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- PDB-5t62: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase L... -

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Entry
Database: PDB / ID: 5t62
TitleNmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
DescriptorEukaryotic translation initiation factor 6
Ubiquitin-60S ribosomal protein L40
Ribosomal Protein uL1
60S ribosomal export protein NMD3
Large Subunit GTPase 1/RNA Complex
(60S ribosomal protein ...) x 39
KeywordsRIBOSOME / Ribosome Biogenesis / 60S / Nmd3 / Lsg1 / Tif6 / cryo-em / Ribosome
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (3.1 Å resolution / Particle / Single particle)
AuthorsMalyutin, A.G. / Musalgaonkar, S. / Patchett, S. / Frank, J. / Johnson, A.W.
CitationEMBO J., 2017, 36, 854-868

EMBO J., 2017, 36, 854-868 Yorodumi Papers
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
Andrey G Malyutin / Sharmishtha Musalgaonkar / Stephanie Patchett / Joachim Frank / Arlen W Johnson

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 2016 / Release: Feb 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 8, 2017Structure modelrepositoryInitial release
1.1Feb 15, 2017Structure modelDatabase references
1.2Feb 22, 2017Structure modelDatabase references
1.3Apr 12, 2017Structure modelDatabase references
1.4Sep 20, 2017Structure modelAuthor supporting evidence / Data collectionem_image_scans / em_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.5Nov 8, 2017Structure modelDerived calculationspdbx_struct_assembly_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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Assembly

Deposited unit
X: Eukaryotic translation initiation factor 6
A: Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA
B: Saccharomyces cerevisiae strain HB_C_OMARUNUI_6 chromosome XII sequence
C: Saccharomyces cerevisiae culture-collection CBS:2888 large subunit ribosomal RNA gene, partial sequence
D: 60S ribosomal protein L2-A
E: 60S ribosomal protein L3
F: 60S ribosomal protein L4-A
G: 60S ribosomal protein L5
H: 60S ribosomal protein L6-A
I: 60S ribosomal protein L7-A
J: 60S ribosomal protein L8-A
K: 60S ribosomal protein L9-A
L: 60S ribosomal protein L10
M: 60S ribosomal protein L11-A
N: 60S ribosomal protein L13-A
O: 60S ribosomal protein L14-A
a: 60S ribosomal protein L15-A
b: 60S ribosomal protein L16-A
c: 60S ribosomal protein L17-A
d: 60S ribosomal protein L18-A
e: 60S ribosomal protein L19-A
f: 60S ribosomal protein L20-A
g: 60S ribosomal protein L21-A
h: 60S ribosomal protein L22-A
i: 60S ribosomal protein L23-A
j: 60S ribosomal protein L24-A
k: 60S ribosomal protein L25
l: 60S ribosomal protein L26-A
m: 60S ribosomal protein L27-A
n: 60S ribosomal protein L28
o: 60S ribosomal protein L29
p: 60S ribosomal protein L30
q: 60S ribosomal protein L31-A
r: 60S ribosomal protein L32
s: 60S ribosomal protein L33-A
t: 60S ribosomal protein L34-A
u: 60S ribosomal protein L35-A
v: 60S ribosomal protein L36-A
w: 60S ribosomal protein L37-A
x: 60S ribosomal protein L38
y: 60S ribosomal protein L39
z: Ubiquitin-60S ribosomal protein L40
Q: 60S ribosomal protein L42-A
R: 60S ribosomal protein L43-A
S: Ribosomal Protein uL1
V: 60S ribosomal export protein NMD3
W: Large subunit GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,110,894210
Polyers2,106,40447
Non-polymers4,489163
Water1086
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)379870
ΔGint (kcal/M)-4424
Surface area (Å2)710130

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Components

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Polypeptide(L) , 5 types, 5 molecules XzSVW

#1: Polypeptide(L)Eukaryotic translation initiation factor 6 / eIF-6


Mass: 28597.959 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12522

Cellular component

Molecular function

Biological process

  • assembly of large subunit precursor of preribosome (GO: 1902626)
  • maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000466)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • mature ribosome assembly (GO: 0042256)
  • ribosomal large subunit biogenesis (GO: 0042273)
  • ribosomal subunit export from nucleus (GO: 0000054)
  • rRNA processing (GO: 0006364)
#42: Polypeptide(L)Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CH08

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)Ribosomal Protein uL1


Mass: 18485.723 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae
#46: Polypeptide(L)60S ribosomal export protein NMD3 / Nonsense-mediated mRNA decay protein 3


Mass: 59995.926 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38861

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)Large subunit GTPase 1


Mass: 71945.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P53145, EC: 3.6.1.-

Cellular component

Molecular function

Biological process

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Saccharomyces cerevisiae ... , 3 types, 3 molecules ABC

#2: RNA chainSaccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c / References: REF: 831416132
#3: RNA chainSaccharomyces cerevisiae strain HB_C_OMARUNUI_6 chromosome XII sequence


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 1039024045
#4: RNA chainSaccharomyces cerevisiae culture-collection CBS:2888 large subunit ribosomal RNA gene, partial sequence


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: GenBank: 1102645687

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60S ribosomal protein ... , 39 types, 39 molecules DEFGHIJKLM...

#5: Polypeptide(L)60S ribosomal protein L2-A / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX45

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14126

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)60S ribosomal protein L4-A / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P10664

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26321

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02326

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05737

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of LSU-rRNA (GO: 0000470)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • ribosomal large subunit biogenesis (GO: 0042273)
#11: Polypeptide(L)60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P17076

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05738

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)60S ribosomal protein L10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P41805

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C0W9

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)60S ribosomal protein L13-A


Mass: 22604.164 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12690

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)60S ribosomal protein L14-A


Mass: 15195.066 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P36105

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05748

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P26784

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)60S ribosomal protein L17-A / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05740

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
#20: Polypeptide(L)60S ribosomal protein L18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX49

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX82

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)60S ribosomal protein L20-A / L18a


Mass: 20478.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX23

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)60S ribosomal protein L21-A


Mass: 18279.266 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q02753

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05749

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)60S ribosomal protein L23-A / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX41

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04449

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04456

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)60S ribosomal protein L26-A / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05743

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)60S ribosomal protein L27-A


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H6

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P02406

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)60S ribosomal protein L29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05747

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P14120

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)60S ribosomal protein L31-A / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0C2H8

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)60S ribosomal protein L32


Mass: 14809.441 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38061

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)60S ribosomal protein L33-A / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05744

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)60S ribosomal protein L34-A


Mass: 13673.196 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P87262

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein L35-A


Mass: 13942.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX84

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)60S ribosomal protein L36-A / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P05745

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49166

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
  • translation (GO: 0006412)
#40: Polypeptide(L)60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P49167

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein L39 / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04650

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein L42-A / L41 / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX27

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein L43-A / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P0CX25

Cellular component

Molecular function

Biological process

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Non-polymers , 4 types, 169 molecules

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


Mass: 24.305 Da / Num. of mol.: 160 / Formula: Mg
#49: ChemicalChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Formula: K
#50: ChemicalChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp (GMPPNP, energy-carrying molecule analogue) *YM


Mass: 522.196 Da / Num. of mol.: 1 / Formula: C10H17N6O13P3
#51: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Formula: H2O

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Details

Sequence detailsIn chain 47 the two UNK segments (135-175 and 276-298) are separated by gaps from the rest of the known sequence and there is not enough information in my EM maps to accurately assign neither the number nor sequence to these regions

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component

Entity ID: 1, 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 / Source: MULTIPLE SOURCES

IDNameTypeParent IDDetails
160S in complex with Nmd3, Lsg1, and Tif6RIBOSOME0
260S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3COMPLEX1This map was acquired by combining 60S-Nmd3 and 60S-Nmd3-Tif6-Lsg1 datasets to increase the number of particles containing 60S-Nmd3 in closed conformation.
Molecular weight
IDUnitsEntity assembly IDExperimental value
1MEGADALTONS1NO
12
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
114932Saccharomyces cerevisiae
224932Saccharomyces cerevisiae
Buffer solution
IDSpecimen IDpH
117.5
227.5
Specimen
IDExperiment IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
11NONONOYES
21NONONOYES
Specimen support
IDSpecimen IDDetailsGrid materialGrid mesh sizeGrid type
1110WGOLD300Made in lab
2210WGOLD300Made in lab
Vitrification

Chamber temperature: 277 kelvins / Cryogen name: ETHANE / Entry ID: 5T62 / Humidity: 100 % / Instrument: FEI VITROBOT MARK IV

IDSpecimen ID
11
22

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company /
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen ID: 1

IDAlignment procedureC2 aperture diameterCalibrated magnificationMicroscope modelCsNominal defocus maxNominal defocus minNominal magnificationSpecimen holder model
1COMA FREE3031000FEI TECNAI F302.264000150027000OTHER
2FEI TITAN KRIOSFEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging IDAverage exposure timeElectron doseDetector modeFilm or detector model
118.040COUNTINGGATAN K2 SUMMIT (4k x 4k)
22859.5COUNTINGGATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging ID
1RELION1.4PARTICLE SELECTION1
2LeginonIMAGE ACQUISITION1
4CTFFIND34.0.18CTF CORRECTION1
7CHIMERAMODEL FITTING
10CootMODEL REFINEMENT
14RELION1.4INITIAL EULER ASSIGNMENT1
15RELION1.4FINAL EULER ASSIGNMENT1
16RELION1.4CLASSIFICATION1
17RELION1.4RECONSTRUCTION1
27MotionCor208-22-10CTF CORRECTION2
30RELION2.0 Open BetaINITIAL EULER ASSIGNMENT2
31RELION2.0 Open BetaFINAL EULER ASSIGNMENT2
32RELION2.0 Open BetaCLASSIFICATION2
33RELION2.0 Open BetaRECONSTRUCTION2
Image processing
IDImage recording ID
11
22
CTF correction
IDEM image processing IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstruction #1Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 226516 / Symmetry type: POINT
3D reconstruction #2Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 19411 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Least-squares processHighest resolution: 3.3 Å
Number of atoms included #1Total: 131777
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.015143315
ELECTRON MICROSCOPYr_bond_other_d0.0020.02091952
ELECTRON MICROSCOPYr_angle_refined_deg1.0341.539208158
ELECTRON MICROSCOPYr_angle_other_deg1.1913.000215337
ELECTRON MICROSCOPYr_dihedral_angle_1_deg16.7078.85322998
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.45122.1062365
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.71315.00010318
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.78115.000579
ELECTRON MICROSCOPYr_chiral_restr0.1070.21123498
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.020106354
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02031969
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.76712.88229293
ELECTRON MICROSCOPYr_mcbond_other5.76712.88129292
ELECTRON MICROSCOPYr_mcangle_it10.57319.29536520
ELECTRON MICROSCOPYr_mcangle_other10.57319.29636521
ELECTRON MICROSCOPYr_scbond_it5.34612.028114022
ELECTRON MICROSCOPYr_scbond_other5.34612.028114023
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other8.97918.080171639
ELECTRON MICROSCOPYr_long_range_B_refined28.252404065
ELECTRON MICROSCOPYr_long_range_B_other28.252404065
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded

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About Yorodumi

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News

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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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

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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

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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Yorodumi

Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

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