[English] 日本語
Yorodumi
- PDB-6yw5: The structure of the small subunit of the mitoribosome from Neuro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yw5
TitleThe structure of the small subunit of the mitoribosome from Neurospora crassa
Components
  • (37S ribosomal protein ...) x 5
  • (40S ribosomal protein ...) x 2
  • (Mito ribosomal protein ...) x 5
  • (Mitochondrial ...Mitochondrion) x 6
  • (Ribosomal protein ...) x 3
  • 16S rRNA
  • 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
  • DUF1713 domain-containing protein
  • Fe superoxide dismutase
  • IF1
  • IGR domain-containing protein
  • Ribosomal_S7 domain-containing protein
  • mS26
  • mS27
  • mS33
  • mS42
  • mS46
  • mS47
  • uS2m
  • uS9m
KeywordsTRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase activity / nuclear pore inner ring / valine catabolic process / nuclear pore organization / ATPase inhibitor activity / negative regulation of ATP-dependent activity / mitochondrial large ribosomal subunit / positive regulation of translational fidelity / mitochondrial small ribosomal subunit / structural constituent of nuclear pore ...3-hydroxyisobutyryl-CoA hydrolase activity / nuclear pore inner ring / valine catabolic process / nuclear pore organization / ATPase inhibitor activity / negative regulation of ATP-dependent activity / mitochondrial large ribosomal subunit / positive regulation of translational fidelity / mitochondrial small ribosomal subunit / structural constituent of nuclear pore / mitochondrial translation / superoxide dismutase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / Ribosomal protein L31p, N-terminal / 54S ribosomal protein L36, yeast / Mitochondrial ribosomal protein MRP51, fungi / Mitochondrial ribosomal protein S25 / Ribosomal protein S24, mitochondrial / Ribosomal protein S23, mitochondrial, fungi / Mitochondrial ribosomal protein subunit / Mitochondrial ribosomal protein S25 / Ribosomal protein MRP10, mitochondrial ...: / Ribosomal protein L31p, N-terminal / 54S ribosomal protein L36, yeast / Mitochondrial ribosomal protein MRP51, fungi / Mitochondrial ribosomal protein S25 / Ribosomal protein S24, mitochondrial / Ribosomal protein S23, mitochondrial, fungi / Mitochondrial ribosomal protein subunit / Mitochondrial ribosomal protein S25 / Ribosomal protein MRP10, mitochondrial / Ribosomal protein S35, mitochondrial / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase domain / IGR protein motif / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Sterile alpha motif/pointed domain superfamily / Ribosomal protein S21 / Ribosomal protein S13, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S14 / Ribosomal protein S2 / Ribosomal protein S4, conserved site / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / Ribosomal protein S11 / RNA-binding S4 domain / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S13 family profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 37S ribosomal protein mrp5 / Ribosomal protein S16, mitochondrial / Ribosomal protein S5, mitochondrial / 37S ribosomal protein S5 ...ADENOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 37S ribosomal protein mrp5 / Ribosomal protein S16, mitochondrial / Ribosomal protein S5, mitochondrial / 37S ribosomal protein S5 / Ribosomal protein S15 / Mitochondrial 37S ribosomal protein S27 / 37S ribosomal protein S24, mitochondrial / Protein FYV4, mitochondrial / Mitochondrial 3-hydroxyisobutyryl-CoA hydrolase / Large ribosomal subunit protein bL31m / Mito ribosomal protein S18 / Mitochondrial ribosomal protein S19 / 37S ribosomal protein S10, mitochondrial / Small ribosomal subunit protein mS27 / 40S ribosomal protein S13 / Fe superoxide dismutase / Mitochondrial 37S ribosomal protein S17 / 37S ribosomal protein mrp10, mitochondrial / Ribosomal_S7 domain-containing protein / 37S ribosomal protein S9, mitochondrial / Mitochondrial 30S ribosomal protein S12 / Mito ribosomal protein S4 / Mito ribosomal protein S21 / Mito ribosomal protein S6 / Small ribosomal subunit protein mS29 / Mitochondrial 40S ribosomal protein MRP2 / Protein FYV4, mitochondrial / Mitochondrial ribosomal protein subunit S18 / Small ribosomal subunit protein mS45 / 40S ribosomal protein S8 / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein uS2m / ATP synthase F1 subunit epsilon
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsAmunts, A. / Itoh, Y. / Naschberger, A.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)(ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology Organization (EMBO)H2020-MSCA-IF-2017European Union
CitationJournal: Nat Commun / Year: 2020
Title: Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Authors: Yuzuru Itoh / Andreas Naschberger / Narges Mortezaei / Johannes M Herrmann / Alexey Amunts /
Abstract: Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each ...Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10958
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10958
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: uS2m
BB: Mito ribosomal protein S2
CC: Ribosomal protein S5, mitochondrial
DD: Mito ribosomal protein S4
EE: 37S ribosomal protein S5
FF: Mito ribosomal protein S6
GG: Ribosomal_S7 domain-containing protein
HH: 40S ribosomal protein S8
II: uS9m
JJ: 37S ribosomal protein S10, mitochondrial
KK: Mitochondrial ribosomal protein subunit S18
LL: Mitochondrial 30S ribosomal protein S12
MM: 40S ribosomal protein S13
NN: Mitochondrial 40S ribosomal protein MRP2
OO: Ribosomal protein S15
PP: Ribosomal protein S16, mitochondrial
QQ: Mitochondrial 37S ribosomal protein S17
RR: Mito ribosomal protein S18
SS: Mitochondrial ribosomal protein S19
TT: Mito ribosomal protein S21
UU: 37S ribosomal protein S25, mitochondrial
VV: mS26
WW: mS27
XX: Mitochondrial ribosomal protein DAP3
YY: mS33
ZZ: 37S ribosomal protein S24, mitochondrial
11: 37S ribosomal protein mrp10, mitochondrial
22: DUF1713 domain-containing protein
33: IGR domain-containing protein
44: Fe superoxide dismutase
55: Fe superoxide dismutase
66: mS42
77: mS46
88: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
00: mS47
99: mS47
aa: 16S rRNA
V: IF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,760,317158
Polymers1,756,59238
Non-polymers3,725120
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 14 types, 16 molecules AAGGIIVVWWYY223344556677880099V

#1: Protein uS2m


Mass: 51596.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: A7UWX2
#7: Protein Ribosomal_S7 domain-containing protein


Mass: 33821.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S6M9
#9: Protein uS9m


Mass: 35319.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S7R6
#22: Protein mS26


Mass: 35312.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHR9
#23: Protein mS27


Mass: 44923.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYW7
#25: Protein mS33


Mass: 12169.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5R0
#28: Protein DUF1713 domain-containing protein


Mass: 38126.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHR6
#29: Protein IGR domain-containing protein


Mass: 26612.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6Q3
#30: Protein Fe superoxide dismutase


Mass: 34270.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S2H6
#31: Protein mS42


Mass: 39274.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHB2
#32: Protein mS46


Mass: 43112.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SG49
#33: Protein 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial / / 3-hydroxyisobutyryl-coenzyme A hydrolase


Mass: 56401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus)
References: UniProt: Q1K7A4, 3-hydroxyisobutyryl-CoA hydrolase
#34: Protein mS47


Mass: 10664.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IRA3
#36: Protein IF1


Mass: 23766.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K7L7

-
Mito ribosomal protein ... , 5 types, 5 molecules BBDDFFRRTT

#2: Protein Mito ribosomal protein S2


Mass: 47197.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5ILE0
#4: Protein Mito ribosomal protein S4


Mass: 51610.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA90
#6: Protein Mito ribosomal protein S6


Mass: 13304.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SB95
#18: Protein Mito ribosomal protein S18


Mass: 28468.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8E0
#20: Protein Mito ribosomal protein S21


Mass: 25679.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SAJ1

-
Ribosomal protein ... , 3 types, 3 molecules CCOOPP

#3: Protein Ribosomal protein S5, mitochondrial / Ribosome


Mass: 58907.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: P23351
#15: Protein Ribosomal protein S15 /


Mass: 35803.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5G1
#16: Protein Ribosomal protein S16, mitochondrial / Ribosome / S24


Mass: 12140.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: P08580

-
37S ribosomal protein ... , 5 types, 5 molecules EEJJUUZZ11

#5: Protein 37S ribosomal protein S5 /


Mass: 53297.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K548
#10: Protein 37S ribosomal protein S10, mitochondrial / Ribosome / Mitochondrial ribosomal small subunit protein 10


Mass: 30377.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYL4
#21: Protein 37S ribosomal protein S25, mitochondrial / Ribosome


Mass: 29553.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q873E4
#26: Protein 37S ribosomal protein S24, mitochondrial / Ribosome


Mass: 44057.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5Z0
#27: Protein 37S ribosomal protein mrp10, mitochondrial / Ribosome


Mass: 9907.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4Y4

-
40S ribosomal protein ... , 2 types, 2 molecules HHMM

#8: Protein 40S ribosomal protein S8 /


Mass: 17743.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHF3
#13: Protein 40S ribosomal protein S13 /


Mass: 13503.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S2C2

-
Mitochondrial ... , 6 types, 6 molecules KKLLNNQQSSXX

#11: Protein Mitochondrial ribosomal protein subunit S18


Mass: 42159.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGU0
#12: Protein Mitochondrial 30S ribosomal protein S12


Mass: 18657.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S9I4
#14: Protein Mitochondrial 40S ribosomal protein MRP2


Mass: 13210.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SF85
#17: Protein Mitochondrial 37S ribosomal protein S17


Mass: 18505.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4E0
#19: Protein Mitochondrial ribosomal protein S19


Mass: 10408.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8V2
#24: Protein Mitochondrial ribosomal protein DAP3


Mass: 51451.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SD06

-
RNA chain , 1 types, 1 molecules aa

#35: RNA chain 16S rRNA /


Mass: 600339.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus)

-
Non-polymers , 3 types, 120 molecules

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


Mass: 24.305 Da / Num. of mol.: 97 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#39: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: K

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Mitoribosome of Neurospora crassa / Type: RIBOSOME / Entity ID: #1-#36 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Neurospora crassa OR74A (fungus)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid-KOHHEPES-KOH1
215 mMPotassium chlorideKCl1
315 mMMagnesium acetateMg(C2H3O2)21
40.05 %n-Dodecyl B-D-maltosideDDM1
50.0075 %1,3-bis(sn-3-phosphatidyl)-sn-glycerolCardiolipin1
62 mMDithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 130000 X / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3172
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_3742refinement
PHENIXdev_3742refinement
EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131806 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 36.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001995706
ELECTRON MICROSCOPYf_angle_d0.356136269
ELECTRON MICROSCOPYf_chiral_restr0.030816157
ELECTRON MICROSCOPYf_plane_restr0.00212174
ELECTRON MICROSCOPYf_dihedral_angle_d18.417140907

+
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