[English] 日本語
Yorodumi
- EMDB-4270: Chloroplast F1Fo conformation 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4270
TitleChloroplast F1Fo conformation 1
Map datachloroplast F1Fo conformation 1
Sample
  • Complex: Chloroplast ATP synthase
    • Protein or peptide: x 9 types
  • Ligand: x 4 types
KeywordsATP synthase / membrane protein complex / molecular motor / MEMBRANE PROTEIN
Function / homology
Function and homology information


photosynthetic electron transport in photosystem I / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism ...photosynthetic electron transport in photosystem I / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b' / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. ...ATP synthase, F0 complex, subunit b' / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase subunit a, chloroplastic / ATP synthase subunit b, chloroplastic / ATP synthase delta chain, chloroplastic / ATP synthase subunit b', chloroplastic / ATP synthase subunit c, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsHahn A / Vonck J
CitationJournal: Science / Year: 2018
Title: Structure, mechanism, and regulation of the chloroplast ATP synthase.
Authors: Alexander Hahn / Janet Vonck / Deryck J Mills / Thomas Meier / Werner Kühlbrandt /
Abstract: The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through ...The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded F motor drive ATP synthesis in the F head by rotary catalysis. We determined the high-resolution structure of the complete cFF complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark.
History
DepositionJan 24, 2018-
Header (metadata) releaseFeb 28, 2018-
Map releaseMay 23, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6fkf
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4270.png

Downloads & links

-
Map

FileDownload / File: emd_4270.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationchloroplast F1Fo conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 350 pix.
= 368.55 Å		1.05 Å/pix.
x 350 pix.
= 368.55 Å		1.05 Å/pix.
x 350 pix.
= 368.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.51132554 - 0.9187655
Average (Standard dev.)-0.000010129011 (±0.022592995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 368.55 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z368.550368.550368.550
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.5110.919-0.000

-
Supplemental data

-
Mask #1

Fileemd_4270_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_4270_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_4270_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Chloroplast ATP synthase

EntireName: Chloroplast ATP synthase
Components
  • Complex: Chloroplast ATP synthase
    • Protein or peptide: ATP synthase subunit alpha, chloroplastic
    • Protein or peptide: ATP synthase subunit beta, chloroplastic
    • Protein or peptide: ATP synthase delta chain, chloroplastic
    • Protein or peptide: ATP synthase epsilon chain, chloroplastic
    • Protein or peptide: ATP synthase gamma chain, chloroplastic
    • Protein or peptide: ATP synthase subunit a, chloroplastic
    • Protein or peptide: ATP synthase subunit b', chloroplastic
    • Protein or peptide: ATP synthase subunit b, chloroplastic
    • Protein or peptide: ATP synthase subunit c, chloroplastic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

+
Supramolecule #1: Chloroplast ATP synthase

SupramoleculeName: Chloroplast ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #9, #3, #7, #5-#6, #8
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 600 KDa

+
Macromolecule #1: ATP synthase subunit alpha, chloroplastic

MacromoleculeName: ATP synthase subunit alpha, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 55.505199 KDa
SequenceString: MATIRADEIS KIIRERIEGY NREVKVVNTG TVLQVGDGIA RIHGLDEVMA GELVEFEEGT IGIALNLESN NVGVVLMGDG LMIQEGSSV KATGRIAQIP VSEAYLGRVI NALAKPIDGR GEITASESRL IESPAPGIMS RRSVYEPLQT GLIAIDAMIP V GRGQRELI ...String:
MATIRADEIS KIIRERIEGY NREVKVVNTG TVLQVGDGIA RIHGLDEVMA GELVEFEEGT IGIALNLESN NVGVVLMGDG LMIQEGSSV KATGRIAQIP VSEAYLGRVI NALAKPIDGR GEITASESRL IESPAPGIMS RRSVYEPLQT GLIAIDAMIP V GRGQRELI IGDRQTGKTA VATDTILNQQ GQNVICVYVA IGQKASSVAQ VVTNFQERGA MEYTIVVAET ADSPATLQYL AP YTGAALA EYFMYRERHT LIIYDDLSKQ AQAYRQMSLL LRRPPGREAY PGDVFYLHSR LLERAAKLSS LLGEGSMTAL PIV ETQAGD VSAYIPTNVI SITDGQIFLS ADLFNAGIRP AINVGISVSR VGSAAQIKAM KKVAGKLKLE LAQFAELEAF AQFA SDLDK ATQNQLARGQ RLRELLKQPQ SAPLTVEEQV MTIYTGTNGY LDSLELDQVR KYLVELRTYV KTNKPEFQEI ISSTK TFTE EAEALLKEAI QEQMERFLLQ EQA

UniProtKB: ATP synthase subunit alpha, chloroplastic

+
Macromolecule #2: ATP synthase subunit beta, chloroplastic

MacromoleculeName: ATP synthase subunit beta, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 53.797367 KDa
SequenceString: MRINPTTSDP GVSTLEKKNL GRIAQIIGPV LDVAFPPGKM PNIYNALIVK GRDTAGQPMN VTCEVQQLLG NNRVRAVAMS ATDGLTRGM EVIDTGAPLS VPVGGATLGR IFNVLGEPVD NLGPVDTRTT SPIHRSAPAF TQLDTKLSIF ETGIKVVDLL A PYRRGGKI ...String:
MRINPTTSDP GVSTLEKKNL GRIAQIIGPV LDVAFPPGKM PNIYNALIVK GRDTAGQPMN VTCEVQQLLG NNRVRAVAMS ATDGLTRGM EVIDTGAPLS VPVGGATLGR IFNVLGEPVD NLGPVDTRTT SPIHRSAPAF TQLDTKLSIF ETGIKVVDLL A PYRRGGKI GLFGGAGVGK TVLIMELINN IAKAHGGVSV FGGVGERTRE GNDLYMEMKE SGVINEQNIA ESKVALVYGQ MN EPPGARM RVGLTALTMA EYFRDVNEQD VLLFIDNIFR FVQAGSEVSA LLGRMPSAVG YQPTLSTEMG SLQERITSTK EGS ITSIQA VYVPADDLTD PAPATTFAHL DATTVLSRGL AAKGIYPAVD PLDSTSTMLQ PRIVGEEHYE IAQRVKETLQ RYKE LQDII AILGLDELSE EDRLTVARAR KIERFLSQPF FVAEVFTGSP GKYVGLAETI RGFQLILSGE LDSLPEQAFY LVGNI DEAT AKAMNLEMES KLKK

UniProtKB: ATP synthase subunit beta, chloroplastic

+
Macromolecule #3: ATP synthase gamma chain, chloroplastic

MacromoleculeName: ATP synthase gamma chain, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 40.119066 KDa
SequenceString: MACSLSFSSS VSTFHLPTTT QSTQAPPNNA TTLPTTNPIQ CANLRELRDR IGSVKNTQKI TEAMKLVAAA KVRRAQEAVV NGRPFSETL VEVLYNMNEQ LQTEDVDVPL TKIRTVKKVA LMVVTGDRGL CGGFNNMLLK KAESRIAELK KLGVDYTIIS I GKKGNTYF ...String:
MACSLSFSSS VSTFHLPTTT QSTQAPPNNA TTLPTTNPIQ CANLRELRDR IGSVKNTQKI TEAMKLVAAA KVRRAQEAVV NGRPFSETL VEVLYNMNEQ LQTEDVDVPL TKIRTVKKVA LMVVTGDRGL CGGFNNMLLK KAESRIAELK KLGVDYTIIS I GKKGNTYF IRRPEIPVDR YFDGTNLPTA KEAQAIADDV FSLFVSEEVD KVEMLYTKFV SLVKSDPVIH TLLPLSPKGE IC DINGKCV DAAEDELFRL TTKEGKLTVE RDMIKTETPA FSPILEFEQD PAQILDALLP LYLNSQILRA LQESLASELA ARM TAMSNA TDNANELKKT LSINYNRARQ AKITGEILEI VAGANACV

UniProtKB: ATP synthase gamma chain, chloroplastic

+
Macromolecule #4: ATP synthase delta chain, chloroplastic

MacromoleculeName: ATP synthase delta chain, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.708582 KDa
SequenceString: MAALQNPVAL QSRTTTAVAA LSTSSTTSTP KPFSLSFSSS TATFNPLRLK ILTASKLTAK PRGGALGTRM VDSTASRYAS ALADVADVT GTLEATNSDV EKLIRIFSEE PVYYFFANPV ISIDNKRSVL DEIITTSGLQ PHTANFINIL IDSERINLVK E ILNEFEDV ...String:
MAALQNPVAL QSRTTTAVAA LSTSSTTSTP KPFSLSFSSS TATFNPLRLK ILTASKLTAK PRGGALGTRM VDSTASRYAS ALADVADVT GTLEATNSDV EKLIRIFSEE PVYYFFANPV ISIDNKRSVL DEIITTSGLQ PHTANFINIL IDSERINLVK E ILNEFEDV FNKITGTEVA VVTSVVKLEN DHLAQIAKGV QKITGAKNVR IKTVIDPSLV AGFTIRYGNE GSKLVDMSVK KQ LEEIAAQ LEMDDVTLAV

UniProtKB: ATP synthase delta chain, chloroplastic

+
Macromolecule #5: ATP synthase subunit b', chloroplastic

MacromoleculeName: ATP synthase subunit b', chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.487596 KDa
SequenceString: MANMLVASSS KTLPTTTTTT ITPKPKFPLL KTPLLKLSPP QLPPLKHLNL SVLKSAAITA TPLTLSFLLP YPSLAEEIEK ASLFDFNLT LPIIMAEFLF LMFALDKIYY TPLGDFMDKR DASIKEQLSG VKDTSSEVKQ LEEQANAVMR AARAEISAAL N KMKKETQL ...String:
MANMLVASSS KTLPTTTTTT ITPKPKFPLL KTPLLKLSPP QLPPLKHLNL SVLKSAAITA TPLTLSFLLP YPSLAEEIEK ASLFDFNLT LPIIMAEFLF LMFALDKIYY TPLGDFMDKR DASIKEQLSG VKDTSSEVKQ LEEQANAVMR AARAEISAAL N KMKKETQL EVEAKLAEGR KKIEVELQEA LGSLEQQKED TIKSLDSQIS ALSDDIVKKV LPVS

UniProtKB: ATP synthase subunit b', chloroplastic

+
Macromolecule #6: ATP synthase subunit b, chloroplastic

MacromoleculeName: ATP synthase subunit b, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 21.013904 KDa
SequenceString:
MKNVTDSFVF LGHWPSAGSF GFNTDILATN LINLSVVLGV LIFFGKGVLS DLLDNRKQRI LNTIRNSEEL RGKAIEQLEK ARARLKKVE MDADQFRVNG YSEIEREKMN LINSTYKTLE QFENYKNETI QFEQQKAINQ VRQRVFQQAL QGALGTLNSC L NNELHLRT INANIGMFGA MNEITD

UniProtKB: ATP synthase subunit b, chloroplastic

+
Macromolecule #7: ATP synthase subunit a, chloroplastic

MacromoleculeName: ATP synthase subunit a, chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.10268 KDa
SequenceString: MNVLSYSINP LKGLYAISGV EVGQHFYWQI GGFQIHGQVL ITSWVVIAIL LGSAAIAVRS PQTIPTGGQN FFEYVLEFIR DVSKTQIGE EYRPWVPFIG TMFLFIFVSN WSGALLPWKI IQLPHGELAA PTNDINTTVA LALLTSVAYF YAGLTKKGLG Y FGKYIQPT ...String:
MNVLSYSINP LKGLYAISGV EVGQHFYWQI GGFQIHGQVL ITSWVVIAIL LGSAAIAVRS PQTIPTGGQN FFEYVLEFIR DVSKTQIGE EYRPWVPFIG TMFLFIFVSN WSGALLPWKI IQLPHGELAA PTNDINTTVA LALLTSVAYF YAGLTKKGLG Y FGKYIQPT PILLPINILE DFTKPLSLSF RLFGNILADE LVVVVLVSLV PLVVPIPVMF LGLFTSGIQA LIFATLAAAY IG ESLEGHH

UniProtKB: ATP synthase subunit a, chloroplastic

+
Macromolecule #8: ATP synthase subunit c, chloroplastic

MacromoleculeName: ATP synthase subunit c, chloroplastic / type: protein_or_peptide / ID: 8 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 7.977366 KDa
SequenceString:
MNPLIAAASV IAAGLAVGLA SIGPGVGQGT AAGQAVEGIA RQPEAEGKIR GTLLLSLAFM EALTIYGLVV ALALLFANPF V

UniProtKB: ATP synthase subunit c, chloroplastic

+
Macromolecule #9: ATP synthase epsilon chain, chloroplastic

MacromoleculeName: ATP synthase epsilon chain, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.715707 KDa
SequenceString:
MTLNLCVLTP NRSIWNSEVK EIILSTNSGQ IGVLPNHAPT ATAVDIGILR IRLNDQWLTL ALMGGFARIG NNEITILVND AERGSDIDP QEAQQTLEIA EANLRKAEGK RQKIEANLAL RRARTRVEAS NTISS

UniProtKB: ATP synthase epsilon chain, chloroplastic

+
Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 25 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationNameFormula
30.0 mMHEPES
2.0 mMMgCl2
0.5 mMEDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 6254 / Average exposure time: 62.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 132953 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 670614
Startup modelType of model: OTHER
Details: unpublished ab initio reconstruction from data from another microscope
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 167171
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 70000 / Software - Name: RELION (ver. 2.1)
Details: three classes with 167,000, 15,000 and 14,000 particles. This is the first one.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Detailsreal space refinement
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6fkf:
Chloroplast F1Fo conformation 1

+
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