[English] 日本語
Yorodumi
- PDB-8oeq: Crystal structure of the Candida albicans 80S ribosome in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oeq
TitleCrystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (250uM)
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 37
  • (Ribosomal protein ...) x 10
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Ribosomal protein
  • Ubiquitin-40S ribosomal protein S31 fusion protein
  • Uncharacterized protein CaJ7.0206
KeywordsRIBOSOME / Candida albicans / paromomycin
Function / homology
Function and homology information


yeast-form cell wall / hyphal cell wall / triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / pre-mRNA 5'-splice site binding / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / translational elongation ...yeast-form cell wall / hyphal cell wall / triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / pre-mRNA 5'-splice site binding / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / translational elongation / TOR signaling / protein-RNA complex assembly / ribosomal subunit export from nucleus / translation regulator activity / translation repressor activity / maturation of LSU-rRNA / cytosolic ribosome / telomere maintenance / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / ubiquitin protein ligase binding / negative regulation of apoptotic process / cell surface / RNA binding / zinc ion binding / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 ...RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L1 signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal_L40e / Ribosomal protein L40e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L40e superfamily / 40S ribosomal protein S4 C-terminus / Ribosomal protein L23/L25, N-terminal
Similarity search - Domain/homology
Chem-3K5 / PAROMOMYCIN / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...Chem-3K5 / PAROMOMYCIN / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL19 / Ribosome-associated protein STM1 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS30 / Small ribosomal subunit protein uS14 / 60S ribosomal protein L42-B / Ribosomal protein S7 / 40S ribosomal protein S17-B / 40S ribosomal protein S26 / Ribosomal protein L22 / 60S ribosomal protein L7-A / 60S ribosomal protein L28 / 60S ribosomal protein L33-A / 40S ribosomal protein S27 / 40S ribosomal protein S10-A / Ribosomal protein S10 / 40S ribosomal protein S3 / 40S ribosomal protein S6 / Ribosomal protein L13 / Ribosomal protein S5 / 60S ribosomal protein L20 / 40S ribosomal protein S28-B / 60S ribosomal protein L8 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S12 / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S24 / 60S ribosomal protein L9-B / 60S ribosomal protein L23-A / 60S ribosomal protein L24-A / 60S ribosomal protein L18-A / 40S ribosomal protein S19-A / 40S ribosomal protein S7 / 40S ribosomal protein S25 / 60S ribosomal protein L29 / 40S ribosomal protein S22-A / 40S ribosomal protein S8 / Ribosomal protein S23 (S12) / 40S ribosomal protein S14-A / 60S ribosomal protein L34-B / 60S ribosomal protein L21-A / 60S ribosomal protein L31-B / 60S ribosomal protein L11-B / Ribosomal protein S4 / 60S ribosomal protein L2-B / 60S ribosomal protein L14-B / Ribosomal protein L24 / 40S ribosomal protein S18-B / Ribosomal protein / 40S ribosomal protein S13 / 60S ribosomal protein L4-B / 60S ribosomal protein L13 / 60S ribosomal protein L25 / Ribosomal protein L29 / Uncharacterized protein CaJ7.0206 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL3 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS21
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKolosova, O. / Zgadzay, Y. / Yusupov, M.
Funding support France, Russian Federation, United States, 5items
OrganizationGrant numberCountry
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)DBF20160635745 France
Foundation for Medical Research (France)FDT202204014886 France
Russian Science Foundation20-65-47031 Russian Federation
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)21 AI138158 United States
CitationJournal: To Be Published
Title: Drug-induced rotational movement of the ribosome is a key factor for read-through enhancement
Authors: Kolosova, O. / Zgadzay, Y. / Stetsenko, A. / Validov, S. / Usachev, K. / Jenner, L. / Dmitriev, S. / Guskov, A. / Yusupov, M.
History
DepositionMar 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: Uncharacterized protein CaJ7.0206
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
i: 60S ribosomal protein CAALFM_C304810CA
B: 18S ribosomal RNA
C: 40S ribosomal protein S0
D: 40S ribosomal protein S1
E: Ribosomal protein S5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S7
I: 40S ribosomal protein S6
J: 40S ribosomal protein S7
K: 40S ribosomal protein S8
L: Ribosomal protein S4
M: 40S ribosomal protein S10-A
N: 40S ribosomal protein S11A
O: 40S ribosomal protein S12
P: 40S ribosomal protein S13
Q: 40S ribosomal protein S14-A
R: 40S ribosomal protein S15
S: 40S ribosomal protein S16
T: 40S ribosomal protein S17-B
U: 40S ribosomal protein S18-B
V: 40S ribosomal protein S19-A
W: Ribosomal protein S10
X: 40S ribosomal protein S21
Y: 40S ribosomal protein S22-A
Z: Ribosomal protein S23 (S12)
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28-B
f: 40S ribosomal protein S29A
g: 40S ribosomal protein S30
h: Ubiquitin-40S ribosomal protein S31 fusion protein
AR: Guanine nucleotide-binding protein subunit beta-like protein
AS: 25S ribosomal RNA
AT: 5S ribosomal RNA
AU: 5.8S ribosomal RNA
AW: 60S ribosomal protein L2-B
AX: 60S ribosomal protein L3
AY: 60S ribosomal protein L4-B
AZ: Uncharacterized protein CaJ7.0206
BA: 60S ribosomal protein L6
BB: 60S ribosomal protein L7-A
BC: 60S ribosomal protein L8
BD: 60S ribosomal protein L9-B
BE: 60S ribosomal protein L10
BF: 60S ribosomal protein L11-B
BG: 60S ribosomal protein L13
BH: 60S ribosomal protein L14-B
BI: 60S ribosomal protein L15-A
BJ: Ribosomal protein L13
BK: Ribosomal protein L22
BL: 60S ribosomal protein L18-A
BM: 60S ribosomal protein L19-A
BN: 60S ribosomal protein L20
BO: 60S ribosomal protein L21-A
BP: 60S ribosomal protein L22-B
BQ: 60S ribosomal protein L23-A
BR: 60S ribosomal protein L24-A
BS: 60S ribosomal protein L25
BT: Ribosomal protein L24
BU: 60S ribosomal protein L27
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L29
BX: 60S ribosomal protein L30
BY: 60S ribosomal protein L31-B
BZ: 60S ribosomal protein L32
CA: 60S ribosomal protein L33-A
CB: 60S ribosomal protein L34-B
CC: Ribosomal protein L29
CD: 60S ribosomal protein L36
CE: 60S ribosomal protein L37-B
CF: 60S ribosomal protein L38
CG: 60S ribosomal protein L39
CH: 60S ribosomal protein L40-B
CI: 60S ribosomal protein L41
CJ: 60S ribosomal protein L42-B
CK: 60S ribosomal protein L43-A
CM: 18S ribosomal RNA
CN: 40S ribosomal protein S0
CO: 40S ribosomal protein S1
CP: Ribosomal protein S5
CQ: Ribosomal protein S3
CR: 40S ribosomal protein S4
CS: Ribosomal protein S7
CT: 40S ribosomal protein S6
CU: 40S ribosomal protein S7
CV: 40S ribosomal protein S8
CW: Ribosomal protein S4
CX: 40S ribosomal protein S10-A
CY: 40S ribosomal protein S11A
CZ: 40S ribosomal protein S12
DA: 40S ribosomal protein S13
DB: 40S ribosomal protein S14-A
DC: 40S ribosomal protein S15
DD: 40S ribosomal protein S16
DE: 40S ribosomal protein S17-B
DF: 40S ribosomal protein S18-B
DG: 40S ribosomal protein S19-A
DH: Ribosomal protein S10
DI: 40S ribosomal protein S21
DJ: 40S ribosomal protein S22-A
DK: Ribosomal protein S23 (S12)
DL: 40S ribosomal protein S24
DM: 40S ribosomal protein S25
DN: 40S ribosomal protein S26
DO: 40S ribosomal protein S27
DP: 40S ribosomal protein S28-B
DQ: 40S ribosomal protein S29A
DR: 40S ribosomal protein S30
DS: Ubiquitin-40S ribosomal protein S31 fusion protein
DT: Guanine nucleotide-binding protein subunit beta-like protein
L1: Ribosomal protein
l1: Ribosomal protein
CL: 60S ribosomal protein CAALFM_C304810CA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,327,5271636
Polymers6,284,909160
Non-polymers42,6181476
Water86548
1
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: Uncharacterized protein CaJ7.0206
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
i: 60S ribosomal protein CAALFM_C304810CA
B: 18S ribosomal RNA
C: 40S ribosomal protein S0
D: 40S ribosomal protein S1
E: Ribosomal protein S5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S7
I: 40S ribosomal protein S6
J: 40S ribosomal protein S7
K: 40S ribosomal protein S8
L: Ribosomal protein S4
M: 40S ribosomal protein S10-A
N: 40S ribosomal protein S11A
O: 40S ribosomal protein S12
P: 40S ribosomal protein S13
Q: 40S ribosomal protein S14-A
R: 40S ribosomal protein S15
S: 40S ribosomal protein S16
T: 40S ribosomal protein S17-B
U: 40S ribosomal protein S18-B
V: 40S ribosomal protein S19-A
W: Ribosomal protein S10
X: 40S ribosomal protein S21
Y: 40S ribosomal protein S22-A
Z: Ribosomal protein S23 (S12)
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28-B
f: 40S ribosomal protein S29A
g: 40S ribosomal protein S30
h: Ubiquitin-40S ribosomal protein S31 fusion protein
AR: Guanine nucleotide-binding protein subunit beta-like protein
l1: Ribosomal protein
hetero molecules


  • defined by author
  • 3.17 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)3,166,766939
Polymers3,142,45580
Non-polymers24,312859
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AS: 25S ribosomal RNA
AT: 5S ribosomal RNA
AU: 5.8S ribosomal RNA
AW: 60S ribosomal protein L2-B
AX: 60S ribosomal protein L3
AY: 60S ribosomal protein L4-B
AZ: Uncharacterized protein CaJ7.0206
BA: 60S ribosomal protein L6
BB: 60S ribosomal protein L7-A
BC: 60S ribosomal protein L8
BD: 60S ribosomal protein L9-B
BE: 60S ribosomal protein L10
BF: 60S ribosomal protein L11-B
BG: 60S ribosomal protein L13
BH: 60S ribosomal protein L14-B
BI: 60S ribosomal protein L15-A
BJ: Ribosomal protein L13
BK: Ribosomal protein L22
BL: 60S ribosomal protein L18-A
BM: 60S ribosomal protein L19-A
BN: 60S ribosomal protein L20
BO: 60S ribosomal protein L21-A
BP: 60S ribosomal protein L22-B
BQ: 60S ribosomal protein L23-A
BR: 60S ribosomal protein L24-A
BS: 60S ribosomal protein L25
BT: Ribosomal protein L24
BU: 60S ribosomal protein L27
BV: 60S ribosomal protein L28
BW: 60S ribosomal protein L29
BX: 60S ribosomal protein L30
BY: 60S ribosomal protein L31-B
BZ: 60S ribosomal protein L32
CA: 60S ribosomal protein L33-A
CB: 60S ribosomal protein L34-B
CC: Ribosomal protein L29
CD: 60S ribosomal protein L36
CE: 60S ribosomal protein L37-B
CF: 60S ribosomal protein L38
CG: 60S ribosomal protein L39
CH: 60S ribosomal protein L40-B
CI: 60S ribosomal protein L41
CJ: 60S ribosomal protein L42-B
CK: 60S ribosomal protein L43-A
CM: 18S ribosomal RNA
CN: 40S ribosomal protein S0
CO: 40S ribosomal protein S1
CP: Ribosomal protein S5
CQ: Ribosomal protein S3
CR: 40S ribosomal protein S4
CS: Ribosomal protein S7
CT: 40S ribosomal protein S6
CU: 40S ribosomal protein S7
CV: 40S ribosomal protein S8
CW: Ribosomal protein S4
CX: 40S ribosomal protein S10-A
CY: 40S ribosomal protein S11A
CZ: 40S ribosomal protein S12
DA: 40S ribosomal protein S13
DB: 40S ribosomal protein S14-A
DC: 40S ribosomal protein S15
DD: 40S ribosomal protein S16
DE: 40S ribosomal protein S17-B
DF: 40S ribosomal protein S18-B
DG: 40S ribosomal protein S19-A
DH: Ribosomal protein S10
DI: 40S ribosomal protein S21
DJ: 40S ribosomal protein S22-A
DK: Ribosomal protein S23 (S12)
DL: 40S ribosomal protein S24
DM: 40S ribosomal protein S25
DN: 40S ribosomal protein S26
DO: 40S ribosomal protein S27
DP: 40S ribosomal protein S28-B
DQ: 40S ribosomal protein S29A
DR: 40S ribosomal protein S30
DS: Ubiquitin-40S ribosomal protein S31 fusion protein
DT: Guanine nucleotide-binding protein subunit beta-like protein
L1: Ribosomal protein
CL: 60S ribosomal protein CAALFM_C304810CA
hetero molecules


  • defined by author
  • 3.16 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)3,160,761697
Polymers3,142,45580
Non-polymers18,306617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)298.320, 293.370, 451.080
Angle α, β, γ (deg.)90.00, 100.16, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
RNA chain , 4 types, 8 molecules 1AS3AT4AUBCM

#1: RNA chain 25S ribosomal RNA


Mass: 1085278.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086444.1
#2: RNA chain 5S ribosomal RNA


Mass: 38943.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: X16634.1
#3: RNA chain 5.8S ribosomal RNA


Mass: 50683.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: OQ195134.1
#46: RNA chain 18S ribosomal RNA


Mass: 575838.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086442.1

+
60S ribosomal protein ... , 37 types, 74 molecules jAWkAXlAYnBAoBBpBCqBDrBEsBFtBGuBHvBIyBLzBM0BN...

#4: Protein 60S ribosomal protein L2-B


Mass: 27366.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X9
#5: Protein 60S ribosomal protein L3


Mass: 44040.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q59LS1
#6: Protein 60S ribosomal protein L4-B


Mass: 39282.352 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4H4
#8: Protein 60S ribosomal protein L6


Mass: 19798.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P834
#9: Protein 60S ribosomal protein L7-A


Mass: 27446.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVN2
#10: Protein 60S ribosomal protein L8


Mass: 28549.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C337
#11: Protein 60S ribosomal protein L9-B


Mass: 21755.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3N3
#12: Protein 60S ribosomal protein L10


Mass: 25236.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5AIB8
#13: Protein 60S ribosomal protein L11-B


Mass: 19859.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1S5
#14: Protein 60S ribosomal protein L13


Mass: 23105.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F5V7
#15: Protein 60S ribosomal protein L14-B


Mass: 14748.476 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F332
#16: Protein 60S ribosomal protein L15-A


Mass: 24389.256 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A6R1
#19: Protein 60S ribosomal protein L18-A


Mass: 20817.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4Y1
#20: Protein 60S ribosomal protein L19-A


Mass: 21942.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK40
#21: Protein 60S ribosomal protein L20


Mass: 20376.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZJ3
#22: Protein 60S ribosomal protein L21-A


Mass: 18049.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1C8
#23: Protein 60S ribosomal protein L22-B


Mass: 14107.862 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM41
#24: Protein 60S ribosomal protein L23-A


Mass: 14494.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C444
#25: Protein 60S ribosomal protein L24-A


Mass: 17430.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4U1
#26: Protein 60S ribosomal protein L25


Mass: 15873.581 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6A1
#28: Protein 60S ribosomal protein L27


Mass: 15551.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P843
#29: Protein 60S ribosomal protein L28


Mass: 16703.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVY8
#30: Protein 60S ribosomal protein L29


Mass: 7135.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0G8
#31: Protein 60S ribosomal protein L30


Mass: 11520.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM75
#32: Protein 60S ribosomal protein L31-B


Mass: 12993.149 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1M1
#33: Protein 60S ribosomal protein L32


Mass: 14993.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94008
#34: Protein 60S ribosomal protein L33-A


Mass: 12138.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BW57
#35: Protein 60S ribosomal protein L34-B


Mass: 12828.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F171
#37: Protein 60S ribosomal protein L36 / L39


Mass: 11096.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P47834
#38: Protein 60S ribosomal protein L37-B


Mass: 10102.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PF45
#39: Protein 60S ribosomal protein L38


Mass: 8911.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PG16
#40: Protein 60S ribosomal protein L39 / L46


Mass: 6347.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q96W55
#41: Protein 60S ribosomal protein L40-B


Mass: 6078.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PL68
#42: Protein/peptide 60S ribosomal protein L41


Mass: 3396.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P9WER7
#43: Protein 60S ribosomal protein L42-B


Mass: 12259.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BR69
#44: Protein 60S ribosomal protein L43-A


Mass: 10136.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PP14
#45: Protein 60S ribosomal protein CAALFM_C304810CA


Mass: 29126.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK71

-
Protein , 4 types, 8 molecules mAZhDSARDTL1l1

#7: Protein Uncharacterized protein CaJ7.0206


Mass: 34557.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UAA6
#78: Protein Ubiquitin-40S ribosomal protein S31 fusion protein


Mass: 22615.525 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A109
#79: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34593.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3E7
#80: Protein Ribosomal protein


Mass: 24416.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4E7

-
Ribosomal protein ... , 10 types, 20 molecules wBJxBK9BTAICCECPFCQHCSLCWWDHZDK

#17: Protein Ribosomal protein L13


Mass: 22685.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ56
#18: Protein Ribosomal protein L22


Mass: 21002.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BUG0
#27: Protein Ribosomal protein L24


Mass: 14215.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3X2
#36: Protein Ribosomal protein L29


Mass: 14118.759 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6B7
#49: Protein Ribosomal protein S5


Mass: 26917.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ90
#50: Protein Ribosomal protein S3


Mass: 27313.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYS1
#52: Protein Ribosomal protein S7


Mass: 25319.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BS29
#56: Protein Ribosomal protein S4


Mass: 21765.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X2
#67: Protein Ribosomal protein S10


Mass: 13366.540 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYJ9
#70: Protein Ribosomal protein S23 (S12)


Mass: 16000.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V0

+
40S ribosomal protein ... , 25 types, 50 molecules CCNDCOGCRICTJCUKCVMCXNCYOCZPDAQDBRDCSDDTDEUDF...

#47: Protein 40S ribosomal protein S0


Mass: 28759.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C395
#48: Protein 40S ribosomal protein S1


Mass: 29041.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C387
#51: Protein 40S ribosomal protein S4


Mass: 29435.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PCI6
#53: Protein 40S ribosomal protein S6


Mass: 27146.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ37
#54: Protein 40S ribosomal protein S7


Mass: 21285.818 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C655
#55: Protein 40S ribosomal protein S8


Mass: 22801.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0S0
#57: Protein 40S ribosomal protein S10-A


Mass: 13836.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWQ8
#58: Protein 40S ribosomal protein S11A


Mass: 17638.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PN83
#59: Protein 40S ribosomal protein S12


Mass: 15715.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3A1
#60: Protein 40S ribosomal protein S13


Mass: 16976.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4G0
#61: Protein 40S ribosomal protein S14-A


Mass: 14052.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V4
#62: Protein 40S ribosomal protein S15


Mass: 15967.796 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK22
#63: Protein 40S ribosomal protein S16


Mass: 15769.456 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94017
#64: Protein 40S ribosomal protein S17-B


Mass: 15770.298 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTR7
#65: Protein 40S ribosomal protein S18-B


Mass: 17023.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3Y8
#66: Protein 40S ribosomal protein S19-A


Mass: 16097.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C5L4
#68: Protein 40S ribosomal protein S21


Mass: 9652.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P844
#69: Protein 40S ribosomal protein S22-A


Mass: 14807.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0N4
#71: Protein 40S ribosomal protein S24


Mass: 15546.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3K1
#72: Protein 40S ribosomal protein S25


Mass: 11633.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6EZQ8
#73: Protein 40S ribosomal protein S26


Mass: 13606.099 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTS1
#74: Protein 40S ribosomal protein S27


Mass: 8982.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWE6
#75: Protein 40S ribosomal protein S28-B


Mass: 7536.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C0A5
#76: Protein 40S ribosomal protein S29A


Mass: 6615.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PTR4
#77: Protein 40S ribosomal protein S30


Mass: 7127.437 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PSK2

-
Non-polymers , 5 types, 1524 molecules

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


Mass: 24.305 Da / Num. of mol.: 1455 / Source method: obtained synthetically / Formula: Mg
#82: Chemical ChemComp-3K5 / 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose / Phyllanthoside


Mass: 804.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O17
#83: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C23H45N5O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: Antimicrobial, medication*YM
#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#85: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 20K, KSCN, Mg Acetate, K - acetate, Bis-Tris-Acetate, Glycerol, Spermidine, phyllanthoside

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→177.03 Å / Num. obs: 1134400 / % possible obs: 99.3 % / Redundancy: 14.4 % / Biso Wilson estimate: 87.83 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.695 / Rpim(I) all: 0.1885 / Rrim(I) all: 0.721 / Net I/σ(I): 4.36
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.3-3.353.382500490.0523.5031
3.35-3.43.266470210.0663.3821
3.4-3.453.151443550.0713.2641
3.45-3.53.015418560.0753.1241
3.5-3.552.889394990.0922.9941
3.55-3.62.722373300.112.8221
3.6-3.652.611353630.1272.7071
3.65-3.72.451336000.1572.5431
3.7-3.752.264316100.1962.3491
3.75-3.82.112299960.2142.1941
3.8-3.91.902544590.2651.9811
3.9-41.755502980.3511.8191
4-4.51.2851905010.6041.331
4.5-70.5853286400.9190.6071
7-100.206787560.9920.2131
10-500.07407810.9990.0721
50-177.030.0512860.9970.0541

-
Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→177.03 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 1824 0.16 %
Rwork0.2541 --
obs0.2542 1133838 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→177.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms181142 222314 1969 0 405425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004433732
X-RAY DIFFRACTIONf_angle_d1.012636243
X-RAY DIFFRACTIONf_dihedral_angle_d16.484196808
X-RAY DIFFRACTIONf_chiral_restr0.05479737
X-RAY DIFFRACTIONf_plane_restr0.00741967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.390.40281410.390786898X-RAY DIFFRACTION99
3.39-3.490.42941400.392986854X-RAY DIFFRACTION99
3.49-3.60.43761390.380486777X-RAY DIFFRACTION99
3.6-3.730.36391410.361587042X-RAY DIFFRACTION99
3.73-3.880.35051380.335185803X-RAY DIFFRACTION98
3.88-4.060.35971400.3187104X-RAY DIFFRACTION99
4.06-4.270.32721410.278987529X-RAY DIFFRACTION100
4.27-4.540.30291410.251387457X-RAY DIFFRACTION100
4.54-4.890.24931410.227287524X-RAY DIFFRACTION100
4.89-5.380.26591390.200686956X-RAY DIFFRACTION99
5.38-6.160.23711400.198686512X-RAY DIFFRACTION99
6.16-7.760.26531410.203587858X-RAY DIFFRACTION100
7.76-177.030.23551420.185887700X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more