[English] 日本語
Yorodumi
- EMDB-14765: Early Pp module assembly intermediate of complex I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14765
TitleEarly Pp module assembly intermediate of complex I
Map dataearly Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin
Sample
  • Complex: Early Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin.
    • Protein or peptide: NADH dehydrogenase subunit 2
    • Protein or peptide: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: Complex I intermediate-associated protein 30-domain-containing protein
    • Protein or peptide: complex I assembly factor CIA84
    • Protein or peptide: Tafazzin family protein
  • Ligand: CARDIOLIPIN
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
Function / homology
Function and homology information


cardiolipin acyl-chain remodeling / 1-acylglycerophosphocholine O-acyltransferase activity / inner mitochondrial membrane organization / mitochondrial respirasome assembly / phospholipid biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial membrane / mitochondrial outer membrane ...cardiolipin acyl-chain remodeling / 1-acylglycerophosphocholine O-acyltransferase activity / inner mitochondrial membrane organization / mitochondrial respirasome assembly / phospholipid biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial membrane / mitochondrial outer membrane / mitochondrial inner membrane / oxidoreductase activity / mitochondrion
Similarity search - Function
Tafazzin / NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Mitochondrial group I intron splicing factor CCM1 / Uncharacterized protein / Complex I intermediate-associated protein 30-domain-containing protein / Tafazzin family protein / NADH-ubiquinone oxidoreductase chain 2
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsSchiller J / Laube E / Vonck J / Zickermann V
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: Sci Adv / Year: 2022
Title: Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.
Authors: Jonathan Schiller / Eike Laube / Ilka Wittig / Werner Kühlbrandt / Janet Vonck / Volker Zickermann /
Abstract: Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly ...Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.
History
DepositionApr 13, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14765.png

Downloads & links

-
Map

FileDownload / File: emd_14765.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationearly Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 208 pix.
= 251.1 Å		1.21 Å/pix.
x 208 pix.
= 251.1 Å		1.21 Å/pix.
x 208 pix.
= 251.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.20721 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.0835288 - 4.681307
Average (Standard dev.)0.0024850257 (±0.10163221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 251.09967 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_14765_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14765_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Early Pp module assembly intermediate of complex I with assembly ...

EntireName: Early Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin.
Components
  • Complex: Early Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin.
    • Protein or peptide: NADH dehydrogenase subunit 2
    • Protein or peptide: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: Complex I intermediate-associated protein 30-domain-containing protein
    • Protein or peptide: complex I assembly factor CIA84
    • Protein or peptide: Tafazzin family protein
  • Ligand: CARDIOLIPIN
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

-
Supramolecule #1: Early Pp module assembly intermediate of complex I with assembly ...

SupramoleculeName: Early Pp module assembly intermediate of complex I with assembly factors NDUFAF1 and CIA84 and cardiolipin remodeling enzyme tafazzin.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Yarrowia lipolytica (yeast)

-
Macromolecule #1: NADH dehydrogenase subunit 2

MacromoleculeName: NADH dehydrogenase subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 53.381367 KDa
SequenceString: (FME)LILAIISLI TFVSMSKLSD NRAIIRLINI YLILVLVLDS FLYLLFLNNQ TYTVMGELLI FNSFTFYIDM LIYFIM IVI SSLYGYNLYN NNLYKTLFEP KKELIILFLI NILGALLIVH SNDFITLFVA IELQSYSIYL ITAIYNSSYK ASKASML YF FMGGILSILI ...String:
(FME)LILAIISLI TFVSMSKLSD NRAIIRLINI YLILVLVLDS FLYLLFLNNQ TYTVMGELLI FNSFTFYIDM LIYFIM IVI SSLYGYNLYN NNLYKTLFEP KKELIILFLI NILGALLIVH SNDFITLFVA IELQSYSIYL ITAIYNSSYK ASKASML YF FMGGILSILI AYSINTYYSV LNSYTLHSLD SLIINTLDLN LILIALSLGL LFKIGIAPLH KWLISIYENT PILITIYI S LIPKISILSY LVLSNISINS LVISILAILT LLVGSVGGLL QIKIKRLLAF SGLTNAGYMM LLLLLNNNEF SYLYYITQY SISHLAIFMI IIFSIYYINY INNQYNPIIY VNQLKGLIHD NAYLVLSMAI VVFSFIGIPP LLGFFGKLNI LMSILNNGYY FISIVLIVA SLISALYYLY LLNVSIQDKN NILINSNETV SSVLSYILSS LIILITFGFI YNSLIIDIFN VYFN

-
Macromolecule #2: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 8.059366 KDa
SequenceString:
MALFTSLVGA SGLGFATKFL SNKIRLKPAG YYPLGYVFSG VAWAGLGLVL HNVHQHSLEV LEKKKTALSE QRTE

-
Macromolecule #3: Complex I intermediate-associated protein 30-domain-containing protein

MacromoleculeName: Complex I intermediate-associated protein 30-domain-containing protein
type: protein_or_peptide / ID: 3 / Details: C-terminal strep tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 31.894016 KDa
Recombinant expressionOrganism: Yarrowia lipolytica (yeast)
SequenceString: MSANPAIVRP TETTEQVLVN FTKPNSLETV LTKCDEELGG YSTVNLALER PTTGKPYGRF FGNLSLDLPK DNKMVTRSGF AMFRTLDQP SSMFKTNAWN WEQYRHLELR VRGDRRKYFV NVQSATPLAS DLYQHRLFIQ TPGEWETVVI PIDDFILTNK G VVQEQMAM ...String:
MSANPAIVRP TETTEQVLVN FTKPNSLETV LTKCDEELGG YSTVNLALER PTTGKPYGRF FGNLSLDLPK DNKMVTRSGF AMFRTLDQP SSMFKTNAWN WEQYRHLELR VRGDRRKYFV NVQSATPLAS DLYQHRLFIQ TPGEWETVVI PIDDFILTNK G VVQEQMAM DTANVYTVGI GLIDRQYGPY NLDIEYIKAV AHPPLEFKPK KEYEVEKETI LLTPGQPMEL GKGKVKELEE NL YFQGAEA AAKEAAAKAW SHPQFEKGGG SGGGSGGSAW SHPQFEK

-
Macromolecule #4: complex I assembly factor CIA84

MacromoleculeName: complex I assembly factor CIA84 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 97.098469 KDa
SequenceString: MPKNALLRSA RQVAISRVFA TSRASHVVSH APILASVRPR SNPAPYRRNF SSSRALRNDY GLDTAERSLK ESLVPFNGAP VDRKVVRDQ LMELISVSPG QVFPISVIPV VKSAYYELFR ENERVLSAGD TKTLFGAVAG NNPEDVQDLP FVLAVYHQAE Q AAETNRDS ...String:
MPKNALLRSA RQVAISRVFA TSRASHVVSH APILASVRPR SNPAPYRRNF SSSRALRNDY GLDTAERSLK ESLVPFNGAP VDRKVVRDQ LMELISVSPG QVFPISVIPV VKSAYYELFR ENERVLSAGD TKTLFGAVAG NNPEDVQDLP FVLAVYHQAE Q AAETNRDS RDNILLLGKY FLFQDRLDNF WKLLEAQIKT HDDVDAGFVK QLLELISVDP HLTLGNVARV LQLKTDNHVS SS DELRNAL SATLEQLYYK ENEGSEFFLS LVENHILDSK DFTPSDSVVA MILNTCVNEG REDLGQSVLR NVVSRVGNLS PGQ EDPQNC WGFWSSVAMD LHGSKTDVKA FISRLEALPH RTKATWDILI RYAVFKADLA GRNDLLQVRA LLAEMQKVGF EPDA ETYFD AYRSSKSIKP DVVHLFEAEL DIEKDTSIFA IEMDKALKNH DTLEALSIFY ESFEQGAQWE NKRLHMEAMT ELLIQ YAGL NDTSVADILQ LVQRIEPICA QGRIPYSAET AIAQNVLQRH SDTANFYTFM NRQYGNTADK VTKQDPQIRP HTYQVI HDY IYSCESERAD LAWEMYGLLH KFYVVPFADY YKAIKFFAQD VKRQDYALLT FQQIRKNHDL HGQPAATSEM VAFLFHE FA KTKYKRGIKR LHEVVALETS FDVNRDVLNE MMAAYVSVED LNRVQDCWAQ LQQLPPSIGA NNRSVDVLLS YFKDNIHY T ERTWQGIPEF GLLPTLENYE QYLINNCRTG NYRRALEITK NMEIDSGLKP TAKIIAAVYN YTFTEQRKLE VEQWAEKAH PEMWLELKEG DKLKSLCLPA NSDNDNVESL LKQASADMDE EMSGGIVKVE SV

-
Macromolecule #5: Tafazzin family protein

MacromoleculeName: Tafazzin family protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: CLIB 122 / E 150
Molecular weightTheoretical: 42.835367 KDa
SequenceString: MSFRNVSLRG SQLLGKLDSR GWGWYVAKKW NIGLVYTMCK VFLRCKKVDI KGLDNLLEAH RQARLEGRGL LTVMNHTSVL DDPVVWGML PNDNGWIPYL MRWATGAKDI CYKNKLYSLF FGAGQVLPIT RFGIGGPFQP GMDMCVRLLN PNNKIKYSAK Y TPYLVHTN ...String:
MSFRNVSLRG SQLLGKLDSR GWGWYVAKKW NIGLVYTMCK VFLRCKKVDI KGLDNLLEAH RQARLEGRGL LTVMNHTSVL DDPVVWGML PNDNGWIPYL MRWATGAKDI CYKNKLYSLF FGAGQVLPIT RFGIGGPFQP GMDMCVRLLN PNNKIKYSAK Y TPYLVHTN ATSYPFWRES NWVHFFPEGY VHQALEPHEG TMRYFRWGTS RAVLEPVTPP IIVPMFSHGL QKVFQEIPKG YE MEGNNTN KDRTISIRIG EPISETTVAG FRNEWINLCH KENVGLNAET MPDVLKNGQE AKDLRSKVAA YLREEVEKLR LTV PNMNPE LPEFKEPEFW SDIDKVHKGV YNHRGKVRML RNPTKGLIEV VEANKD

-
Macromolecule #6: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 6 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

-
Macromolecule #7: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 7 / Number of copies: 1 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

-
Macromolecule #8: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 276 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was a mixture of assembly intermediates associated with the assembly factor NDUFAF1

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6229 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
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: 2048808
Startup modelType of model: OTHER / Details: Ab initio model in CryoSPARC 3.3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 376810
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7o71

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7zkq:
Early Pp module assembly intermediate of complex I

+
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