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- EMDB-11879: Cryo-EM structure of Polytomella Complex-I (peripheral arm) -

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Basic information

Entry
Database: EMDB / ID: EMD-11879
TitleCryo-EM structure of Polytomella Complex-I (peripheral arm)
Map data
Sample
  • Complex: Polytomella complex I - Peripheral arm
    • Protein or peptide: x 16 types
  • Ligand: x 7 types
KeywordsComplex-I / ELECTRON TRANSPORT
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKlusch N / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 23, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7arc
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11879.png

Downloads & links

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Map

FileDownload / File: emd_11879.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 502.2 Å		0.84 Å/pix.
x 600 pix.
= 502.2 Å		0.84 Å/pix.
x 600 pix.
= 502.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.060136966 - 0.118719615
Average (Standard dev.)0.000032826472 (±0.0011616133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 502.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z502.200502.200502.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0600.1190.000

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Supplemental data

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Half map: #2

Fileemd_11879_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11879_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polytomella complex I - Peripheral arm

EntireName: Polytomella complex I - Peripheral arm
Components
  • Complex: Polytomella complex I - Peripheral arm
    • Protein or peptide: PSST
    • Protein or peptide: ND9
    • Protein or peptide: ND7
    • Protein or peptide: 24 kDa
    • Protein or peptide: 51 kDa
    • Protein or peptide: 75 kDa
    • Protein or peptide: TYKY
    • Protein or peptide: 39 kDa
    • Protein or peptide: 18 kDa
    • Protein or peptide: 13 kDa
    • Protein or peptide: B8
    • Protein or peptide: SDAP2
    • Protein or peptide: B13
    • Protein or peptide: B14
    • Protein or peptide: B17.2
    • Protein or peptide: B14.5a
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ZINC ION
  • Ligand: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
  • Ligand: water

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Supramolecule #1: Polytomella complex I - Peripheral arm

SupramoleculeName: Polytomella complex I - Peripheral arm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)

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Macromolecule #1: PSST

MacromoleculeName: PSST / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 18.158168 KDa
SequenceString:
MSKAVAAAKG ADFIVSKVDT VVNWARAGSM WPMTFGLACC AVEMMHAGAS RYDLDRFGII FRPSPRQSDV MIVAGTLTNK MAPALRKVY DQMPEPKWVV SMGSCANGGG YYHYSYSVVR GCDRVVPVDV YVPGCPPTAE GLLYGLLQLQ KKIYRSKNTQ L WWNK

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Macromolecule #2: ND9

MacromoleculeName: ND9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 25.689066 KDa
SequenceString: MSYCYARKMT DKDYIAYDNI KNFGDNYLTD YIIKTVPKYV TMAVNGPAQS SVLYQEPTIY TTPEHIYALC AFLRDHVNLQ YKTLIDITA VDYPERSARF EVVYHLLSPR LNNRIRIKVV VDEVTSVPSV SRIWNAANWF ERETWDMFGV FFSNHPDLRR V LTDYGFTG ...String:
MSYCYARKMT DKDYIAYDNI KNFGDNYLTD YIIKTVPKYV TMAVNGPAQS SVLYQEPTIY TTPEHIYALC AFLRDHVNLQ YKTLIDITA VDYPERSARF EVVYHLLSPR LNNRIRIKVV VDEVTSVPSV SRIWNAANWF ERETWDMFGV FFSNHPDLRR V LTDYGFTG HPLRKDFPLT GYTEVRYDYG KKRVISEPLE LTQEFRYFDF SSPWDTLSR

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Macromolecule #3: ND7

MacromoleculeName: ND7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 45.263047 KDa
SequenceString: MKPLTPSKVS NFTINFGPQH PAAHGVLRLV LEMDGEIIKR ADPHIGLLHR GTEKLLEYKT YNQGIPYFDR LDYVSMMCME HSYVLAIEQ LLNVAVPLRG QYIRVLFSEI TRIMNHILAI TCHSMDVGAL TPFLWAFEER EKLFEFYERV SGARMHAAYF R VGGVAQDL ...String:
MKPLTPSKVS NFTINFGPQH PAAHGVLRLV LEMDGEIIKR ADPHIGLLHR GTEKLLEYKT YNQGIPYFDR LDYVSMMCME HSYVLAIEQ LLNVAVPLRG QYIRVLFSEI TRIMNHILAI TCHSMDVGAL TPFLWAFEER EKLFEFYERV SGARMHAAYF R VGGVAQDL PIGLLRDIYD WSRQFASRVD EMEELLTGNR IWKERTIDVG LVTAQQAWDW GCSGPILRGS GIDWDLRKNQ PY DVYGRMD FNVPIAGHGD CYDRYLVRVQ EMRESLRIIY QCLNEMPDGL YKTPDQKVSP PSRGQMKQSM ESLIHHFKLF SEG YHVPAG ETYRAVEAPK GEFGVYLVSR GGNRPYRCKI RSPGYAHLQM LDMVAKGAML ADVVTIIGTL DVVFGEIDR

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Macromolecule #4: 24 kDa

MacromoleculeName: 24 kDa / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 30.186473 KDa
SequenceString: MFSRFTSLVV RAAVVASSHN KAATPIISVT LPSLRSFATN STDVFNVHHD TPENNKDTKF DFTEANYKLV NKIMSNYPSN YKASAMIPL LDLAQQQNGG VVSLAVMNRV AQILEVPPIK VYEVATFFTM FNRSKMGKYH VCICGTTPCR LQGAQKIEEA I TKHLGVGI ...String:
MFSRFTSLVV RAAVVASSHN KAATPIISVT LPSLRSFATN STDVFNVHHD TPENNKDTKF DFTEANYKLV NKIMSNYPSN YKASAMIPL LDLAQQQNGG VVSLAVMNRV AQILEVPPIK VYEVATFFTM FNRSKMGKYH VCICGTTPCR LQGAQKIEEA I TKHLGVGI GQTTADGTFT LGEMECMGAC VNAPMIAVAD YRNGVEGFSY NYYEDLTPQD AVNILEKLKK GEKPKLGSQH RQ TAEPAGA VVGDKWIPSS GEQTLMGELP GPYCRDLSK

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Macromolecule #5: 51 kDa

MacromoleculeName: 51 kDa / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 51.593879 KDa
SequenceString: MQRSTGAALR FAGFRSRCLS LLRTFSTQAP PAAAPEKTTF GGLRDQDRIF TNIYGRHDPY IKGAEARGDW YMTKDLVGKG RDWIIDQIK KSGLRGRGGA GFASGLKWSF MPKVSDGRPS YLVVNGDESE PGTCKDREIM RHEPHKLVEG CLVAGTAMGA R AGYIYIRG ...String:
MQRSTGAALR FAGFRSRCLS LLRTFSTQAP PAAAPEKTTF GGLRDQDRIF TNIYGRHDPY IKGAEARGDW YMTKDLVGKG RDWIIDQIK KSGLRGRGGA GFASGLKWSF MPKVSDGRPS YLVVNGDESE PGTCKDREIM RHEPHKLVEG CLVAGTAMGA R AGYIYIRG EFVNERKAVE RAVAEAYAKG YLGKNACGSG VDFDLFVHYG AGAYICGEET ALIESLEGKQ GKPRLKPPFP AG MGLYGCP TTVTNVETVA VSPTILRRGP EWFSSFGRKN NAGTKLFAIS GHVNRPVTVE EEMSIPLREL IERHAGGVRG GWD NLLAII PGGSSVPLLP KKMCDDVIMD FDALRTAQSG LGTAAVIVMN KDTDVIDAIA RLSYFYKHES CGQCTPCREG TGWL YDIMS RMRKGDARLE EIDMLWEITK QIEGHTICAL GDAAAWPVQG LIRHFRSEME DRIKNADQQR ISAH

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Macromolecule #6: 75 kDa

MacromoleculeName: 75 kDa / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 77.364305 KDa
SequenceString: MISKKAIQAI SQLGAKQPAV RAISSSVSAL NQAAAAPALP ADKMEVFVNG EAVVVPKNFT VLQACDAAGV DVPRFCYHQR LSIAGNCRM CLVEIEKAPK PVASCAFPAG PGMKIKTDTP VIKKAREGVM EFLLINHPLD CPICDQGGEC DLQDQAMIFG S DRSRFIEY ...String:
MISKKAIQAI SQLGAKQPAV RAISSSVSAL NQAAAAPALP ADKMEVFVNG EAVVVPKNFT VLQACDAAGV DVPRFCYHQR LSIAGNCRM CLVEIEKAPK PVASCAFPAG PGMKIKTDTP VIKKAREGVM EFLLINHPLD CPICDQGGEC DLQDQAMIFG S DRSRFIEY KRAVADKNLG PLIKTSMNRC IHCTRCVRFT HEVAGTSELG ITGRGRDSEV GTYIEKLHSS ELSGNVIDLC PV GALLSKP YAFTARSWEL KGTETIDVSD ALGSNIKVDC RGTEVMRITP RLNDAINEEW LSDKGRFQYD GLKRQRLNTP LVK GAKGLE NATWSAAFDA IRTAIAGAKG NELKAIAGKL ADAESMIALK DLFNKLGSGN LIHEDGSATL SADVRSSYIA NTTI ASIEK ADVILLVGTN PRFESPVFNA RLRKVFLDGA KVGLVGEKVD LTYAYQHLGA DVAALESLAS GKGAFFEALK GAKNP VVIV GSSVLRRDDR EAVLKTVNDL VDAAGVVKEG WNGFNVLHDN ASRVAALDIG FVPSASARTN PVPAKVVYLL GSDDFK DEE IPADAFVIYQ GHHGDKGAAR ANVVLPGAAY TEKASLFANT EGRVQTTRTA VPVLGDARED WKIIRALSEV VGQQLPY DS QPQVRARLAE VAPHFAEIGK AESALWLNGQ YFKGVKDLVA KAARSTASLA TNISNYYMTD AISRASRTMA KCTAVRQQ

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Macromolecule #7: TYKY

MacromoleculeName: TYKY / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 26.140525 KDa
SequenceString: MSLINRAAQR LLSMPSVSSM GGLTQFTRSM GTERRPGQSG AWKQVDKQRY SSEWEQDPTF KQVPKNVSEV LDDSVSVLFL TDIVRGMMY SASGFFDDKV TILYPFEKGA VSPRFRGEHA LRRYPTGEER CISCKLCEAI CPAQAITIEA EEREDGSRKT T RYDIDMTK ...String:
MSLINRAAQR LLSMPSVSSM GGLTQFTRSM GTERRPGQSG AWKQVDKQRY SSEWEQDPTF KQVPKNVSEV LDDSVSVLFL TDIVRGMMY SASGFFDDKV TILYPFEKGA VSPRFRGEHA LRRYPTGEER CISCKLCEAI CPAQAITIEA EEREDGSRKT T RYDIDMTK CIYCGFCQEA CPVDAIVEGP NFEFSTETRE ELLYDKQKLL ENGDKWEQEI AANLRTESLY R

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Macromolecule #8: 39 kDa

MacromoleculeName: 39 kDa / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 41.233008 KDa
SequenceString: MSTLKPFDLN ANNAVRNGPG GRSSIGGVVA TVFGANGFIG SYVVNEISKR GNQVVCPYRC NENKVQPLKQ MGDLGQVVLL PEFDIHDDE YIRRAISRSN VVINCVGIRQ ETKNYSYKDV HVDFPTRLAK IVAESGKVER FIQVSEMGAD VSHASRRLQT K AVGDEAIM ...String:
MSTLKPFDLN ANNAVRNGPG GRSSIGGVVA TVFGANGFIG SYVVNEISKR GNQVVCPYRC NENKVQPLKQ MGDLGQVVLL PEFDIHDDE YIRRAISRSN VVINCVGIRQ ETKNYSYKDV HVDFPTRLAK IVAESGKVER FIQVSEMGAD VSHASRRLQT K AVGDEAIM KYIPDATIIR PGNVVGIEDY FYNNLIFQLS YTIVAPVINN GANKVQPTYI LDVADAVVKI LKDKKTSGKT YY LGGPETL TMRQIYDHLI DTLRLSNDDT VNLRYELAKM LYKPLDTLRT KLPEFPFLGF MMSSDYAEEQ VADSVAPAGS LGY KDLSIS PAKVTEGLAI EGVRFIRVGG YDWGDMNKVS SNIPEHIRKY YNLK

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Macromolecule #9: 18 kDa

MacromoleculeName: 18 kDa / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 20.800783 KDa
SequenceString:
MLRKAVSTLF NLEKRVLYQQ AGFATAPQDF SLAMKKADEI YSGKTVKAGD IGFSAGVPLE TYNRKVRIFC PAKAASQSGL GRTLHPSSK APQWKIVFEN LSKWENPLMG WTSTADPLEN VGRSTLLFYT KEEAAAFCAK HGWEYVVDEP NPRKHIRQKR Y LGYGDNYS IKRKGVPDLA HLPSNRS

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Macromolecule #10: 13 kDa

MacromoleculeName: 13 kDa / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 14.346163 KDa
SequenceString:
MSFVRSSFSL VRRFASEAVI AEKNKIPETV GGAAFKGDLR GTSAVGLGDG LYSHTSKWMQ GNGKSPMDYI NEVEPIKVKG LVVASHGSD DPALGCPVEY ISLKGTSYEN PAVCKYTGNR YYSDCWKHGA HHH

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Macromolecule #11: B8

MacromoleculeName: B8 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 10.509916 KDa
SequenceString:
MAWKTALTTT FQELRITLSQ SSSSSAGARE FVLGQYAELK AANPLLPILV RESNAAQASL TARYDFGVEK KVSIENDSAS GILSKLEGL VKHGQSLAK

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Macromolecule #12: SDAP2

MacromoleculeName: SDAP2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 13.393094 KDa
SequenceString:
MAFLTSALRS AVLSNLRVAA STVEFKSISV VSAFTRNFSS FLPKEEVESR IIAQVKEQNL AAGIKVELSS RFDKDLGLDS LDKVELLIS LEEDFGVEVP DAEIDKIHTV EDAVNFFISN PSS

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Macromolecule #13: B13

MacromoleculeName: B13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 17.745182 KDa
SequenceString:
MIRNISSRFS TCLRQALPSA SSNRTFKAVA DVEIDFSNRA VLKKYVGVDH LSKEQGTKAK FIVSLNSLLE AVKSVPETAE YRKAIEATC QYRLKVCGEN NSDAAIEEVL DAHLEELIAE SKEELRILPV LLESKPWDVP ADYSAPVFDY VDASTILDKK

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Macromolecule #14: B14

MacromoleculeName: B14 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 16.134878 KDa
SequenceString:
MTSRFAYVAK AAAPAAPVTC QKARNLYLEA CRCLPFIHRL HKLEEITSLK EMRLIIKDKF RVNSPVTDSR VTDLLIFKGR EELETYLFM YKQRHHAITE YIEPYQIKKL LIERKSSNSA FLDSFYEKAY PLVHSKYA

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Macromolecule #15: B17.2

MacromoleculeName: B17.2 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 18.178396 KDa
SequenceString:
MSLTKYLNNL VSTSGKKSLA GFFVSWEFAK MIVDGNLHNN VVRPQSGAQV GIDKFGNKYF EDNEESYGRR RWIVFADKFD YKISSIPPE WHGWLNYIND YKPSDYETID NKKPMYHAEW TISATGTQEC YNPKGSWFNP AKRNWKKVEI WQPPQV

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Macromolecule #16: B14.5a

MacromoleculeName: B14.5a / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Polytomella sp. Pringsheim 198.80 (plant)
Molecular weightTheoretical: 13.827012 KDa
SequenceString:
MSGILKTVQS IFYSVGLKEP WKMTGIRSLP DFEYYLPFGL TYRGISPGNQ PIKAVVPHDV PKLVYDIKYF ARDYRRNNSY TVRSVDSKT PFDYSKVFGS APLKPADVKT VRIPEVMPHR GC

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Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 18 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #19: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 19 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #20: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 20 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #22: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
type: ligand / ID: 22 / Number of copies: 1 / Formula: 8Q1
Molecular weightTheoretical: 540.651 Da
Chemical component information

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

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Macromolecule #23: water

MacromoleculeName: water / type: ligand / ID: 23 / Number of copies: 418 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42350
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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

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