[English] 日本語
Yorodumi
- EMDB-73966: Cryo-EM structure of Leishmania tarentolae respiratory complex IV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73966
TitleCryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)
Map data
Sample
  • Complex: Leishmania tarentolae mitochondria Complex IV
    • Protein or peptide: x 17 types
  • Ligand: x 2 types
KeywordsElectron transport chain / respiratory complex / cytochrome c oxidase / mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


aerobic electron transport chain / respiratory chain complex IV / mitochondrial envelope / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / mitochondrial inner membrane / copper ion binding ...aerobic electron transport chain / respiratory chain complex IV / mitochondrial envelope / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / membrane
Similarity search - Function
Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) ...Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cupredoxin
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome c oxidase subunit iv / Cytochrome c oxidase subunit 10 / Cytochrome c oxidase subunit V, putative / P27 protein / Cytochrome C oxidase subunit VI, putative / Cytochrome c oxidase VIII, putative / Cytochrome c oxidase VII, putative ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome c oxidase subunit iv / Cytochrome c oxidase subunit 10 / Cytochrome c oxidase subunit V, putative / P27 protein / Cytochrome C oxidase subunit VI, putative / Cytochrome c oxidase VIII, putative / Cytochrome c oxidase VII, putative / Uncharacterized protein / Uncharacterized protein / Cytochrome-c oxidase / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsLiao YT / Chao L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2026
Title: Conserved and divergent mitochondrial assemblies in kinetoplastid parasites
Authors: Solayman M / Liao YT / Calvo SE / Vacas AF / Papanastasiou M / Rivera KD / Mani D / Boyle BW / Deng FG / Betsinger CN / Carr SA / Chen MZ / Duraisingh MT / Fry MY / Goyal M / Issa TM / Kim M ...Authors: Solayman M / Liao YT / Calvo SE / Vacas AF / Papanastasiou M / Rivera KD / Mani D / Boyle BW / Deng FG / Betsinger CN / Carr SA / Chen MZ / Duraisingh MT / Fry MY / Goyal M / Issa TM / Kim M / Lian CG / Luce BE / Mian SY / Nguyen K / Paul AS / Samuelson J / Stefely JA / Udeshi ND / Mootha VK / Aphasizheva I / Chao LH / Aphasizhev R
History
DepositionNov 19, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73966.png

Downloads & links

-
Map

FileDownload / File: emd_73966.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 640 pix.
= 471.04 Å		0.74 Å/pix.
x 640 pix.
= 471.04 Å		0.74 Å/pix.
x 640 pix.
= 471.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0728
Minimum - Maximum-0.13428007 - 0.28947794
Average (Standard dev.)0.0004963049 (±0.010952361)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 471.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharp.map

Fileemd_73966_additional_1.map
Annotationsharp.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_73966_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_73966_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Leishmania tarentolae mitochondria Complex IV

EntireName: Leishmania tarentolae mitochondria Complex IV
Components
  • Complex: Leishmania tarentolae mitochondria Complex IV
    • Protein or peptide: Cytochrome c oxidase subunit iv
    • Protein or peptide: Cytochrome-c oxidase
    • Protein or peptide: Hypothetical protein, conserved, LtaP04.0630
    • Protein or peptide: Cytochrome c oxidase subunit V, putative
    • Protein or peptide: Cytochrome c oxidase VII, putative
    • Protein or peptide: Cytochrome c oxidase assembly factor like protein
    • Protein or peptide: Hypothetical protein, conserved, LtaP36.1760
    • Protein or peptide: Cytochrome C oxidase subunit VI, putative
    • Protein or peptide: Cytochrome c oxidase subunit I
    • Protein or peptide: Hypothetical protein, conserved, LtaP09.0030
    • Protein or peptide: Cytochrome c oxidase subunit 10
    • Protein or peptide: P27 protein
    • Protein or peptide: Cytochrome c oxidase VIII, putative
    • Protein or peptide: Hypothetical protein, conserved, LtaP33.2260
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase subunit 2
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A

+
Supramolecule #1: Leishmania tarentolae mitochondria Complex IV

SupramoleculeName: Leishmania tarentolae mitochondria Complex IV / type: complex / ID: 1 / Parent: 0
Macromolecule list: #16, #9, #5, #2, #8, #17, #15, #4, #11, #7, #10, #1, #6, #14, #12-#13, #3
Details: Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, ...Details: Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, followed by centrifuging at 14,000 x g for 10 min. The supernatant was filtered prior to grid preparation.
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)

+
Macromolecule #1: P27 protein

MacromoleculeName: P27 protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 25.912838 KDa
SequenceString: MSRCTTKISG GMARANLVDH GVYVKPMSLN PFLGAVHDGT STGYCQGYSA KPMHWLYRFR YNLLPQGISG GFFSRNPYGR YVHWLEVST IEKLRVQLLS LEAMPVSVLT TIVIIYTLWF SYRLAFLHPD ITLYNLGLWS TKPWVQQQRF NKKIDIDQQV Y RWVHRVPE ...String:
MSRCTTKISG GMARANLVDH GVYVKPMSLN PFLGAVHDGT STGYCQGYSA KPMHWLYRFR YNLLPQGISG GFFSRNPYGR YVHWLEVST IEKLRVQLLS LEAMPVSVLT TIVIIYTLWF SYRLAFLHPD ITLYNLGLWS TKPWVQQQRF NKKIDIDQQV Y RWVHRVPE FAITDPIREM YRLEISANEP YLEHVRDLGR EKELTLYANE RTGGAGNIRP LNIPH

UniProtKB: P27 protein

+
Macromolecule #2: Cytochrome c oxidase subunit V, putative

MacromoleculeName: Cytochrome c oxidase subunit V, putative / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 20.361264 KDa
SequenceString:
FFGKGWDNAA LDTIFSSMLR KPEVNDRIRT QYASTMDPRD ADVLRRLGEV SKENKTFIRV FLPPHLGDPH RLLKCYSLMA YPILDDKGG QLKVEMDGCK LDAFADPDDD YSKVVIPHIE LVEYLAKSLL ETMKWEATPR GAASLLESLY RGAEIPDHVF Q TPAVIERL EDYKDGNKVI S

UniProtKB: Cytochrome c oxidase subunit V, putative

+
Macromolecule #3: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 23.988639 KDa
SequenceString: MAFILSFWMI FLLDSVIVLL SFVCFVCVWI CALLFSTVLL VSKLNNIYCT WDFTASKFID VYWFTIGGMF SLGLLLRLCL LLYFGHLNF VSFDLCKVVG FQWYWVYFIF GETTIFSNLI LESDYMIGDL RLLQCNHVLT LLSLVIYKLW LSAVDVIHSF A ISSLGVKV ...String:
MAFILSFWMI FLLDSVIVLL SFVCFVCVWI CALLFSTVLL VSKLNNIYCT WDFTASKFID VYWFTIGGMF SLGLLLRLCL LLYFGHLNF VSFDLCKVVG FQWYWVYFIF GETTIFSNLI LESDYMIGDL RLLQCNHVLT LLSLVIYKLW LSAVDVIHSF A ISSLGVKV DCIPGRCNEI VLFSSNNATV YGQCSELCGV LHGFMPIVIC FI

UniProtKB: Cytochrome c oxidase subunit 2

+
Macromolecule #4: Cytochrome C oxidase subunit VI, putative

MacromoleculeName: Cytochrome C oxidase subunit VI, putative / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 19.310088 KDa
SequenceString:
MPHEDHRKYK VQREELPRMP HFNDFNDPRF CGTTNKQKNG ILAYYQWLHC IGNWGEEHSM CKKMRWYVER MMHETWLEKW EEKRALGHF DHTILYGVKP WKEFEPLYQP VKKNRKGAYE YWLDRDFEPL YDADAADWRE KAPILHDMFV LGKKPVAE

UniProtKB: Cytochrome C oxidase subunit VI, putative

+
Macromolecule #5: Hypothetical protein, conserved, LtaP04.0630

MacromoleculeName: Hypothetical protein, conserved, LtaP04.0630 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 23.408184 KDa
SequenceString: MTMNFGNMTL GGAMATFGGQ SNPMCNYTSP LAKKFVYKEV GKVHYPLRRH VFRTKVRTAA EIRFNEIVKR YMKEKMTFKR GCYAATITN TVELDHMGSI IPKDEYEVKR LTSYMTSKKM SSDYKKHMQE LWTRVLFVCE STNLVGVTEN AMHQNSRPGT D EEFMSIIW ...String:
MTMNFGNMTL GGAMATFGGQ SNPMCNYTSP LAKKFVYKEV GKVHYPLRRH VFRTKVRTAA EIRFNEIVKR YMKEKMTFKR GCYAATITN TVELDHMGSI IPKDEYEVKR LTSYMTSKKM SSDYKKHMQE LWTRVLFVCE STNLVGVTEN AMHQNSRPGT D EEFMSIIW YSSFVTTLMA FVVTLFIWWY RYGQAPQYAE FK

UniProtKB: Uncharacterized protein

+
Macromolecule #6: Cytochrome c oxidase VIII, putative

MacromoleculeName: Cytochrome c oxidase VIII, putative / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 15.495813 KDa
SequenceString:
MHSSDRFKAA WDEIPLHMLG ASHKQMFEWY WRAMYQLGLR DPYRLTKLRS MLNWAALFSF MYLTYISIFY SSFYHVYMMD WPEHFKREN AREYALSHGH DVWAGDGKFI RPYFHINPPM LTMTSEDI

UniProtKB: Cytochrome c oxidase VIII, putative

+
Macromolecule #7: Hypothetical protein, conserved, LtaP09.0030

MacromoleculeName: Hypothetical protein, conserved, LtaP09.0030 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 12.414288 KDa
SequenceString:
MASCRTGRLP MPDDPLFNST HMHGLRHSSR IAGLGMIAVI WIMYEKLRHS HHYITYKGPE NPFARIRHRR FPGGAFMFGW GNNGLNRDC GIKEFECWAG YTGKEYTY

UniProtKB: Uncharacterized protein

+
Macromolecule #8: Cytochrome c oxidase VII, putative

MacromoleculeName: Cytochrome c oxidase VII, putative / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 19.136926 KDa
SequenceString:
MPRPFGVWAP ATTLAEYRAR IPNPFAYSFK WVYSMKREVF YPPEALAHFK DPQQFKDAVD TVIAMRVSDK IFGEGQKLPR HPVILMLMV LATHGFIIFS GLKYYYGTYM PANNPTWRKT VNKEWEEAIN NSPWDHMSHV WQYSDEYAAA LGDTAAPGQR K FYIPA

UniProtKB: Cytochrome c oxidase VII, putative

+
Macromolecule #9: Cytochrome-c oxidase

MacromoleculeName: Cytochrome-c oxidase / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 23.705305 KDa
SequenceString: GPTPYQDKSY PVQPHNLDEL QQPPDSWRKS PIMSKLMDQS LPVYDDVVTG VGRLYWQEPA RVWHLFEADD TLMLEEHDRE EWNDRPYVA VNHLYEPPIG SEERPIRVEG TGNPGDQQIV LCFGNCAPHV PQSNYYMMMK GYNKTKCPMC QQWFYIHNRP W LVMHPDWT ...String:
GPTPYQDKSY PVQPHNLDEL QQPPDSWRKS PIMSKLMDQS LPVYDDVVTG VGRLYWQEPA RVWHLFEADD TLMLEEHDRE EWNDRPYVA VNHLYEPPIG SEERPIRVEG TGNPGDQQIV LCFGNCAPHV PQSNYYMMMK GYNKTKCPMC QQWFYIHNRP W LVMHPDWT DEPAADEGPA YTFSEIEAEF DRDFHEFGVY LNAE

UniProtKB: Cytochrome-c oxidase

+
Macromolecule #10: Cytochrome c oxidase subunit 10

MacromoleculeName: Cytochrome c oxidase subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 11.616062 KDa
SequenceString:
HFPLSPPPIE IDYLDSDPLE FAVRTEARRW GFDDLQYMRE LAFVRIKENP SIGDFRRMTP EERRDLFWGS DRQDFFRYIT LKLTGHPEH LYHRGW

UniProtKB: Cytochrome c oxidase subunit 10

+
Macromolecule #11: Cytochrome c oxidase subunit I

MacromoleculeName: Cytochrome c oxidase subunit I / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 12.034609 KDa
SequenceString:
YMLAFNSKAK ARPNFGLRGV GYWTSEVYHK PGQNYWMVVC CAGPFLLVGA IMMDGFWSKL DDIAGGGPSA LDYGWRSQDR KPWDFSFDI GEGYAAGPAV YRPASGAVDL G

UniProtKB: Cytochrome c oxidase subunit I

+
Macromolecule #12: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 63.297883 KDa
SequenceString: MFWLCLVCLS VSHKMIGLCY LLVAILSGFV GYVYSLFIRL ELSLIGCGIL FGDYQFYNVL ITSHGLIMVF AFIMPVMMGG LVNYFIPVM AGFPDMVFPR LNNMSFWMYL AGFGCVVNGF LTEEGMGVGW TLYPTLICID FHSSLACDFV MFAVHLLGIS S ILNSINLL ...String:
MFWLCLVCLS VSHKMIGLCY LLVAILSGFV GYVYSLFIRL ELSLIGCGIL FGDYQFYNVL ITSHGLIMVF AFIMPVMMGG LVNYFIPVM AGFPDMVFPR LNNMSFWMYL AGFGCVVNGF LTEEGMGVGW TLYPTLICID FHSSLACDFV MFAVHLLGIS S ILNSINLL GTLFCCRRKF FSFLSWSLFI WAALITAILL IITLPVLAGG VTLILCDRNF NTSFYDVVGG GDLILFQHIF WF FGHPEVY IILLPVFGLI STIVEVIGFR CVFSTVAMIY SMILIAILGM FVWAHHMFVV GMDVDSRAYF GGVSILIGLP TCV KLFNWI YSFLYTDMII TFEVYFVIMF IFMFLIGAVT GLFLSNVGID IMLHDTYFVV GHFHYVLSLG AVVGFFTGFI HFLA KWLPI ELYLFWMFYF ISTLFIGSNM LFFPMHSLGM YAFPRRISDY PVSFLFWSSF MLYGMLLLAS LILFLCALFC VFLFW DYCL FFVSLFVFSL YCFFYFSTWL PCVMVLYLLL VDFAHIVLDY LFLILCFCFV FFIFFWQSLF LFFYI

UniProtKB: Cytochrome c oxidase subunit 1

+
Macromolecule #13: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 34.184578 KDa
SequenceString: MFVRVIFVGV SGVFVFLSLP AICIVYLTFC LCGLFCIMFG SFIFIDYCFI CFFACLLFCL VCLLCDLFVD SLRGLFDVCC FIRCIQYCF VWFIISELLL FLSLFYVVFS LVLFVSVEFA FVFVIPVMFS CLICDFGFVF YWYFIDIFNL LINTFLLFVS G LFVNFVLF ...String:
MFVRVIFVGV SGVFVFLSLP AICIVYLTFC LCGLFCIMFG SFIFIDYCFI CFFACLLFCL VCLLCDLFVD SLRGLFDVCC FIRCIQYCF VWFIISELLL FLSLFYVVFS LVLFVSVEFA FVFVIPVMFS CLICDFGFVF YWYFIDIFNL LINTFLLFVS G LFVNFVLF LFWFRFFLCV LFMLWVGILF GFLFLWNQVW EFALLFVTCS CGVFGSILFL IDLLHFSHVF LGIFLLFLCF SR CFNFLCM DTRFVFLYVV CLYWHFVDCV WFFLLRFVYF DVLSVVYLYA

UniProtKB: Cytochrome c oxidase subunit 3

+
Macromolecule #14: Hypothetical protein, conserved, LtaP33.2260

MacromoleculeName: Hypothetical protein, conserved, LtaP33.2260 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 10.566061 KDa
SequenceString:
FYANCGETGI SGATMQVLLK LTLACCVVQV FAIRYFVFQR LTTKKQFVED STDLWESDGT EMDGEEAVAN LRIQHERIMP FMNDIKDKL DAQA

UniProtKB: Uncharacterized protein

+
Macromolecule #15: Hypothetical protein, conserved, LtaP36.1760

MacromoleculeName: Hypothetical protein, conserved, LtaP36.1760 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 9.70411 KDa
SequenceString:
SYTELSHMKF PVYYGAVGVV LGYFVVMWVV FLRMGSKHTA RSEFKNDYLR VWRRRLGTGY EWADAWGPEM GTFFKDLPEE VE

UniProtKB: Uncharacterized protein

+
Macromolecule #16: Cytochrome c oxidase subunit iv

MacromoleculeName: Cytochrome c oxidase subunit iv / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 35.969211 KDa
SequenceString: HDRWYGHALE LDTHNYKFNG EPPSWMKTHA KTEEETSFAK SVLPHIDFAS SYECLLFDAD RLNTNLNRKE FGNEIKYRLE KQANTVARA QQLLKDKKAG TGPDAAKIEN TLIARIFDEE HVQAEMKYVK CIRANELAED NRLDILPGGS PNSLREKTRW N LNTELHPA ...String:
HDRWYGHALE LDTHNYKFNG EPPSWMKTHA KTEEETSFAK SVLPHIDFAS SYECLLFDAD RLNTNLNRKE FGNEIKYRLE KQANTVARA QQLLKDKKAG TGPDAAKIEN TLIARIFDEE HVQAEMKYVK CIRANELAED NRLDILPGGS PNSLREKTRW N LNTELHPA DRAEIGARLT AWLPEKYHIV YFDDFQTVAA NDATARREML EIVESVQKEY TAEAKEGGYE SDLKETVAEL MD DVDPTRA ITMEAIKSCK DLQQLEDWSR QVHEYNGDDR IIEIYARAAE ITKNAEHQAL VKQMREWRKL ATKN

UniProtKB: Cytochrome c oxidase subunit iv

+
Macromolecule #17: Cytochrome c oxidase assembly factor like protein

MacromoleculeName: Cytochrome c oxidase assembly factor like protein / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: Leishmania tarentolae promastigotes (UC strain)
Molecular weightTheoretical: 15.137333 KDa
SequenceString:
TVAKISSIER ASTYLRFSTL RVHPHHEPNF RARPVGWKAW NSKQYMDPWA PYPLTSPVRH VDRPFSGMWF GMGHFALKNF FGPLNWKFW ARVSFFGTLG WAYSLSSYAL RMHRNGWEWK NRGAVFSMD

UniProtKB: Uncharacterized protein

+
Macromolecule #18: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

+
Macromolecule #19: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 19 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
Details: 50 mM HEPES pH 7.9, 300 mM NaCl, 4 mM MgCl2, 20 uM CaCl2, 0.1 mM Dithiothreitol, and 0.5% n-dodecyl-beta-D-maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 5392
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: Built de novo using ModelAngelo (v1.014), guided by the cryo-EM density map
Output model

PDB-9zak:
Cryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)

+
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