[English] 日本語
Yorodumi
- EMDB-4981: 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4981
Title3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules
Map data
Sample
  • Complex: Spinach Cytochrome b6f complex with native bound plastoquinone and thylakoid lipids
    • Protein or peptide: x 8 types
  • Ligand: x 10 types
Function / homology
Function and homology information


plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / mitochondrial respiratory chain complex III / photosynthetic electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane ...plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / mitochondrial respiratory chain complex III / photosynthetic electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily ...Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rudiment single hybrid motif / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome b6-f complex iron-sulfur subunit, chloroplastic / Cytochrome f / Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 6
Similarity search - Component
Biological speciesSpinacia oleracea (spinach) / Spinach (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsMalone LA / Qian P / Mayneord GE / Hitchcock A / Farmer D / Thompson R / Swainsbury DJK / Ranson N / Hunter CN / Johnson MP
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000265/1 United Kingdom
Leverhulme TrustRPG-2016-161 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P002005/1 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structure of the spinach cytochrome bf complex at 3.6 Å resolution.
Authors: Lorna A Malone / Pu Qian / Guy E Mayneord / Andrew Hitchcock / David A Farmer / Rebecca F Thompson / David J K Swainsbury / Neil A Ranson / C Neil Hunter / Matthew P Johnson /
Abstract: The cytochrome b f (cytb f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane ...The cytochrome b f (cytb f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane proton gradient for ATP synthesis. Electron transfer within cytb f occurs via the quinol (Q) cycle, which catalyses the oxidation of plastoquinol (PQH) and the reduction of both plastocyanin (PC) and plastoquinone (PQ) at two separate sites via electron bifurcation. In higher plants, cytb f also acts as a redox-sensing hub, pivotal to the regulation of light harvesting and cyclic electron transfer that protect against metabolic and environmental stresses. Here we present a 3.6 Å resolution cryo-electron microscopy (cryo-EM) structure of the dimeric cytb f complex from spinach, which reveals the structural basis for operation of the Q cycle and its redox-sensing function. The complex contains up to three natively bound PQ molecules. The first, PQ1, is located in one cytb f monomer near the PQ oxidation site (Q) adjacent to haem b and chlorophyll a. Two conformations of the chlorophyll a phytyl tail were resolved, one that prevents access to the Q site and another that permits it, supporting a gating function for the chlorophyll a involved in redox sensing. PQ2 straddles the intermonomer cavity, partially obstructing the PQ reduction site (Q) on the PQ1 side and committing the electron transfer network to turnover at the occupied Q site in the neighbouring monomer. A conformational switch involving the haem c propionate promotes two-electron, two-proton reduction at the Q site and avoids formation of the reactive intermediate semiquinone. The location of a tentatively assigned third PQ molecule is consistent with a transition between the Q and Q sites in opposite monomers during the Q cycle. The spinach cytb f structure therefore provides new insights into how the complex fulfils its catalytic and regulatory roles in photosynthesis.
History
DepositionMay 15, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseNov 13, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rqf
  • Surface level: 0.0144
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4981.png

Downloads & links

-
Map

FileDownload / File: emd_4981.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.0144 / Movie #1: 0.02
Minimum - Maximum-0.06678099 - 0.114864625
Average (Standard dev.)0.00013588773 (±0.0032125697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 330.15002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z310310310
origin x/y/z0.0000.0000.000
length x/y/z330.150330.150330.150
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS310310310
D min/max/mean-0.0670.1150.000

-
Supplemental data

-
Mask #1

Fileemd_4981_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_4981_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_4981_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Spinach Cytochrome b6f complex with native bound plastoquinone an...

EntireName: Spinach Cytochrome b6f complex with native bound plastoquinone and thylakoid lipids
Components
  • Complex: Spinach Cytochrome b6f complex with native bound plastoquinone and thylakoid lipids
    • Protein or peptide: Cytochrome b6Cytochrome b
    • Protein or peptide: Cytochrome b6-f complex subunit 4
    • Protein or peptide: Cytochrome f
    • Protein or peptide: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
    • Protein or peptide: Cytochrome b6-f complex subunit 6
    • Protein or peptide: Cytochrome b6-f complex subunit 7
    • Protein or peptide: Cytochrome b6-f complex subunit 5
    • Protein or peptide: Cytochrome b6-f complex subunit 8
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Supramolecule #1: Spinach Cytochrome b6f complex with native bound plastoquinone an...

SupramoleculeName: Spinach Cytochrome b6f complex with native bound plastoquinone and thylakoid lipids
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Spinacia oleracea (spinach)

+
Macromolecule #1: Cytochrome b6

MacromoleculeName: Cytochrome b6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 24.186504 KDa
SequenceString: MSKVYDWFEE RLEIQAIADD ITSKYVPPHV NIFYCLGGIT LTCFLVQVAT GFAMTFYYRP TVTDAFASVQ YIMTEVNFGW LIRSVHRWS ASMMVLMMIL HVFRVYLTGG FKKPRELTWV TGVVLGVLTA SFGVTGYSLP WDQIGYWAVK IVTGVPDAIP V IGSPLVEL ...String:
MSKVYDWFEE RLEIQAIADD ITSKYVPPHV NIFYCLGGIT LTCFLVQVAT GFAMTFYYRP TVTDAFASVQ YIMTEVNFGW LIRSVHRWS ASMMVLMMIL HVFRVYLTGG FKKPRELTWV TGVVLGVLTA SFGVTGYSLP WDQIGYWAVK IVTGVPDAIP V IGSPLVEL LRGSASVGQS TLTRFYSLHT FVLPLLTAVF MLMHFLMIRK QGISGPL

+
Macromolecule #2: Cytochrome b6-f complex subunit 4

MacromoleculeName: Cytochrome b6-f complex subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 17.456662 KDa
SequenceString:
MGVTKKPDLN DPVLRAKLAK GMGHNYYGEP AWPNDLLYIF PVVILGTIAC NVGLAVLEPS MIGEPADPFA TPLEILPEWY FFPVFQILR TVPNKLLGVL LMASVPAGLL TVPFLENVNK FQNPFRRPVA TTVFLVGTVV ALWLGIGATL PIDKSLTLGL F

+
Macromolecule #3: Cytochrome f

MacromoleculeName: Cytochrome f / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 31.35702 KDa
SequenceString: YPIFAQQGYE NPREATGRIV CANCHLANKP VDIEVPQAVL PDTVFEAVVR IPYDMQLKQV LANGKKGGLN VGAVLILPEG FELAPPDRI SPEMKEKMGN LSFQSYRPNK QNILVIGPVP GQKYSEITFP ILAPDPATKK DVHFLKYPIY VGGNRGRGQI Y PDGSKSNN ...String:
YPIFAQQGYE NPREATGRIV CANCHLANKP VDIEVPQAVL PDTVFEAVVR IPYDMQLKQV LANGKKGGLN VGAVLILPEG FELAPPDRI SPEMKEKMGN LSFQSYRPNK QNILVIGPVP GQKYSEITFP ILAPDPATKK DVHFLKYPIY VGGNRGRGQI Y PDGSKSNN TVYNSTATGI VKKIVRKEKG GYEINIADAS DGREVVDIIP RGPELLVSEG ESIKLDQPLT SNPNVGGFGQ GD AEVVLQD PLRIQGLLFF FASVILAQIF LVLKKKQFEK VQLSEMNF

+
Macromolecule #4: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

MacromoleculeName: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: plastoquinol-plastocyanin reductase
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 18.95648 KDa
SequenceString:
ATSIPADNVP DMQKRETLNL LLLGALSLPT GYMLLPYASF FVPPGGGAGT GGTIAKDALG NDVIAAEWLK THAPGDRTLT QGLKGDPTY LVVESDKTLA TFGINAVCTH LGCVVPFNAA ENKFICPCHG SQYNNQGRVV RGPAPLSLAL AHCDVDDGKV V FVPWTETD FRTGEAPWWS A

+
Macromolecule #5: Cytochrome b6-f complex subunit 6

MacromoleculeName: Cytochrome b6-f complex subunit 6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 3.4522 KDa
SequenceString:
MFTLTSYFGF LLAALTITSA LFIGLNKIRL I

+
Macromolecule #6: Cytochrome b6-f complex subunit 7

MacromoleculeName: Cytochrome b6-f complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 3.774431 KDa
SequenceString:
NAAAEIFRIA AVMNGLTLVG VAIGFVLLRI EATVEE

+
Macromolecule #7: Cytochrome b6-f complex subunit 5

MacromoleculeName: Cytochrome b6-f complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 4.171985 KDa
SequenceString:
MIEVFLFGIV LGLIPITLAG LFVTAYLQYR RGDQLDL

+
Macromolecule #8: Cytochrome b6-f complex subunit 8

MacromoleculeName: Cytochrome b6-f complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinach (spinach)
Molecular weightTheoretical: 3.170809 KDa
SequenceString:
MDIVSLAWAA LMVVFTFSLS LVVWGRSGL

+
Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 9 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
Macromolecule #10: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 10 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

+
Macromolecule #11: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 2 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #12: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 12 / Number of copies: 2 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #13: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
type: ligand / ID: 13 / Number of copies: 3 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / Plastoquinone

+
Macromolecule #14: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...

MacromoleculeName: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 14 / Number of copies: 3 / Formula: 6PL
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-6PL:
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

+
Macromolecule #15: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 15 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+
Macromolecule #16: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 16 / Number of copies: 4 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #17: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 17 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

+
Macromolecule #18: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 18 / Number of copies: 3 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.15 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 422660
CTF correctionSoftware - Name: RELION (ver. 2.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 108560
FSC plot (resolution estimation)

+
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