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- PDB-5mmi: Structure of the large subunit of the chloroplast ribosome -

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Basic information

Entry
Database: PDB / ID: 5mmi
TitleStructure of the large subunit of the chloroplast ribosome
Components
  • (50S ribosomal protein ...) x 17
  • (plastid ribosomal protein ...) x 14
  • 23S ribosomal RNA
  • 4.5S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNA
KeywordsRIBOSOME / chloroplast / translation / cryo-EM
Function / homology
Function and homology information


plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 ...Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal Protein L22; Chain A / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / Ribosomal protein L10 / RRM (RNA recognition motif) domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Single Sheet / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Nucleic acid-binding proteins / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein uL10c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein uL2cz/uL2cy / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein uL14c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Large ribosomal subunit protein uL16c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Large ribosomal subunit protein uL11c / Large ribosomal subunit protein uL10c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL31c / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBieri, P. / Leibundgut, M. / Saurer, M. / Boehringer, D. / Ban, N.
CitationJournal: EMBO J / Year: 2017
Title: The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Authors: Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban /
Abstract: Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, ...Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.
History
DepositionDec 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Derived calculations
Category: em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name
Revision 1.3Oct 17, 2018Group: Data collection / Other / Refinement description / Category: cell / refine / Item: _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
0: 50S ribosomal protein L31
1: 50S ribosomal protein L32, chloroplastic
2: 50S ribosomal protein L33, chloroplastic
3: 50S ribosomal protein L34, chloroplastic
4: 50S ribosomal protein L35, chloroplastic
5: 50S ribosomal protein L36, chloroplastic
6: plastid ribosomal protein cL37, PSRP5
7: 50S ribosomal protein 6, chloroplastic
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2, chloroplastic
D: plastid ribosomal protein uL3c
E: plastid ribosomal protein uL4c
F: plastid ribosomal protein uL5c
G: plastid ribosomal protein uL6c
H: plastid ribosomal protein bL9c
I: plastid ribosomal protein uL10c
J: 50S ribosomal protein L11, chloroplastic
K: 50S ribosomal protein L13, chloroplastic
L: 50S ribosomal protein L14, chloroplastic
M: plastid ribosomal protein uL15c
N: 50S ribosomal protein L16, chloroplastic
O: plastid ribosomal protein bL17c
P: plastid ribosomal protein uL18c
Q: 50S ribosomal protein L19, chloroplastic
R: 50S ribosomal protein L20, chloroplastic
S: 50S ribosomal protein L21, chloroplastic
T: 50S ribosomal protein L22, chloroplastic
U: 50S ribosomal protein L23, chloroplastic
V: plastid ribosomal protein uL24c
W: 4.5S ribosomal RNA
X: plastid ribosomal protein bL27c
Y: plastid ribosomal protein bL28c
Z: plastid ribosomal protein uL29c
z: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,625,172538
Polymers1,612,86435
Non-polymers12,308503
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-101 kcal/mol
Surface area31260 Å2
MethodPISA

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Components

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50S ribosomal protein ... , 17 types, 17 molecules 0123457CJKLNQRSTU

#1: Protein 50S ribosomal protein L31 / / plastid ribosomal protein bL31c


Mass: 14748.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS
#2: Protein 50S ribosomal protein L32, chloroplastic / Ribosome / plastid ribosomal protein bL32c


Mass: 6650.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#3: Protein 50S ribosomal protein L33, chloroplastic / Ribosome / plastid ribosomal protein bL33c


Mass: 7668.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Zn-binding protein / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#4: Protein 50S ribosomal protein L34, chloroplastic / Ribosome / plastid ribosomal protein bL34c / CL34


Mass: 16126.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#5: Protein 50S ribosomal protein L35, chloroplastic / Ribosome / plastid ribosomal protein bL35c / CL35


Mass: 17376.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#6: Protein/peptide 50S ribosomal protein L36, chloroplastic / Ribosome / plastid ribosomal protein bL36c


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Zn-binding protein / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230
#8: Protein 50S ribosomal protein 6, chloroplastic / Ribosome / plastid ribosomal protein cL38 / PSRP6 / CL25 / Plastid-specific 50S ribosomal protein 6 / PSRP-6


Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82411
#11: Protein 50S ribosomal protein L2, chloroplastic / Ribosome / plastid ribosomal protein uL2c / Ribosomal protein CS-L4


Mass: 29853.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#18: Protein 50S ribosomal protein L11, chloroplastic / Ribosome / plastid ribosomal protein uL11c / CL11


Mass: 23689.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P31164
#19: Protein 50S ribosomal protein L13, chloroplastic / Ribosome / plastid ribosomal protein uL13c / CL13


Mass: 28211.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#20: Protein 50S ribosomal protein L14, chloroplastic / Ribosome / plastid ribosomal protein uL14c / Ribosomal protein CS-L29


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09596
#22: Protein 50S ribosomal protein L16, chloroplastic / Ribosome / plastid ribosomal protein uL16c / Ribosomal protein CS-L24


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353
#25: Protein 50S ribosomal protein L19, chloroplastic / Ribosome / plastid ribosomal protein bL19c / CL19


Mass: 26121.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#26: Protein 50S ribosomal protein L20, chloroplastic / Ribosome / plastid ribosomal protein bL20c


Mass: 15725.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#27: Protein 50S ribosomal protein L21, chloroplastic / Ribosome / plastid ribosomal protein bL21c / CL21 / CS-L7


Mass: 28441.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 68-81 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#28: Protein 50S ribosomal protein L22, chloroplastic / Ribosome / plastid ribosomal protein uL22c / Ribosomal protein CS-L13


Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594
#29: Protein 50S ribosomal protein L23, chloroplastic / Ribosome / plastid ribosomal protein uL23c / PRPL23


Mass: 21832.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5

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Plastid ribosomal protein ... , 14 types, 14 molecules 6DEFGHIMOPVXYZ

#7: Protein plastid ribosomal protein cL37, PSRP5


Mass: 15694.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S2M7, UniProt: P27684*PLUS
#12: Protein plastid ribosomal protein uL3c


Mass: 33034.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QEC7, UniProt: P82191*PLUS
#13: Protein plastid ribosomal protein uL4c


Mass: 32541.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RVQ9, UniProt: O49937*PLUS
#14: Protein plastid ribosomal protein uL5c


Mass: 28182.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 39-52 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RJX4, UniProt: P82192*PLUS
#15: Protein plastid ribosomal protein uL6c


Mass: 24516.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS
#16: Protein plastid ribosomal protein bL9c


Mass: 22038.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RQ91, UniProt: P82180*PLUS
#17: Protein plastid ribosomal protein uL10c


Mass: 26128.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R3N5, UniProt: P82139*PLUS
#21: Protein plastid ribosomal protein uL15c


Mass: 29081.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS
#23: Protein plastid ribosomal protein bL17c


Mass: 14577.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS
#24: Protein plastid ribosomal protein uL18c


Mass: 18410.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS
#30: Protein plastid ribosomal protein uL24c


Mass: 21417.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QFU9, UniProt: P27683*PLUS
#32: Protein plastid ribosomal protein bL27c


Mass: 21366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS
#33: Protein plastid ribosomal protein bL28c


Mass: 16460.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS
#34: Protein plastid ribosomal protein uL29c


Mass: 19083.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS

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RNA chain , 4 types, 4 molecules ABWz

#9: RNA chain 23S ribosomal RNA / / plastid 23S rRNA


Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084
#10: RNA chain 5S ribosomal RNA / / plastid 5S rRNA


Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#31: RNA chain 4.5S ribosomal RNA / plastid 4.5S rRNA


Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 12299
#35: RNA chain E-site tRNA


Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CA-3' end of E-site tRNA / Source: (natural) Spinacia oleracea (spinach)

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Non-polymers , 2 types, 503 molecules

#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#37: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 501 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Chloroplast 70S ribosome / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Molecular weightValue: 2.4 MDa / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach) / Organelle: chloroplast / Tissue: leaf
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris hydrochlorideTris-HClTris1
225 mMPotassium chlorideKCl1
325 mMMagnesium acetateMg(CH3COO)21
42 mMDithiothreitolDTT1
50.05 mMSpermine1
62 mMSpermidine1
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 K

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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 / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2796
Image scansMovie frames/image: 8 / Used frames/image: 2-8

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN1.9particle selectionBatchboxer
2EPUimage acquisition
4CTFFIND3CTF correctionCTF estimation
5RELION1.4CTF correctionAmplitude correction
8UCSF Chimera1.11.2model fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 326094
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154332 / Symmetry type: POINT
Atomic model buildingB value: 56.9 / Protocol: OTHER / Space: RECIPROCAL
RefinementResolution: 3.25→212.302 Å / SU ML: 0.44 / σ(F): 1.06 / Phase error: 26.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2471 41351 2.5 %
Rwork0.2343 --
obs0.2346 1650858 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008103202
ELECTRON MICROSCOPYf_angle_d1.1154296
ELECTRON MICROSCOPYf_dihedral_angle_d16.6248326
ELECTRON MICROSCOPYf_chiral_restr0.04619619
ELECTRON MICROSCOPYf_plane_restr0.0068225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2501-3.2870.456313950.461454328ELECTRON MICROSCOPY100
3.287-3.32570.396613890.36953061ELECTRON MICROSCOPY100
3.3257-3.36620.363713600.353853815ELECTRON MICROSCOPY100
3.3662-3.40890.361613930.34753861ELECTRON MICROSCOPY100
3.4089-3.45370.354513970.335853596ELECTRON MICROSCOPY100
3.4537-3.5010.352614240.325853475ELECTRON MICROSCOPY100
3.501-3.5510.34113900.315553622ELECTRON MICROSCOPY100
3.551-3.60410.32813700.304353704ELECTRON MICROSCOPY100
3.6041-3.66040.313712880.294954345ELECTRON MICROSCOPY100
3.6604-3.72040.302414300.283653187ELECTRON MICROSCOPY100
3.7204-3.78460.292314130.270553519ELECTRON MICROSCOPY100
3.7846-3.85340.279712800.265153784ELECTRON MICROSCOPY100
3.8534-3.92750.264614170.252453678ELECTRON MICROSCOPY100
3.9275-4.00770.259813680.242553529ELECTRON MICROSCOPY100
4.0077-4.09480.243713960.234453910ELECTRON MICROSCOPY100
4.0948-4.19010.222913180.225253189ELECTRON MICROSCOPY100
4.1901-4.29490.241914020.216353886ELECTRON MICROSCOPY100
4.2949-4.4110.222413630.209954042ELECTRON MICROSCOPY100
4.411-4.54080.215714030.201653423ELECTRON MICROSCOPY100
4.5408-4.68740.203813560.195153684ELECTRON MICROSCOPY100
4.6874-4.85490.206913750.189353742ELECTRON MICROSCOPY100
4.8549-5.04930.199513310.18353608ELECTRON MICROSCOPY100
5.0493-5.27920.186314190.174753354ELECTRON MICROSCOPY100
5.2792-5.55750.177113550.167853915ELECTRON MICROSCOPY100
5.5575-5.90570.176613010.167853805ELECTRON MICROSCOPY100
5.9057-6.36170.178814240.164353373ELECTRON MICROSCOPY100
6.3617-7.0020.169414100.162553715ELECTRON MICROSCOPY100
7.002-8.01520.162513740.156953652ELECTRON MICROSCOPY100
8.0152-10.09840.173914450.161953681ELECTRON MICROSCOPY100
10.0984-212.7560.162713650.157253024ELECTRON MICROSCOPY99

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