[English] 日本語
Yorodumi
- PDB-6gzz: T. thermophilus hibernating 100S ribosome (amc) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6gzz
TitleT. thermophilus hibernating 100S ribosome (amc)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • (Ribosome hibernation promoting ...) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / Ribosome / hibernation / 100S / dimer / cryo-EM
Function / homologyRibosomal protein S8 superfamily / Ribosomal protein S18 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L35 superfamily ...Ribosomal protein S8 superfamily / Ribosomal protein S18 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosome hibernation promotion factor-like / Ribosomal protein S20 superfamily / Ribosomal protein L25, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein S19 / Ribosomal protein L33 superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L19 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L17 superfamily / Ribosomal protein S2 / Ribosomal protein L4 domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L31 type A / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal L18e/L15P superfamily / L28p-like / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L27 signature. / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / Ribosome hibernation promoting factor, long/plastid / Ribosomal protein L25 / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / 30S ribosomal protein Thx / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 30S ribosomal protein / Ribosomal protein S15 / Ribosomal protein L30p/L7e / Ribosomal protein L35 / Ribosomal protein S7 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein L14 signature. / Ribosomal protein S9 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 30S ribosomal protein Thx / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein TL5, C-terminal domain / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal protein L5 signature. / Ribosomal protein S10 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein L33 signature. / Ribosomal protein L13 signature. / Ribosomal protein L9 signature. / Ribosomal protein S13 signature. / Ribosomal protein L30 signature. / Ribosomal protein S4 signature. / Ribosomal protein S5 signature. / Ribosomal protein L29 signature. / Ribosomal protein S15 signature.
Function and homology information
Specimen sourceThermus thermophilus (bacteria)
Thermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.13 Å resolution
AuthorsFlygaard, R.K. / Jenner, L.B.
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
Authors: Rasmus Kock Flygaard / Niels Boegholm / Marat Yusupov / Lasse B Jenner
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2018 / Release: Oct 24, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C1: 50S ribosomal protein L2
D1: 50S ribosomal protein L3
E1: 50S ribosomal protein L4
F1: 50S ribosomal protein L5
G1: 50S ribosomal protein L6
H1: 50S ribosomal protein L9
I1: 50S ribosomal protein L13
J1: 50S ribosomal protein L14
K1: 50S ribosomal protein L15
L1: 50S ribosomal protein L16
M1: 50S ribosomal protein L17
N1: 50S ribosomal protein L18
O1: 50S ribosomal protein L19
P1: 50S ribosomal protein L20
Q1: 50S ribosomal protein L21
R1: 50S ribosomal protein L22
S1: 50S ribosomal protein L23
T1: 50S ribosomal protein L24
U1: 50S ribosomal protein L25
V1: 50S ribosomal protein L27
W1: 50S ribosomal protein L28
X1: 50S ribosomal protein L29
Y1: 50S ribosomal protein L30
Z1: 50S ribosomal protein L31
a1: 50S ribosomal protein L32
b1: 50S ribosomal protein L33
c1: 50S ribosomal protein L34
d1: 50S ribosomal protein L35
A1: 23S ribosomal RNA
B1: 5S ribosomal RNA
e1: 50S ribosomal protein L36
C2: 50S ribosomal protein L2
D2: 50S ribosomal protein L3
E2: 50S ribosomal protein L4
F2: 50S ribosomal protein L5
G2: 50S ribosomal protein L6
H2: 50S ribosomal protein L9
I2: 50S ribosomal protein L13
J2: 50S ribosomal protein L14
K2: 50S ribosomal protein L15
L2: 50S ribosomal protein L16
M2: 50S ribosomal protein L17
N2: 50S ribosomal protein L18
O2: 50S ribosomal protein L19
P2: 50S ribosomal protein L20
Q2: 50S ribosomal protein L21
R2: 50S ribosomal protein L22
S2: 50S ribosomal protein L23
T2: 50S ribosomal protein L24
U2: 50S ribosomal protein L25
V2: 50S ribosomal protein L27
W2: 50S ribosomal protein L28
X2: 50S ribosomal protein L29
Y2: 50S ribosomal protein L30
Z2: 50S ribosomal protein L31
a2: 50S ribosomal protein L32
b2: 50S ribosomal protein L33
c2: 50S ribosomal protein L34
d2: 50S ribosomal protein L35
A2: 23S ribosomal RNA
B2: 5S ribosomal RNA
e2: 50S ribosomal protein L36
B3: 30S ribosomal protein S2
C3: 30S ribosomal protein S3
D3: 30S ribosomal protein S4
E3: 30S ribosomal protein S5
F3: 30S ribosomal protein S6
G3: 30S ribosomal protein S7
H3: 30S ribosomal protein S8
I3: 30S ribosomal protein S9
J3: 30S ribosomal protein S10
K3: 30S ribosomal protein S11
L3: 30S ribosomal protein S12
M3: 30S ribosomal protein S13
N3: 30S ribosomal protein S14 type Z
O3: 30S ribosomal protein S15
P3: 30S ribosomal protein S16
Q3: 30S ribosomal protein S17
R3: 30S ribosomal protein S18
S3: 30S ribosomal protein S19
T3: 30S ribosomal protein S20
U3: 30S ribosomal protein Thx
X3: Ribosome hibernation promoting factor
A3: 16S ribosomal RNA
V3: Ribosome hibernation promoting factor
B4: 30S ribosomal protein S2
C4: 30S ribosomal protein S3
D4: 30S ribosomal protein S4
E4: 30S ribosomal protein S5
F4: 30S ribosomal protein S6
G4: 30S ribosomal protein S7
H4: 30S ribosomal protein S8
I4: 30S ribosomal protein S9
J4: 30S ribosomal protein S10
K4: 30S ribosomal protein S11
L4: 30S ribosomal protein S12
M4: 30S ribosomal protein S13
N4: 30S ribosomal protein S14 type Z
O4: 30S ribosomal protein S15
P4: 30S ribosomal protein S16
Q4: 30S ribosomal protein S17
R4: 30S ribosomal protein S18
S4: 30S ribosomal protein S19
T4: 30S ribosomal protein S20
U4: 30S ribosomal protein Thx
W4: Ribosome hibernation promoting factor
A4: 16S ribosomal RNA
V4: Ribosome hibernation promoting factor


Theoretical massNumber of molelcules
Total (without water)4,284,947108
Polyers4,284,947108
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
50S ribosomal protein ... , 29 types, 58 molecules C1C2D1D2E1E2F1F2G1G2H1H2I1I2J1J2K1K2L1L2M1M2N1N2O1O2P1P2Q1Q2...

#1: Protein/peptide 50S ribosomal protein L2 /


Mass: 29985.799 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60405
#2: Protein/peptide 50S ribosomal protein L3 /


Mass: 22321.031 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN8
#3: Protein/peptide 50S ribosomal protein L4 / / L1e


Mass: 23071.721 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN9
#4: Protein/peptide 50S ribosomal protein L5 /


Mass: 20930.400 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ0
#5: Protein/peptide 50S ribosomal protein L6 /


Mass: 18567.633 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY8
#6: Protein/peptide 50S ribosomal protein L9 /


Mass: 5454.388 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ1
#7: Protein/peptide 50S ribosomal protein L13 /


Mass: 15699.658 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60488
#8: Protein/peptide 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP8
#9: Protein/peptide 50S ribosomal protein L15 /


Mass: 16319.142 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ7
#10: Protein/peptide 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60489
#11: Protein/peptide 50S ribosomal protein L17 /


Mass: 13618.952 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q9Z9H5
#12: Protein/peptide 50S ribosomal protein L18 / / TL24


Mass: 12508.649 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ4
#13: Protein/peptide 50S ribosomal protein L19 /


Mass: 16218.812 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60490
#14: Protein/peptide 50S ribosomal protein L20 /


Mass: 13648.081 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60491
#15: Protein/peptide 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60492
#16: Protein/peptide 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP3
#17: Protein/peptide 50S ribosomal protein L23 /


Mass: 10273.117 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP0
#18: Protein/peptide 50S ribosomal protein L24 /


Mass: 11238.710 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP9
#19: Protein/peptide 50S ribosomal protein L25 / / TL5


Mass: 20268.330 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHZ1
#20: Protein/peptide 50S ribosomal protein L27 /


Mass: 8703.032 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60493
#21: Protein/peptide 50S ribosomal protein L28 /


Mass: 10872.965 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60494
#22: Protein/peptide 50S ribosomal protein L29 /


Mass: 8296.725 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP6
#23: Protein/peptide 50S ribosomal protein L30 /


Mass: 6667.931 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ6
#24: Protein/peptide 50S ribosomal protein L31 /


Mass: 7377.532 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJE1
#25: Protein/peptide 50S ribosomal protein L32 /


Mass: 6590.854 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80339
#26: Protein/peptide 50S ribosomal protein L33 /


Mass: 5602.612 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P35871
#27: Protein/peptide 50S ribosomal protein L34 /


Mass: 6132.449 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80340
#28: Protein/peptide 50S ribosomal protein L35 /


Mass: 6985.579 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SKU1
#31: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4304.215 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHR2

-
RNA chain , 3 types, 6 molecules A1A2B1B2A3A4

#29: RNA chain 23S ribosomal RNA /


Mass: 947013.000 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#30: RNA chain 5S ribosomal RNA /


Mass: 39540.617 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#53: RNA chain 16S ribosomal RNA /


Mass: 489002.531 Da / Num. of mol.: 2 / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382

+
30S ribosomal protein ... , 20 types, 40 molecules B3B4C3C4D3D4E3E4F3F4G3G4H3H4I3I4J3J4K3K4L3L4M3M4N3N4O3O4P3P4...

#32: Protein/peptide 30S ribosomal protein S2 /


Mass: 27330.648 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80371
#33: Protein/peptide 30S ribosomal protein S3 /


Mass: 22862.430 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80372
#34: Protein/peptide 30S ribosomal protein S4 /


Mass: 24242.254 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80373
#35: Protein/peptide 30S ribosomal protein S5 /


Mass: 16460.193 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ5
#36: Protein/peptide 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLP8
#37: Protein/peptide 30S ribosomal protein S7 /


Mass: 17919.775 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P17291
#38: Protein/peptide 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY9
#39: Protein/peptide 30S ribosomal protein S9 /


Mass: 14279.419 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80374
#40: Protein/peptide 30S ribosomal protein S10 /


Mass: 11398.308 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN7
#41: Protein/peptide 30S ribosomal protein S11 /


Mass: 12519.292 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80376
#42: Protein/peptide 30S ribosomal protein S12 /


Mass: 13875.388 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN3
#43: Protein/peptide 30S ribosomal protein S13 /


Mass: 13308.508 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80377
#44: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY6
#45: Protein/peptide 30S ribosomal protein S15 /


Mass: 10447.213 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJ76
#46: Protein/peptide 30S ribosomal protein S16 /


Mass: 9995.546 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJH3
#47: Protein/peptide 30S ribosomal protein S17 /


Mass: 11880.098 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY7
#48: Protein/peptide 30S ribosomal protein S18 /


Mass: 7312.723 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ0
#49: Protein/peptide 30S ribosomal protein S19 /


Mass: 8872.271 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP2
#50: Protein/peptide 30S ribosomal protein S20 /


Mass: 10921.086 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80380
#51: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3089.655 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SIH3

-
Ribosome hibernation promoting ... , 2 types, 4 molecules X3W4V3V4

#52: Protein/peptide Ribosome hibernation promoting factor / HPF


Mass: 6769.808 Da / Num. of mol.: 2
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: hpf, TTHA1294 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIS0
#54: Protein/peptide Ribosome hibernation promoting factor / HPF


Mass: 13694.619 Da / Num. of mol.: 2
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: hpf, TTHA1294 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIS0

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent IDSource
1Thermus thermophilus hibernating 100S ribosome (amc)RIBOSOMET. thermophilus hibernating 100S ribosome cryo-EM structure from grids coated with continuous amorphous carbon1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 540MULTIPLE SOURCES
2100S ribosomeRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 541NATURAL
3Ribosome hibernation promoting factorCOMPLEX52, 541RECOMBINANT
Molecular weightValue: 2.35 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12300852Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
23300852Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 1.06 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12126 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more