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- PDB-8oi5: Crystal structure of the Candida albicans 80S ribosome in complex... -

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Basic information

Entry
Database: PDB / ID: 8oi5
TitleCrystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (2mM)
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 37
  • (Ribosomal protein ...) x 10
  • 18S
  • 25S
  • 5.8S
  • 5S
  • Guanine nucleotide-binding protein subunit beta-like 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 S5, eukaryotic/archaeal / Ribosomal protein L29e / Ribosomal L29e protein family / 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 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 / Ribosomal protein L23, N-terminal domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein S8e, conserved site
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 / 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 / SAD / Resolution: 2.9 Å
AuthorsKolosova, O. / Zgadzay, Y. / Yusupov, M.
Funding support France, Russian Federation, 4items
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
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. / Yusupov, M.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 25S
3: 5S
4: 5.8S
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
B: 18S
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
AT: 5S
AU: 5.8S
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
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
i: 60S ribosomal protein CAALFM_C304810CA
CL: 60S ribosomal protein CAALFM_C304810CA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,240,8641230
Polymers6,180,759156
Non-polymers60,1061074
Water00
1
1: 25S
3: 5S
4: 5.8S
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
B: 18S
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
i: 60S ribosomal protein CAALFM_C304810CA
hetero molecules


  • defined by author
  • 3.16 MDa, 79 polymers
Theoretical massNumber of molelcules
Total (without water)3,155,057640
Polymers3,118,98479
Non-polymers36,073561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AS: 25S
AT: 5S
AU: 5.8S
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
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
CL: 60S ribosomal protein CAALFM_C304810CA
hetero molecules


  • defined by author
  • 3.09 MDa, 77 polymers
Theoretical massNumber of molelcules
Total (without water)3,085,807590
Polymers3,061,77577
Non-polymers24,032513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)297.300, 292.540, 442.980
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 4 types, 8 molecules 1AS3AT4AUBCM

#1: RNA chain 25S


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


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


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


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

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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: 13774.282 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
#79: 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 , 3 types, 4 molecules mAZhAR

#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
#77: Protein Ubiquitin-40S ribosomal protein S31 fusion protein


Mass: 22615.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A109
#78: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34593.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3E7

-
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
#48: 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
#49: 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
#51: 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
#55: 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
#66: 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
#69: 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...

#46: 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
#47: 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
#50: 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
#52: 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
#53: 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
#54: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#67: 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
#68: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: 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
#76: 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 , 4 types, 1074 molecules

#80: 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.: 1 / Source method: obtained synthetically / Formula: C40H52O17
#81: Chemical...
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C23H45N5O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: Antimicrobial, medication*YM
#82: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1001 / Source method: obtained synthetically / Formula: Mg
#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60 %
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: May 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→163 Å / Num. obs: 1631597 / % possible obs: 99.2 % / Redundancy: 21.7 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.556 / Rpim(I) all: 0.2205 / Rrim(I) all: 0.599 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.9-2.953.28816920.0693.5261
2.95-33.169763330.0663.4061
3-3.053.026713300.0823.2521
3.05-3.12.883668380.0963.0991
3.1-3.152.719625830.1232.9241
3.15-3.22.557587970.1412.7511
3.2-3.252.38552170.1662.5621
3.25-3.32.233518830.192.4051
3.3-3.352.106487460.2282.2691
3.35-3.41.932459470.2552.0831
3.4-3.451.792432470.2871.9341
3.45-3.51.633406350.3311.7651
3.5-3.61.414735730.381.5361
3.6-3.81.1441274960.5551.2331
3.8-40.8741038950.7130.9381
4-70.365058530.9460.3881
7-100.128768750.9930.1381
10-500.055394560.9990.0591
50-1630.0362630.9980.0391

-
Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→163 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 1999 0.12 %
Rwork0.2573 --
obs0.2573 1631597 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms174348 219747 3385 0 397480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006425733
X-RAY DIFFRACTIONf_angle_d1.12625020
X-RAY DIFFRACTIONf_dihedral_angle_d15.778149614
X-RAY DIFFRACTIONf_chiral_restr0.06178894
X-RAY DIFFRACTIONf_plane_restr0.00840639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.42611440.4068116509X-RAY DIFFRACTION100
2.97-3.050.42811420.3935116512X-RAY DIFFRACTION100
3.05-3.140.42411430.3771116521X-RAY DIFFRACTION100
3.14-3.240.38111430.3549116359X-RAY DIFFRACTION99
3.24-3.360.35251430.3358116475X-RAY DIFFRACTION99
3.36-3.490.31131420.3175116124X-RAY DIFFRACTION99
3.49-3.650.37271410.2974114430X-RAY DIFFRACTION98
3.65-3.850.28311440.2671117033X-RAY DIFFRACTION100
3.85-4.090.24551430.245117030X-RAY DIFFRACTION100
4.09-4.40.30841420.2278116760X-RAY DIFFRACTION100
4.4-4.850.21871430.2089116807X-RAY DIFFRACTION100
4.85-5.550.25591410.2041114886X-RAY DIFFRACTION98
5.55-6.990.23941440.2092117350X-RAY DIFFRACTION100
6.99-1630.20961440.2081116802X-RAY DIFFRACTION99

+
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