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- PDB-4v5o: CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMP... -

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Basic information

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Database: PDB / ID: 4v5o
TitleCRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH INITIATION FACTOR 1.
Components
  • (40S RIBOSOMAL PROTEIN ...) x 4
  • (RIBOSOMAL PROTEIN ...) x 9
  • 18S RRNA
  • EIF1
  • KH DOMAIN CONTAINING PROTEIN
  • PLECTIN/S10 DOMAIN CONTAINING PROTEIN
  • RACK1
  • RPS0E
  • RPS13E
  • RPS14E
  • RPS15E
  • RPS16E, 40S RIBOSOMAL PROTEIN RPS16E
  • RPS17E
  • RPS18E
  • RPS19E
  • RPS21E
  • RPS24E
  • RPS25E
  • RPS27E
  • RPS29E
  • RPS30E
  • RPS31E
  • RPS6E
  • RPS7E
KeywordsRIBOSOME / TRANSLATION
Function / homology
Function and homology information


kinase activity / small ribosomal subunit / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / metal ion binding
Similarity search - Function
: / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal ...: / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S10 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S12 signature. / Ribosomal protein S12/S23
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S6 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS4 / 40S ribosomal protein S8 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S6 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS4 / 40S ribosomal protein S8 / 40S ribosomal protein S3 / 40S ribosomal protein S11, putative / 40S ribosomal protein S27 / 40S ribosomal protein S20 / 40S ribosomal protein S29 / 40S ribosomal protein S12 / 40S ribosomal protein S5 / Ribosomal protein S9 component of cytosolic 80S ribosome and 40S small subunit / 40S ribosomal protein S28e, putative / Uncharacterized protein / Small ribosomal subunit protein eS1 / 40S ribosomal protein S2, putative / Uncharacterized protein / Receptor of activated kinase C 1A, component of 40S small ribosomal subunit / 40S ribosomal protein S10, putative
Similarity search - Component
Biological speciesTETRAHYMENA THERMOPHILA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.93 Å
AuthorsRabl, J. / Leibundgut, M. / Ataide, S.F. / Haag, A. / Ban, N.
CitationJournal: Science / Year: 2011
Title: Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1.
Authors: Rabl, J. / Leibundgut, M. / Ataide, S.F. / Haag, A. / Ban, N.
History
DepositionNov 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2XZM, 2XZN
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2C" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2C" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: RIBOSOMAL PROTEIN S28E CONTAINING PROTEIN
A2: 40S RIBOSOMAL PROTEIN S8
A3: RPS7E
A4: 40S RIBOSOMAL PROTEIN S3A
A5: RIBOSOMAL PROTEIN S26E CONTAINING PROTEIN
A6: RPS27E
A7: PLECTIN/S10 DOMAIN CONTAINING PROTEIN
A8: RPS25E
A9: RPS31E
AA: 18S RRNA
AB: RPS0E
AC: KH DOMAIN CONTAINING PROTEIN
AD: RIBOSOMAL PROTEIN S4 CONTAINING PROTEIN
AE: RIBOSOMAL PROTEIN S5 CONTAINING PROTEIN
AF: EIF1
AG: RIBOSOMAL PROTEIN S7 CONTAINING PROTEIN
AH: RIBOSOMAL PROTEIN S8 CONTAINING PROTEIN
AI: RPS16E, 40S RIBOSOMAL PROTEIN RPS16E
AJ: RIBOSOMAL PROTEIN S10 CONTAINING PROTEIN
AK: RPS14E
AL: 40S RIBOSOMAL PROTEIN S12
AM: RPS18E
AN: RPS29E
AO: RPS13E
AP: RPS24E
AQ: RIBOSOMAL PROTEIN S17 CONTAINING PROTEIN
AR: RACK1
AS: RPS15E
AT: RPS19E
AU: RIBOSOMAL PROTEIN L7AE CONTAINING PROTEIN
AV: RPS17E
AW: 40S RIBOSOMAL PROTEIN S4
AX: RPS30E
AY: RPS6E
AZ: RPS21E
B1: RIBOSOMAL PROTEIN S28E CONTAINING PROTEIN
B2: 40S RIBOSOMAL PROTEIN S8
B3: RPS7E
B4: 40S RIBOSOMAL PROTEIN S3A
B5: RIBOSOMAL PROTEIN S26E CONTAINING PROTEIN
B6: RPS27E
B7: PLECTIN/S10 DOMAIN CONTAINING PROTEIN
B8: RPS25E
B9: RPS31E
BA: 18S RRNA
BB: RPS0E
BC: KH DOMAIN CONTAINING PROTEIN
BD: RIBOSOMAL PROTEIN S4 CONTAINING PROTEIN
BE: RIBOSOMAL PROTEIN S5 CONTAINING PROTEIN
BF: EIF1
BG: RIBOSOMAL PROTEIN S7 CONTAINING PROTEIN
BH: RIBOSOMAL PROTEIN S8 CONTAINING PROTEIN
BI: RPS16E, 40S RIBOSOMAL PROTEIN RPS16E
BJ: RIBOSOMAL PROTEIN S10 CONTAINING PROTEIN
BK: RPS14E
BL: 40S RIBOSOMAL PROTEIN S12
BM: RPS18E
BN: RPS29E
BO: RPS13E
BP: RPS24E
BQ: RIBOSOMAL PROTEIN S17 CONTAINING PROTEIN
BR: RACK1
BS: RPS15E
BT: RPS19E
BU: RIBOSOMAL PROTEIN L7AE CONTAINING PROTEIN
BV: RPS17E
BW: 40S RIBOSOMAL PROTEIN S4
BX: RPS30E
BY: RPS6E
BZ: RPS21E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,424,399262
Polymers2,419,40370
Non-polymers4,995192
Water19,8891104
1
A1: RIBOSOMAL PROTEIN S28E CONTAINING PROTEIN
A2: 40S RIBOSOMAL PROTEIN S8
A3: RPS7E
A4: 40S RIBOSOMAL PROTEIN S3A
A5: RIBOSOMAL PROTEIN S26E CONTAINING PROTEIN
A6: RPS27E
A7: PLECTIN/S10 DOMAIN CONTAINING PROTEIN
A8: RPS25E
A9: RPS31E
AA: 18S RRNA
AB: RPS0E
AC: KH DOMAIN CONTAINING PROTEIN
AD: RIBOSOMAL PROTEIN S4 CONTAINING PROTEIN
AE: RIBOSOMAL PROTEIN S5 CONTAINING PROTEIN
AF: EIF1
AG: RIBOSOMAL PROTEIN S7 CONTAINING PROTEIN
AH: RIBOSOMAL PROTEIN S8 CONTAINING PROTEIN
AI: RPS16E, 40S RIBOSOMAL PROTEIN RPS16E
AJ: RIBOSOMAL PROTEIN S10 CONTAINING PROTEIN
AK: RPS14E
AL: 40S RIBOSOMAL PROTEIN S12
AM: RPS18E
AN: RPS29E
AO: RPS13E
AP: RPS24E
AQ: RIBOSOMAL PROTEIN S17 CONTAINING PROTEIN
AR: RACK1
AS: RPS15E
AT: RPS19E
AU: RIBOSOMAL PROTEIN L7AE CONTAINING PROTEIN
AV: RPS17E
AW: 40S RIBOSOMAL PROTEIN S4
AX: RPS30E
AY: RPS6E
AZ: RPS21E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,212,199131
Polymers1,209,70235
Non-polymers2,49896
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B1: RIBOSOMAL PROTEIN S28E CONTAINING PROTEIN
B2: 40S RIBOSOMAL PROTEIN S8
B3: RPS7E
B4: 40S RIBOSOMAL PROTEIN S3A
B5: RIBOSOMAL PROTEIN S26E CONTAINING PROTEIN
B6: RPS27E
B7: PLECTIN/S10 DOMAIN CONTAINING PROTEIN
B8: RPS25E
B9: RPS31E
BA: 18S RRNA
BB: RPS0E
BC: KH DOMAIN CONTAINING PROTEIN
BD: RIBOSOMAL PROTEIN S4 CONTAINING PROTEIN
BE: RIBOSOMAL PROTEIN S5 CONTAINING PROTEIN
BF: EIF1
BG: RIBOSOMAL PROTEIN S7 CONTAINING PROTEIN
BH: RIBOSOMAL PROTEIN S8 CONTAINING PROTEIN
BI: RPS16E, 40S RIBOSOMAL PROTEIN RPS16E
BJ: RIBOSOMAL PROTEIN S10 CONTAINING PROTEIN
BK: RPS14E
BL: 40S RIBOSOMAL PROTEIN S12
BM: RPS18E
BN: RPS29E
BO: RPS13E
BP: RPS24E
BQ: RIBOSOMAL PROTEIN S17 CONTAINING PROTEIN
BR: RACK1
BS: RPS15E
BT: RPS19E
BU: RIBOSOMAL PROTEIN L7AE CONTAINING PROTEIN
BV: RPS17E
BW: 40S RIBOSOMAL PROTEIN S4
BX: RPS30E
BY: RPS6E
BZ: RPS21E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,212,199131
Polymers1,209,70235
Non-polymers2,49896
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)320.520, 362.210, 412.110
Angle α, β, γ (deg.)90.00, 109.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RIBOSOMAL PROTEIN ... , 9 types, 18 molecules A1B1A5B5ADBDAEBEAGBGAHBHAJBJAQBQAUBU

#1: Protein RIBOSOMAL PROTEIN S28E CONTAINING PROTEIN / RPS28E / 40S RIBOSOMAL PROTEIN RPS28E


Mass: 7628.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q234G5
#5: Protein RIBOSOMAL PROTEIN S26E CONTAINING PROTEIN / RPS26E / 40S RIBOSOMAL PROTEIN RPS26E


Mass: 13844.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23PT4, UniProt: E6PBU4*PLUS
#13: Protein RIBOSOMAL PROTEIN S4 CONTAINING PROTEIN / RPS9E / 40S RIBOSOMAL PROTEIN RPS9E


Mass: 21190.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q230V2
#14: Protein RIBOSOMAL PROTEIN S5 CONTAINING PROTEIN / RPS2E / 40S RIBOSOMAL PROTEIN RPS2E


Mass: 33743.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23KG1
#16: Protein RIBOSOMAL PROTEIN S7 CONTAINING PROTEIN / RPS5E / 40S RIBOSOMAL PROTEIN RPS5E


Mass: 22513.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22WU7
#17: Protein RIBOSOMAL PROTEIN S8 CONTAINING PROTEIN / RPS22E / 40S RIBOSOMAL PROTEIN RPS22E


Mass: 14931.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q238Q8
#19: Protein RIBOSOMAL PROTEIN S10 CONTAINING PROTEIN / RPS20E / 40S RIBOSOMAL PROTEIN RPS20E


Mass: 13696.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22DC6
#26: Protein RIBOSOMAL PROTEIN S17 CONTAINING PROTEIN / RPS11E / 40S RIBOSOMAL PROTEIN RPS11E


Mass: 18142.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22B78
#30: Protein RIBOSOMAL PROTEIN L7AE CONTAINING PROTEIN / RPS12E / 40S RIBOSOMAL PROTEIN RPS12E


Mass: 13832.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22W26

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40S RIBOSOMAL PROTEIN ... , 4 types, 8 molecules A2B2A4B4ALBLAWBW

#2: Protein 40S RIBOSOMAL PROTEIN S8 / RPS8E / 40S RIBOSOMAL PROTEIN RPS8E


Mass: 24250.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22AV0
#4: Protein 40S RIBOSOMAL PROTEIN S3A / RPS1E / 40S RIBOSOMAL PROTEIN RPS1E


Mass: 29709.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q23DE3
#21: Protein 40S RIBOSOMAL PROTEIN S12 / RPS23E / 40S RIBOSOMAL PROTEIN RPS23E


Mass: 15777.714 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P06147
#32: Protein 40S RIBOSOMAL PROTEIN S4 / RPS4E / 40S RIBOSOMAL PROTEIN S7 / 40S RIBOSOMAL PROTEIN RPS4E


Mass: 29643.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: P0C233

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Protein , 21 types, 42 molecules A3B3A6B6A7B7A8B8A9B9ABBBACBCAFBFAIBIAKBKAMBMANBNAOBOAPBPARBR...

#3: Protein RPS7E / 40S RIBOSOMAL PROTEIN RPS7E


Mass: 23231.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#6: Protein RPS27E / 40S RIBOSOMAL PROTEIN RPS27E


Mass: 9245.880 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22CK0
#7: Protein PLECTIN/S10 DOMAIN CONTAINING PROTEIN / RPS10E / 40S RIBOSOMAL PROTEIN RPS10E


Mass: 18614.869 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q24F70
#8: Protein RPS25E / 40S RIBOSOMAL PROTEIN RPS25E


Mass: 15297.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#9: Protein RPS31E / 40S RIBOSOMAL PROTEIN RPS31E


Mass: 20377.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#11: Protein RPS0E / 40S RIBOSOMAL PROTEIN RPS0E


Mass: 27533.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#12: Protein KH DOMAIN CONTAINING PROTEIN / RPS3E / 40S RIBOSOMAL PROTEIN RPS3E


Mass: 27577.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22AV9
#15: Protein EIF1


Mass: 11956.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TETRAHYMENA THERMOPHILA (eukaryote) / Production host: ESCHERICHIA COLI (E. coli)
#18: Protein RPS16E, 40S RIBOSOMAL PROTEIN RPS16E


Mass: 16417.256 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#20: Protein RPS14E / 40S RIBOSOMAL PROTEIN RPS14E


Mass: 16401.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#22: Protein RPS18E / 40S RIBOSOMAL PROTEIN RPS18E


Mass: 17801.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#23: Protein RPS29E / 40S RIBOSOMAL PROTEIN RPS29E


Mass: 6663.876 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22MB0
#24: Protein RPS13E / 40S RIBOSOMAL PROTEIN RPS13E


Mass: 17623.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#25: Protein RPS24E / 40S RIBOSOMAL PROTEIN RPS24E


Mass: 17128.072 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q22MB0
#27: Protein RACK1


Mass: 38523.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: Q24D42
#28: Protein RPS15E / 40S RIBOSOMAL PROTEIN RPS15E


Mass: 15905.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#29: Protein RPS19E / 40S RIBOSOMAL PROTEIN RPS19E


Mass: 17774.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#31: Protein RPS17E / 40S RIBOSOMAL PROTEIN RPS17E


Mass: 14963.514 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#33: Protein RPS30E / 40S RIBOSOMAL PROTEIN RPS30E


Mass: 9249.011 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)
#34: Protein RPS6E / 40S RIBOSOMAL PROTEIN RPS6E


Mass: 32614.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: UniProt: A4VD76
#35: Protein RPS21E / 40S RIBOSOMAL PROTEIN RPS21E


Mass: 10704.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote)

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RNA chain , 1 types, 2 molecules AABA

#10: RNA chain 18S RRNA


Mass: 565193.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TETRAHYMENA THERMOPHILA (eukaryote) / References: GenBank: X56165

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Non-polymers , 3 types, 1296 molecules

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


Mass: 24.305 Da / Num. of mol.: 184 / Source method: obtained synthetically / Formula: Mg
#37: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsHEXACOORDINATED MAGNESIUM ION (MO6): HEXACOORDINATED MAGNESIUM ION REFINED IN HEXACOORDINATED FORM. ...HEXACOORDINATED MAGNESIUM ION (MO6): HEXACOORDINATED MAGNESIUM ION REFINED IN HEXACOORDINATED FORM. WATER WAS DEPOSITED SEPARATELY. ZINC ION (ZN): COORDINATED BY ZINC FINGER PROTEIN.
Sequence detailsRESIDUES 697-704 OF THE 18S RRNA WERE NOT BUILT. RESIDUES 145-169 WERE BUILT AS POLY-SERINE AND ...RESIDUES 697-704 OF THE 18S RRNA WERE NOT BUILT. RESIDUES 145-169 WERE BUILT AS POLY-SERINE AND DEPOSITED AS UNK RESIDUES.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 6.5
Details: 50MM MES-KOH PH6.5, 80MM MGCL2, 200MM KCL, 0.495MM PUTRESCEINE, 4.4-5.4% (W/V) PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS / Detector: PIXEL / Date: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.93→100 Å / Num. obs: 364651 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.8
Reflection shellResolution: 3.93→4.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.05 / % possible all: 61

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Processing

Software
NameVersionClassification
SHARPmodel building
PHASERmodel building
DMmodel building
CNSmodel building
PHENIXmodel building
CNS1.3refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
PHASERphasing
DMphasing
CNSphasing
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2J02

2j02
PDB Unreleased entry


Resolution: 3.93→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 25089988.51 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: REGION 697-704 OF THE 18S RRNA (CHAINS AA AND BA) WAS OMITTED FROM THE MODEL DUE TO DISORDER. (RESIDUES 145-169 OF RPS31E (CHAINS A9 AND B9) WERE BUILT AND REFINED AS POLY-SER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 6635 2 %RANDOM
Rwork0.2065 ---
obs0.2065 332261 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.5375 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 148.4 Å2
Baniso -1Baniso -2Baniso -3
1-22.55 Å20 Å24.908 Å2
2--14.527 Å20 Å2
3----37.076 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 3.93→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40937 37231 96 552 78816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007318
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_deg1.33835
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.93→4.07 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.362 262 2 %
Rwork0.345 13109 -
obs--34.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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