[English] 日本語
Yorodumi
- PDB-4v6m: Structure of the ribosome-SecYE complex in the membrane environment -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4v6m
TitleStructure of the ribosome-SecYE complex in the membrane environment
DescriptorPROTEIN/RNA Complex
KeywordsRIBOSOME/RIBOSOMAL PROTEIN / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / TRANSLATION / ZINC-FINGER / 70S RIBOSOME / RIBOSOME / TRANSLOCON / SECYEG / NANODISC / RIBOSOME-RIBOSOMAL PROTEIN complex
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Escherichia coli dh1 / bacteria / FtsQ nascent chain / image: Escherichia coli
Escherichia coli o157:h7 / bacteria / image: Escherichia coli
Escherichia coli k-12 / bacteria / image: Escherichia coli
Escherichia coli 536 / bacteria / image: Escherichia coli
Homo sapiens / human
MethodElectron microscopy (7.1 Å resolution / Particle / Single particle)
AuthorsFrauenfeld, J. / Gumbart, J. / van der Sluis, E.O. / Funes, S. / Gartmann, M. / Beatrix, B. / Mielke, T. / Berninghausen, O. / Becker, T. / Schulten, K. / Beckmann, R.
CitationNat. Struct. Mol. Biol., 2011, 18, 614-621

Nat. Struct. Mol. Biol., 2011, 18, 614-621 Yorodumi Papers
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
Jens Frauenfeld / James Gumbart / Eli O van der Sluis / Soledad Funes / Marco Gartmann / Birgitta Beatrix / Thorsten Mielke / Otto Berninghausen / Thomas Becker / Klaus Schulten / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 8, 2011 / Release: Jul 9, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Aug 20, 2014Structure modelDatabase references / Structure summary
1.2Dec 10, 2014Structure modelOther
1.3Apr 1, 2015Structure modelOther

-
Structure visualization

Movie
  • Deposited structure unit
  • 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
AA: 16S RIBOSOMAL RNA
AX: mRNA
AV: FtsQ nascent chain
AZ: Cell division protein FtsQ
A0: Apolipoprotein A-I
A1: Apolipoprotein A-I
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
B7: 5S RIBOSOMAL RNA
B8: 23S RIBOSOMAL RNA
BA: Preprotein translocase secY subunit
BB: Preprotein translocase secE subunit
B5: 50S ribosomal protein L1
B6: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,410,929193
Polyers2,314,24060
Non-polymers96,689133
Water0
#1


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

-
Components

+
RNA chain , 5 types, 5 molecules AAAXAVB7B8

#1: RNA chain16S RIBOSOMAL RNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: J01695
#2: RNA chainmRNA


Mass: 3442.106 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli
#3: RNA chainFtsQ nascent chain


Mass: 24876.777 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli DH1 / References: GenBank: AP012030
#26: RNA chain5S RIBOSOMAL RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli DH1 / References: GenBank: AP012030
#27: RNA chain23S RIBOSOMAL RNA


Mass: 941612.375 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli DH1 / References: GenBank: AP012030

+
Polypeptide(L) , 2 types, 3 molecules AZA0A1

#4: Polypeptide(L)Cell division protein FtsQ / Cell division protein / ingrowth of wall at septum


Mass: 11085.822 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli O157:H7 / References: UniProt: Q8X9Y5

Cellular component

Biological process

#5: Polypeptide(L)Apolipoprotein A-I / Apo-AI / ApoA-I / Apolipoprotein A1 / Apolipoprotein A-I(1-242)


Mass: 23309.361 Da / Num. of mol.: 2 / Source: (synth.) Homo sapiens / References: UniProt: P02647

Cellular component

Molecular function

Biological process

+
30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAK...

#6: Polypeptide(L)30S ribosomal protein S2


Mass: 26650.475 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7V0

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S3


Mass: 25900.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7V3

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7V8

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S5


Mass: 17498.203 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7W1

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)30S ribosomal protein S6 / 30S ribosomal protein S6 / fully modified isoform / 30S ribosomal protein S6 / non-modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P02358

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein S7


Mass: 19923.959 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P02359

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7W7

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S9


Mass: 14755.074 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7X3

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#14: Polypeptide(L)30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7R5

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S11


Mass: 13739.778 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7R9

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#16: Polypeptide(L)30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S13


Mass: 12997.271 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0ADZ4
#18: Polypeptide(L)30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG59

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S15


Mass: 10188.687 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7T3

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG63

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)30S ribosomal protein S18


Mass: 8874.276 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7T7

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)30S ribosomal protein S19


Mass: 10324.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7U3

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7U7

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)30S ribosomal protein S21


Mass: 8392.844 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P68679

Cellular component

Molecular function

Biological process

+
Preprotein translocase ... , 2 types, 2 molecules BABB

#28: Polypeptide(L)Preprotein translocase secY subunit


Mass: 47669.277 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli 536 / References: UniProt: Q0TCG1
#29: Polypeptide(L)Preprotein translocase secE subunit / Inner membrane preprotein translocase


Mass: 12623.296 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli 536 / References: UniProt: Q0TA84

+
50S ribosomal protein ... , 30 types, 30 molecules B5B6BDBEBFBGBHBIBJBK...

#30: Polypeptide(L)50S ribosomal protein L1


Mass: 24765.660 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7L0

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L2


Mass: 29792.424 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P60422

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P60438

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P60723

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S ribosomal protein L5


Mass: 20202.416 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P62399

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S ribosomal protein L6


Mass: 18801.598 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG55

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7R1

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)50S ribosomal protein L11


Mass: 14763.165 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AA10

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0ADY3

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P02413

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0ADY7

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG44

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0C018

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7K6

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7L3

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG48

Cellular component

Molecular function

Biological process

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


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P61175

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0ADZ0

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)50S ribosomal protein L24


Mass: 11208.054 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P60624

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P68919

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)50S ribosomal protein L27


Mass: 9015.344 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7L8

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7M2

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7M6

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)50S ribosomal protein L30


Mass: 6423.625 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG51

Cellular component

Molecular function

Biological process

#55: Polypeptide(L)50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7N4

Cellular component

Molecular function

Biological process

#56: Polypeptide(L)50S ribosomal protein L33


Mass: 6257.436 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7N9

Cellular component

Molecular function

Biological process

#57: Polypeptide(L)50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7P5

Cellular component

Molecular function

Biological process

#58: Polypeptide(L)50S ribosomal protein L35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7Q1

Cellular component

Molecular function

Biological process

#59: Polypeptide(L)50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7Q6

Cellular component

Molecular function

Biological process

+
Non-polymers , 2 types, 133 molecules

#60: Chemical...
ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / POPE (phospholipid) *YM


Mass: 720.012 Da / Num. of mol.: 101 / Formula: C39H78NO8P
#61: Chemical...
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / phospholipid *YM


Mass: 749.007 Da / Num. of mol.: 32 / Formula: C40H77O10P

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: An active E. coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E. coli ribosome
Type: RIBOSOME
Details: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc)
Buffer solutionName: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
Details: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
pH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: liquid ethane was used as a cryogen

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 / Calibrated magnification: 38000 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm
Image recordingElectron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1MDFFMODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: DEFOCUS GROUP VOLUMES
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.1 Å / Number of particles: 85664 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--flexible fitting / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Number of atoms included #LASTProtein: 24247 / Nucleic acid: 34960 / Ligand: 6581 / Solvent: 0 / Total: 65788

+
About Yorodumi

-
News

-
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

-
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)

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