[English] 日本語
Yorodumi
- PDB-4v7e: Model of the small subunit RNA based on a 5.5 A cryo-EM map of Tr... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4v7e
TitleModel of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome
DescriptorRibosome
KeywordsRIBOSOME / eukaryotic ribosome / homology modeling / de novo modeling / ribosomal RNA / rRNA / RNA expansion segments
Specimen sourceTriticum aestivum / plant / wheat / コムギ /
MethodElectron microscopy (5.5 Å resolution / Particle / Single particle)
AuthorsBarrio-Garcia, C. / Armache, J.-P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. / Marquez, V. / Mielke, T. / Thomm, M. / Berninghausen, O. / Beatrix, B. / Soeding, J. / Westhof, E. / Wilson, D.N. / Beckmann, R.
CitationNature, 2014, 506, 107-110

primary. Nature, 2014, 506, 107-110 StrPapers
Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.
Marko Gogala / Thomas Becker / Birgitta Beatrix / Jean-Paul Armache / Clara Barrio-Garcia / Otto Berninghausen / Roland Beckmann

#1. Proc.Natl.Acad.Sci.USA, 2010, 107, 19748-19753 StrPapers
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
Armache, J.P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. / Marquez, V. / Mielke, T. / Thomm, M. / Berninghausen, O. / Beatrix, B. / Soding, J. / Westhof, E. / Wilson, D.N. / Beckmann, R.

#2. Proc.Natl.Acad.Sci.USA, 2010, 107, 19754-19759 StrPapers
Localization of eukaryote-specific ribosomal proteins in a 5.5- angstrom cryo-EM map of the 80S eukaryotic ribosome.
Armache, J.P. / Jarasch, A. / Anger, A.M. / Villa, E. / Becker, T. / Bhushan, S. / Jossinet, F. / Habeck, M. / Dindar, G. / Franckenberg, S. / Marquez, V. / Mielke, T. / Thomm, M. / Berninghausen, O. / Beatrix, B. / Soding, J. / Westhof, E. / Wilson, D.N. / Beckmann, R.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 22, 2013 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 15, 2015Structure modelOther

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1780
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
Ad: 18S ribosomal RNA
Ae: P-site tRNA
Af: 5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'
BY: 40S ribosomal protein S24E
BI: 40S ribosomal protein S8E
BK: 40S ribosomal protein S10E
BM: 40S ribosomal protein S12E
Bf: 40S ribosomal protein S31e
BX: 40S ribosomal protein S12
Bg: RACK1
BD: 40S ribosomal protein S3
BE: 40S ribosomal protein S4E
BF: 40S ribosomal protein S7
BQ: 40S ribosomal protein S9
BU: 40S ribosomal protein S10
BO: 40S ribosomal protein S11
BS: 40S ribosomal protein S13
BN: 40S ribosomal protein S15
BL: 40S ribosomal protein S17
BT: 40S ribosomal protein S19E
BP: 40S ribosomal protein S19
BZ: 40S ribosomal protein S25E
Bc: 40S ribosomal protein S28E
BW: 40S ribosomal protein S8
Bd: 40S ribosomal protein S14
Bb: 40S ribosomal protein S27E
Be: 40S ribosomal protein S30E
BA: 40S ribosomal protein S2
BR: 40S ribosomal protein S17E
BB: 40S ribosomal protein S1E
BV: 40S ribosomal protein S21E
Ba: 40S ribosomal protein S26E
BJ: 40S ribosomal protein S4
BC: 40S ribosomal protein S5
BG: 40S ribosomal protein S6
BH: 40S ribosomal protein S7E
CG: 60S ribosomal protein L8E
CT: 60S ribosomal protein L21E
CZ: 60S ribosomal protein L27E
Cz: 60S ribosomal protein L1
CA: 60S ribosomal protein L2
CJ: 60S ribosomal protein L5
CH: 60S ribosomal protein L6
CV: 60S ribosomal protein L14
CN: 60S ribosomal protein L15E
Ca: 60S ribosomal protein L15
CQ: 60S ribosomal protein L18E
CD: 60S ribosomal protein L18
CR: 60S ribosomal protein L19E
CP: 60S ribosomal protein L22
CX: 60S ribosomal protein L23
CW: 60S ribosomal protein L24E
CY: 60S ribosomal protein L24
Cr: 60S ribosomal protein L28E
Cc: 60S ribosomal protein L30E
Cd: 60S ribosomal protein L31E
Ce: 60S ribosomal protein L32E
Cj: 60S ribosomal protein L37E
Cl: 60S ribosomal protein L39E
Co: 60S ribosomal protein L44E
CM: 60S ribosomal protein L14E
CS: 60S ribosomal protein L20
CU: 60S ribosomal protein L22E
Ci: 60S ribosomal protein L36E
CK: 60S ribosomal protein L11
Cu: 60S ribosomal protein P1
Cv: 60S ribosomal protein P1
Cs: Acidic ribosomal protein P2
Ct: Acidic ribosomal protein P2
Ch: 60S ribosomal protein L29
CF: 60S ribosomal protein L30
Cq: 60S acidic ribosomal protein P0
CB: 60S ribosomal protein L3
CC: 60S ribosomal protein L4
CO: 60S ribosomal protein L13
Cp: 60S ribosomal protein L43E
CI: 60S ribosomal protein L16
Cn: 60S ribosomal protein L41E
Cm: 60S ribosomal protein L40E
CL: 60S ribosomal protein L13E
CE: 60S ribosomal protein L6E
Cf: 60S ribosomal protein L33E
Ck: 60S ribosomal protein L38E
Cb: 60S ribosomal protein L29E
Cg: 60S ribosomal protein L34E
Aa: 60S ribosomal RNA
Ac: 5.8S ribosomal RNA
Ab: 5S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)3,326,87888
Polyers3,326,87888
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 6 types, 6 molecules AdAeAfAaAcAb

#1: RNA chain18S ribosomal RNA


Mass: 583613.562 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: GenBank: AY049040.1
#2: RNA chainP-site tRNA


Mass: 24135.262 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: GenBank: M25599.1
#3: RNA chain5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'


Mass: 3498.178 Da / Num. of mol.: 1 / Details: messenger RNA / Source: (natural) Triticum aestivum
#84: RNA chain60S ribosomal RNA


Mass: 1097289.250 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#85: RNA chain5.8S ribosomal RNA


Mass: 51535.613 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#86: RNA chain5S ribosomal RNA


Mass: 38716.957 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: GenBank: X06094.1

+
40S ribosomal protein ... , 32 types, 32 molecules BYBIBKBMBfBXBDBEBFBQ...

#4: Polypeptide(L)40S ribosomal protein S24E


Mass: 15788.734 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#5: Polypeptide(L)40S ribosomal protein S8E


Mass: 24883.594 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#6: Polypeptide(L)40S ribosomal protein S10E


Mass: 20292.812 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#7: Polypeptide(L)40S ribosomal protein S12E


Mass: 18404.377 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#8: Polypeptide(L)40S ribosomal protein S31e


Mass: 17720.691 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#9: Polypeptide(L)40S ribosomal protein S12


Mass: 15696.476 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#11: Polypeptide(L)40S ribosomal protein S3


Mass: 23255.113 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q8L804

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)40S ribosomal protein S4E


Mass: 29922.018 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#13: Polypeptide(L)40S ribosomal protein S7


Mass: 21249.539 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#14: Polypeptide(L)40S ribosomal protein S9


Mass: 16852.977 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#15: Polypeptide(L)40S ribosomal protein S10


Mass: 14070.350 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#16: Polypeptide(L)40S ribosomal protein S11


Mass: 16351.802 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#17: Polypeptide(L)40S ribosomal protein S13


Mass: 17702.686 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q8L806

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)40S ribosomal protein S15


Mass: 17152.379 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#19: Polypeptide(L)40S ribosomal protein S17


Mass: 18027.361 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#20: Polypeptide(L)40S ribosomal protein S19E


Mass: 16414.846 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#21: Polypeptide(L)40S ribosomal protein S19


Mass: 17449.520 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#22: Polypeptide(L)40S ribosomal protein S25E


Mass: 11944.909 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#23: Polypeptide(L)40S ribosomal protein S28E


Mass: 7477.787 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q7X9K4

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)40S ribosomal protein S8


Mass: 14825.377 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#25: Polypeptide(L)40S ribosomal protein S14


Mass: 6392.440 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K3

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)40S ribosomal protein S27E


Mass: 9542.145 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#27: Polypeptide(L)40S ribosomal protein S30E


Mass: 6953.253 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#28: Polypeptide(L)40S ribosomal protein S2


Mass: 28723.594 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#29: Polypeptide(L)40S ribosomal protein S17E


Mass: 16461.135 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#30: Polypeptide(L)40S ribosomal protein S1E


Mass: 29781.682 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#31: Polypeptide(L)40S ribosomal protein S21E


Mass: 9266.369 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#32: Polypeptide(L)40S ribosomal protein S26E


Mass: 15029.448 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#33: Polypeptide(L)40S ribosomal protein S4


Mass: 22629.166 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#34: Polypeptide(L)40S ribosomal protein S5


Mass: 28859.619 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#35: Polypeptide(L)40S ribosomal protein S6


Mass: 28106.990 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#36: Polypeptide(L)40S ribosomal protein S7E


Mass: 21902.414 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K2

Cellular component

Molecular function

Biological process

-
Polypeptide(L) , 3 types, 4 molecules BgCsCtCq

#10: Polypeptide(L)RACK1


Mass: 41794.809 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q8LNY6

Cellular component

Biological process

#67: Polypeptide(L)Acidic ribosomal protein P2


Mass: 11596.995 Da / Num. of mol.: 2 / Source: (natural) Triticum aestivum
#70: Polypeptide(L)60S acidic ribosomal protein P0


Mass: 34418.574 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum

+
60S ribosomal protein ... , 45 types, 46 molecules CGCTCZCzCACJCHCVCNCa...

#37: Polypeptide(L)60S ribosomal protein L8E


Mass: 29236.938 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#38: Polypeptide(L)60S ribosomal protein L21E


Mass: 18719.801 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: F4YWL9

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)60S ribosomal protein L27E


Mass: 15508.620 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#40: Polypeptide(L)60S ribosomal protein L1


Mass: 24604.240 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7L3

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein L2


Mass: 28309.662 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#42: Polypeptide(L)60S ribosomal protein L5


Mass: 20727.090 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7L2

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein L6


Mass: 21382.818 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#44: Polypeptide(L)60S ribosomal protein L14


Mass: 15040.856 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K4

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein L15E


Mass: 23760.797 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#46: Polypeptide(L)60S ribosomal protein L15


Mass: 15834.768 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#47: Polypeptide(L)60S ribosomal protein L18E


Mass: 21379.338 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7L0

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)60S ribosomal protein L18


Mass: 34723.168 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#49: Polypeptide(L)60S ribosomal protein L19E


Mass: 24485.947 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q7XY20

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)60S ribosomal protein L22


Mass: 19536.494 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#51: Polypeptide(L)60S ribosomal protein L23


Mass: 17091.447 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#52: Polypeptide(L)60S ribosomal protein L24E


Mass: 18504.867 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#53: Polypeptide(L)60S ribosomal protein L24


Mass: 16971.777 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#54: Polypeptide(L)60S ribosomal protein L28E


Mass: 16639.441 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#55: Polypeptide(L)60S ribosomal protein L30E


Mass: 12294.396 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K9

Cellular component

#56: Polypeptide(L)60S ribosomal protein L31E


Mass: 14092.330 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#57: Polypeptide(L)60S ribosomal protein L32E


Mass: 15740.655 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#58: Polypeptide(L)60S ribosomal protein L37E


Mass: 10823.657 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#59: Polypeptide(L)60S ribosomal protein L39E


Mass: 6528.786 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K7

Cellular component

Molecular function

Biological process

#60: Polypeptide(L)60S ribosomal protein L44E


Mass: 12174.439 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#61: Polypeptide(L)60S ribosomal protein L14E


Mass: 15418.365 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#62: Polypeptide(L)60S ribosomal protein L20


Mass: 21444.225 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#63: Polypeptide(L)60S ribosomal protein L22E


Mass: 14443.594 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#64: Polypeptide(L)60S ribosomal protein L36E


Mass: 12563.044 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7L5

Cellular component

Molecular function

Biological process

#65: Polypeptide(L)60S ribosomal protein L11


Mass: 17775.705 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#66: Polypeptide(L)60S ribosomal protein P1


Mass: 11204.584 Da / Num. of mol.: 2 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K5

Cellular component

Molecular function

Biological process

#68: Polypeptide(L)60S ribosomal protein L29


Mass: 14401.041 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q8L805

Cellular component

Molecular function

Biological process

#69: Polypeptide(L)60S ribosomal protein L30


Mass: 28175.119 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K6

Cellular component

#71: Polypeptide(L)60S ribosomal protein L3


Mass: 44720.387 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q7X744

Cellular component

Molecular function

Biological process

#72: Polypeptide(L)60S ribosomal protein L4


Mass: 44822.043 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#73: Polypeptide(L)60S ribosomal protein L13


Mass: 23581.172 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7L1

Cellular component

Molecular function

Biological process

#74: Polypeptide(L)60S ribosomal protein L43E


Mass: 10266.146 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: D8L9P6

Cellular component

Molecular function

Biological process

#75: Polypeptide(L)60S ribosomal protein L16


Mass: 25400.791 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#76: Polypeptide(L)60S ribosomal protein L41E


Mass: 3445.437 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#77: Polypeptide(L)60S ribosomal protein L40E


Mass: 6295.639 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#78: Polypeptide(L)60S ribosomal protein L13E


Mass: 24070.221 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#79: Polypeptide(L)60S ribosomal protein L6E


Mass: 24589.756 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7L4

Cellular component

Molecular function

Biological process

#80: Polypeptide(L)60S ribosomal protein L33E


Mass: 12684.730 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#81: Polypeptide(L)60S ribosomal protein L38E


Mass: 8053.604 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#82: Polypeptide(L)60S ribosomal protein L29E


Mass: 7069.020 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum
#83: Polypeptide(L)60S ribosomal protein L34E


Mass: 13808.402 Da / Num. of mol.: 1 / Source: (natural) Triticum aestivum / References: UniProt: Q5I7K8

Cellular component

Molecular function

Biological process

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent ID
1Programmed Wheat Germ 80S RibosomeRIBOSOME0
2Tritcum aestivum 80S ribosomeRIBOSOME1
Molecular weightValue: 4.2 deg. / Units: MEGADALTONS / Experimental value: YES
Buffer solutionName: 20 mM HEPES/KOH, pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.01 mg/mL cycloheximide, 1 mM DTT, 0.01% Nikkol
Details: 20 mM HEPES/KOH, pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.01 mg/mL cycloheximide, 1 mM DTT, 0.01% Nikkol
pH: 7.5
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil Grid with 2 nm carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 10 seconds (using 2 layers of filter paper) before plunging into liquid ethane (FEI VITROBOT).
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 / Calibrated magnification: 38900 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: FEI Polara Cartridge System
Image recordingElectron dose: 25 e/Å2
Details: Scanned at 5334 dpi on a Heidelberg Primescan Drum Scanner
Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 1374
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: SPIDER / Category: RECONSTRUCTION
CTF correctionDetails: Wiener Filter on 3D volumes (SPIDER)
SymmetryPoint symmetry: C1
3D reconstructionMethod: Projection Matching / Resolution: 5.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 2108230 / Nominal pixel size: 1.24 / Actual pixel size: 1.24 / Symmetry type: POINT
Number of atoms included #LASTProtein: 0 / Nucleic acid: 39411 / Ligand: 0 / Solvent: 0 / Total: 39411

+
About Yorodumi

-
News

-
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

-
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

+
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)

+
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)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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

Read more