S RIBOSOMAL PROTEIN L27
DX: 50S RIBOSOMAL PROTEIN L29
DY: 50S RIBOSOMAL PROTEIN L30
DZ: 50S RIBOSOMAL PROTEIN L31
D0: 50S RIBOSOMAL PROTEIN L32
D1: 50S RIBOSOMAL PROTEIN L33
D2: 50S RIBOSOMAL PROTEIN L34
D3: 50S RIBOSOMAL PROTEIN L35
D4: 50S RIBOSOMAL PROTEIN L36
DI: 50S RIBOSOMAL PROTEIN L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,150,538226
Polymers2,145,95452
Non-polymers4,584174
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.848, 379.202, 739.283
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 , 3 types, 6 molecules AACABADABBDB

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 499690.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357879
#22: RNA chain 5S RIBOSOMAL RNA /


Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357928
#23: RNA chain 23S RIBOSOMAL RNA /


Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357927

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

#2: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 26031.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V3
#3: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 23514.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V8
#4: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 17629.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1
#5: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02358
#6: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 20055.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02359
#7: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 14146.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W7
#8: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14886.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7X3
#9: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R5
#10: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 13870.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R9
#11: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 13768.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3
#12: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 13128.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S9
#13: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 11606.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG59
#14: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10319.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: Q8X9M2, UniProt: P0ADZ4*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S16 /


Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T3
#16: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 9724.491 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG63
#17: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 9005.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T7
#18: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10455.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U3
#19: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 9708.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U7
#20: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 26781.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V0
#21: Protein 30S RIBOSOMAL PROTEIN S21 /


Mass: 8524.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68679

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

#24: Protein 50S RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68919
#25: Protein 50S RIBOSOMAL PROTEIN L2 /


Mass: 29923.619 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60422
#26: Protein 50S RIBOSOMAL PROTEIN L3 /


Mass: 22277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60438
#27: Protein 50S RIBOSOMAL PROTEIN L4 /


Mass: 22121.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60723
#28: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 20333.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P62399
#29: Protein 50S RIBOSOMAL PROTEIN L6 /


Mass: 18932.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02390, UniProt: P0AG56*PLUS
#30: Protein 50S RIBOSOMAL PROTEIN L9 /


Mass: 15789.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R1
#31: Protein 50S RIBOSOMAL PROTEIN L13 /


Mass: 16050.606 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02410, UniProt: P0AA12*PLUS
#32: Protein 50S RIBOSOMAL PROTEIN L14 /


Mass: 13565.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02411, UniProt: P0ADY3*PLUS
#33: Protein 50S RIBOSOMAL PROTEIN L15 /


Mass: 15008.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02413
#34: Protein 50S RIBOSOMAL PROTEIN L16 /


Mass: 15312.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02414, UniProt: P0ADY7*PLUS
#35: Protein 50S RIBOSOMAL PROTEIN L17 /


Mass: 14393.657 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02416, UniProt: P0AG44*PLUS
#36: Protein 50S RIBOSOMAL PROTEIN L18 /


Mass: 12794.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#37: Protein 50S RIBOSOMAL PROTEIN L19 /


Mass: 13159.278 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7K6
#38: Protein 50S RIBOSOMAL PROTEIN L20 /


Mass: 13528.024 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L3
#39: Protein 50S RIBOSOMAL PROTEIN L21 /


Mass: 11586.374 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02422, UniProt: P0AG48*PLUS
#40: Protein 50S RIBOSOMAL PROTEIN L22 /


Mass: 12253.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P61175
#41: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 11222.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02424, UniProt: P0ADZ0*PLUS
#42: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 11339.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60624
#43: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9146.540 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L8
#44: Protein 50S RIBOSOMAL PROTEIN L29 /


Mass: 7286.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M6
#45: Protein 50S RIBOSOMAL PROTEIN L30 /


Mass: 6554.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02430, UniProt: P0AG51*PLUS
#46: Protein 50S RIBOSOMAL PROTEIN L31 /


Mass: 7887.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M9
#47: Protein 50S RIBOSOMAL PROTEIN L32 /


Mass: 6463.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7N4
#48: Protein 50S RIBOSOMAL PROTEIN L33 /


Mass: 6388.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7N9
#49: Protein/peptide 50S RIBOSOMAL PROTEIN L34 /


Mass: 5397.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7P5
#50: Protein 50S RIBOSOMAL PROTEIN L35 / / RIBOSOMAL PROTEIN A


Mass: 7313.032 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#51: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / / RIBOSOMAL PROTEIN B


Mass: 4377.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q6
#52: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 14894.362 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7J7

-
Non-polymers , 3 types, 1972 molecules

#53: Chemical ChemComp-KSG / (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE / KASUGAMYCIN / Kasugamycin


Mass: 379.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O9 / Comment: antibiotic*YM
#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 343 / Source method: obtained synthetically / Formula: Mg
#55: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1627 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growpH: 7.5
Details: MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS-HCL, EDTA, PH 7.5, BATCH, TEMPERATURE 277K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2PEG 800011
3MgCl211
4NH4Cl11
5spermine11
6spermidine11
7TRIS-HCLTris11
8EDTAEthylenediaminetetraacetic acid11
9H2O11
10MPD12
11PEG 800012
12MgCl212
13NH4Cl12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.46→70 Å / Num. obs: 693093 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.4
Reflection shellResolution: 3.46→3.55 Å / Redundancy: 0 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / % possible all: 87.9

-
Processing

Software
NameClassification
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1PNS, 1PNU

1pns
PDB Unreleased entry

1pnu
PDB Unreleased entry


Resolution: 3.46→70 Å / Isotropic thermal model: GROUPED BY RESIDUE / σ(F): 0 / Stereochemistry target values: TORSIONAL DYNAMICS
RfactorNum. reflection% reflectionSelection details
Rfree0.331 --RANDOM 5%
Rwork0.279 ---
obs0.279 692904 91.6 %-
Displacement parametersBiso mean: 58.69 Å2
Refinement stepCycle: LAST / Resolution: 3.46→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18538 32831 386 0 51755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.16
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 3.46→3.48 Å
RfactorNum. reflection% reflection
Rfree0.398 359 -
Rwork0.342 --
obs--87.9 %

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