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- EMDB-13093: Immature 60S Ribosomal Subunit from C. thermophilum -

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Basic information

Entry
Database: EMDB / ID: EMD-13093
TitleImmature 60S Ribosomal Subunit from C. thermophilum
Map dataImmature 60S Ribosomal Subunit from C.thermophilum, Main Map
Sample
  • Complex: Native 60-mer core of Pyruvate Dehydrogenase Complex
    • Protein or peptide: x 1 types
  • Protein or peptide: x 20 types
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.52 Å
AuthorsSkalidis I / Kastritis PL
CitationJournal: Structure / Year: 2022
Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis /
Abstract: Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts.
History
DepositionJun 16, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13093.png

Downloads & links

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Map

FileDownload / File: emd_13093.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImmature 60S Ribosomal Subunit from C.thermophilum, Main Map
Voxel sizeX=Y=Z: 1.5678 Å
Density
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-0.99596155 - 3.4253058
Average (Standard dev.)0.008825258 (±0.18437766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 401.3568 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.567800781251.567800781251.56780078125
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z401.357401.357401.357
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.9963.4250.009

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Supplemental data

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Additional map: Signature 4 Map

Fileemd_13093_additional_1.map
AnnotationSignature 4 Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Immature 60S Ribosomal Subunit from C.thermophilum, Half-Map A

Fileemd_13093_half_map_1.map
AnnotationImmature 60S Ribosomal Subunit from C.thermophilum, Half-Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Immature 60S Ribosomal Subunit from C.thermophilum, Half-Map B

Fileemd_13093_half_map_2.map
AnnotationImmature 60S Ribosomal Subunit from C.thermophilum, Half-Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native 60-mer core of Pyruvate Dehydrogenase Complex

EntireName: Native 60-mer core of Pyruvate Dehydrogenase Complex
Components
  • Complex: Native 60-mer core of Pyruvate Dehydrogenase Complex
    • Protein or peptide: uL13
  • Protein or peptide: eL21
  • Protein or peptide: eL13
  • Protein or peptide: eL15List of Subaru engines
  • Protein or peptide: eL18
  • Protein or peptide: uL15
  • Protein or peptide: eL36
  • Protein or peptide: eL32CD59
  • Protein or peptide: eL20
  • Protein or peptide: uL22
  • Protein or peptide: eL8
  • Protein or peptide: uL29
  • Protein or peptide: uL6
  • Protein or peptide: eL6
  • Protein or peptide: uL5
  • Protein or peptide: uL18
  • Protein or peptide: eL14
  • Protein or peptide: uL30
  • Protein or peptide: eL33
  • Protein or peptide: uL24
  • Protein or peptide: uL4

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Supramolecule #1: Native 60-mer core of Pyruvate Dehydrogenase Complex

SupramoleculeName: Native 60-mer core of Pyruvate Dehydrogenase Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 3 MDa

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Macromolecule #1: uL13

MacromoleculeName: uL13 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MSSFESVVVI DGKGHLLGRL ASIVAKQLLS GQKIVVVRCE ALNISGEFFR AKLKYHAYLR KMTRYNPTRG GPFHFRAPSR IFYKAVRGMI PHKTARGAAA LERLKVFEGV PPPYDKKKKM VVPQALRVLR LQPGRKYCTV GRLSHEVGWK YQDVVARLEE RRKAKGAAYY ...String:
MSSFESVVVI DGKGHLLGRL ASIVAKQLLS GQKIVVVRCE ALNISGEFFR AKLKYHAYLR KMTRYNPTRG GPFHFRAPSR IFYKAVRGMI PHKTARGAAA LERLKVFEGV PPPYDKKKKM VVPQALRVLR LQPGRKYCTV GRLSHEVGWK YQDVVARLEE RRKAKGAAYY ERKKLAARQL SEAKKAAAAK VDPKVSEALA AYGY

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Macromolecule #2: eL21

MacromoleculeName: eL21 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MGHAAGLRSG TRYAFSRGFR KHGQIPLSTY LRTYRVGDIV DIKVNGAVQK GMPHKFYHGK TGVVYNVTKS AVGVIVYKRV KHRYIEKRIN VRIEHVKPSR SREDFLRRVK ENAELKKKAK AEGVPVQLKR QPAMPREAHT VSIADNKPVT LAPVAYETTI

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Macromolecule #3: eL13

MacromoleculeName: eL13 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MAIKHNQQIP NNHFRKHWQR RVRCHFDQPG KKVTRRLARR AKAAALAPRP VDKLRPIVRC PTVKYNRRTR LGRGFTLEEL KAAGIPRLLA PTIGIAVDHR RKNLSEESLA ANVQRLKDYK ARLILFPRKS NKPKKADTPK DQQTAETTTS LRTSFGVEQP LAPGFTEISK ...String:
MAIKHNQQIP NNHFRKHWQR RVRCHFDQPG KKVTRRLARR AKAAALAPRP VDKLRPIVRC PTVKYNRRTR LGRGFTLEEL KAAGIPRLLA PTIGIAVDHR RKNLSEESLA ANVQRLKDYK ARLILFPRKS NKPKKADTPK DQQTAETTTS LRTSFGVEQP LAPGFTEISK SEIPAGIEGG AYRALRKARS DARLVGVREK RAKEKAEAEA NKK

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Macromolecule #4: eL15

MacromoleculeName: eL15 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MGALKYLEEL SKKKQSDVVR FLLRVRCWEY RQLNVIHRAS RPSRPDKARR LGYKAKQGYV IYRVRVRRGG RKRPVPKGAT YGKPTNQGVN QLKYQRSLRA TAEERVGRRC SNLRVLNSYW VNQDSTYKYY EVILVDPNHK AIRRDPRINW ICNPVHKHRE CRGLTSTGKK ...String:
MGALKYLEEL SKKKQSDVVR FLLRVRCWEY RQLNVIHRAS RPSRPDKARR LGYKAKQGYV IYRVRVRRGG RKRPVPKGAT YGKPTNQGVN QLKYQRSLRA TAEERVGRRC SNLRVLNSYW VNQDSTYKYY EVILVDPNHK AIRRDPRINW ICNPVHKHRE CRGLTSTGKK SRGLNKGHRF NKTRAGRRKT WKRHNTLSLW RYR

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Macromolecule #5: eL18

MacromoleculeName: eL18 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MDLVCAFIGP LFAPGARRLN LEEIAAESSS GIDLRWKHVR SSHRKAPKSD NVYLKLLVKL YRFLARRTEA PFNKVVLRRL FMSRINRPPV SLSRIARNLK NGNEKKTVVV VATVTDDNRL LQVPKMEVAA LRFTAKARAR IEAAGGRTLT LDQLALEKPT GANTLLLRGP ...String:
MDLVCAFIGP LFAPGARRLN LEEIAAESSS GIDLRWKHVR SSHRKAPKSD NVYLKLLVKL YRFLARRTEA PFNKVVLRRL FMSRINRPPV SLSRIARNLK NGNEKKTVVV VATVTDDNRL LQVPKMEVAA LRFTAKARAR IEAAGGRTLT LDQLALEKPT GANTLLLRGP KNAREAVKHF GFGPHKHKKP YVRSKGRKFE RARGRRRSRG FKV

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Macromolecule #6: uL15

MacromoleculeName: uL15 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MVRQLTSGRF EREMLTFAAY PVFQDKKAPR PRVRRRVGKH RKHPGGRGMA GGQHHHRTNL DKYHPGYFGK VGMRHFHLLR NHYWRPSINI DKLWSLVPSD VREQYLSGQK KDTAPVIDLL SHGYAKLLGK GRLPEIPVVV RARYVSAEAE RKVKEAGGVV ELVA

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Macromolecule #7: eL36

MacromoleculeName: eL36 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MSEDATPKAP VERTGLIRGL NKGHKTTRRV LKERPSRRKG AQSKRTQFVR SLIREVAGLA PYERRVIELL RNGKDKRARK FSKKKLGTFG RAKRKCEELQ RIIAESRRAH

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Macromolecule #8: eL32

MacromoleculeName: eL32 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MVAAKKHVPI VKKRTKRFMR HQSDRFKCLD SAWRKPKGID NRVRRRFKGN LAMPSIGYGS NKKTKHMMPS GHKAFLVHNV KDVELLLMHN RTYAAEIAHN VSSRKRIDII TRAKQLGVKV TNAKAKVTTE V

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Macromolecule #9: eL20

MacromoleculeName: eL20 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MGRLQEYQVI GRHLPTEANP NPALYRMRIF APNEVVAKSR FWYFLRGLKK VKKATGEIVS VNVISEKHPL KVKNFGIWLR YDSRSGTHNM YKEYRETSRV AAVEAMYADM AARHRARFRS IHILKVVELE KTEDVKRPYI KQLVAKNLSF PLPHRVPKIS TKKIFSAKRP STFS

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Macromolecule #10: uL22

MacromoleculeName: uL22 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MVRYAATEIA PTKSARARGS YLRVSFKNTR ETAQAINGWK LQRALTFLQN VIDKKEAVPM RRYAGSTGRT AQGKQWGVSR ARWPVKSAQF LIGLLKNAEA NADAKGLDTG NLIIKHIQVN QAPKQRRRTY RAHGRINPYM SNPCHIELIL TEAEETVQKS EAVVRDVESH LSSRQRGVRI RRALTAA

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Macromolecule #11: eL8

MacromoleculeName: eL8 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MPPKSGKKVA PAPFPQGKAG AKKAPKNPLL EKRPRNFGIG QDIQPKRNLS RMVKWPEYIR LQRQKKILRM RLKVPPAIAQ FQYTLDKNLA AQAFKLLNKY RPETKQEKKE RLLREATAIK EGKKKEDVSK KPYTVKYGLN HVVGLIENKK ASLVLIANDV DPIELVVFLP ...String:
MPPKSGKKVA PAPFPQGKAG AKKAPKNPLL EKRPRNFGIG QDIQPKRNLS RMVKWPEYIR LQRQKKILRM RLKVPPAIAQ FQYTLDKNLA AQAFKLLNKY RPETKQEKKE RLLREATAIK EGKKKEDVSK KPYTVKYGLN HVVGLIENKK ASLVLIANDV DPIELVVFLP ALCRKMGIPY AIIKGKARLG TLVHKKTAAV VAITEVRSED KNELAKLISA VKEGYLEKVE DTRKRWGGGI MGFKAQKREE KRKKSLETAI KV

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Macromolecule #12: uL29

MacromoleculeName: uL29 / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MSSNGKVKAG QLWSKNKEEL TKILGELKTE LSQLRIQKIS SSGAKLNKIH DLRKSIARVL TVINAKQRAQ LRLFYKNKKY LPLDLRPKLT RALRRRLSKE DASRVLEKTK KRLTHFPQRK YAVKAATYSE GPALSIYHSH QREARCSLVQ CCTFEPELRE SLLLLPVAAS ...String:
MSSNGKVKAG QLWSKNKEEL TKILGELKTE LSQLRIQKIS SSGAKLNKIH DLRKSIARVL TVINAKQRAQ LRLFYKNKKY LPLDLRPKLT RALRRRLSKE DASRVLEKTK KRLTHFPQRK YAVKAATYSE GPALSIYHSH QREARCSLVQ CCTFEPELRE SLLLLPVAAS LKGPNFTRRE RQHRNPSEAT MSAAEPLKLL ASAGKGKSTR SVLRVAILVL IAGAAVASRL FSVIRFESII HEFDPWFNFR ATKYLVANGF YKFWDWFDDR TWHPLGRVTG GTLYPGLMVT SGVIYHLLRF LTVPVDIRNI CVLLAPGFSG LTAIAAYLLT NEMTTSPSAG LLAAAFMGIA PGYISRSVAG SYDNEAIAIF LLVFTFFLWI KALKQGSMLW GALCALFYGY MVASWGGYAF ITCLLPLHSF VLICMGRYST RLYVAYTTWY ALGTLASMQI PFVGFLPVKT SEHMPALGIF GFLQLLAFLD YVRSTISSRQ FQTFLWLFAG GIFGLGLLGL VIATSAGLIA PWSGRFYSLW DTGYAKIHIP IIASVSEHQP TAWPAFFFDL NMLVWLFPVG VYLCFQQLGD EHVFIIVYAL FGSYFAGVMV RLMLTLTPVV CVAAAIAFSS LLDTYLNLKT PNPGQAQATE DAGKKKSGLK AASKPAVGVY ALWGKTMMIS GLTIYLLLFV LHCTWVTSNA YSSPSVVLAS RLPDGSQHII DDYREAYQWL RQNTREDAKI MSWWDYGYQI GGMADRPTLV DNNTWNNTHI ATVGKAMASR EEVSYPIMRQ HEVDYVLVVF GGLLGYSGDD INKFLWMVRI AEGIWPDEVS ERAFFTPRGE YRVDAEATDT MKNSLMYKMC YYNYNNLFPP GQAVDRMRGV RLPEVGPTLN TLEEAFTSEN WIIRIYKVKD LDNLGRDHAS AAAFERGHKK KKATKKRGPR VLRVE

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Macromolecule #13: uL6

MacromoleculeName: uL6 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MRYIHSEETI PVPENGTFRK FRRNDYTFGR TRGREKKRGT TSSKIGELDI NGLKVSIKSR LVTVEGPRGK LQKDLSHIAV NFSVVKKGVI GLEIHHGSRK DVAALRTVRT IINNMIIGVT KGFKYKMRYV YAHFPINVNV EKNAETGCYE VEIRNFIGEK IVRKVVMAPG ...String:
MRYIHSEETI PVPENGTFRK FRRNDYTFGR TRGREKKRGT TSSKIGELDI NGLKVSIKSR LVTVEGPRGK LQKDLSHIAV NFSVVKKGVI GLEIHHGSRK DVAALRTVRT IINNMIIGVT KGFKYKMRYV YAHFPINVNV EKNAETGCYE VEIRNFIGEK IVRKVVMAPG VEVEISKAQK DELILSGNSL EAVSQSAADI QQICKVRNKD IRKFLDGIYV SEKGNIVED

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Macromolecule #14: eL6

MacromoleculeName: eL6 / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MSAAPTTKTF GKGTRTVPAP SEKAQKWYPA EDEAQPKKVR KAVRPWTPRK SLQPGTVLIL LAGRFRGKRV VLLKCLDQGV LLVTGPFKIN GVPLRRVNAR YVIATSVKVD LTGVDQAKID EVAQPKYFTA EKAKEKASEE AFFKQGEKPQ KKPVSSTRAA DQKAIDKALI ...String:
MSAAPTTKTF GKGTRTVPAP SEKAQKWYPA EDEAQPKKVR KAVRPWTPRK SLQPGTVLIL LAGRFRGKRV VLLKCLDQGV LLVTGPFKIN GVPLRRVNAR YVIATSVKVD LTGVDQAKID EVAQPKYFTA EKAKEKASEE AFFKQGEKPQ KKPVSSTRAA DQKAIDKALI ANIKKVDMLA SYLASSFSLR KGDKPHLMKF

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Macromolecule #15: uL5

MacromoleculeName: uL5 / type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MSSEKAQNPM RELRIQKLVL NISVGESGDR LTRAAKVLEQ LSGQTPVYSK ARYTVRQFGI RRNEKIAVHV TVRGPKAEEI LERGLKVKEY ELRRRNFSET GNFGFGISEH IDLGIKYDPS IGIYGMDFYC CMTRPGERVA KRRRCKSRIG ASHRITREET IRWFKQRFDG IVR

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Macromolecule #16: uL18

MacromoleculeName: uL18 / type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MAFHKLVKNS AYYSRFQTKF KRRRQGKTDY YARKRLITQA KNKYNAPKYR LVVRFTNRDI ITQMVTSEIN GDKIFAAAYS HELRAYGINH GLTNWAAAYA TGLLLARRVL AKLGLDKTFT GVEEPNGEYT LTEAAETEDG ERRPFKAILD VGLARTSTGA RVFGVMKGAS ...String:
MAFHKLVKNS AYYSRFQTKF KRRRQGKTDY YARKRLITQA KNKYNAPKYR LVVRFTNRDI ITQMVTSEIN GDKIFAAAYS HELRAYGINH GLTNWAAAYA TGLLLARRVL AKLGLDKTFT GVEEPNGEYT LTEAAETEDG ERRPFKAILD VGLARTSTGA RVFGVMKGAS DGGIFIPHSE NRFPGYDIET EELDTEVLKK YIYGGHVAEY METLADDDEE RYKSQFVKYI EDDVEADSLE ELYAEAHKQI RADPFRKYVS DAPKKSKEEW KAESLKYKKA KLSREERKAR VEAKIKQLLA EQDE

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Macromolecule #17: eL14

MacromoleculeName: eL14 / type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MAEINVEATS WRRVEVGRVL KLENGSLAAI VEIIDHKRVL ADGPSSDPKL ATPRGIVPLS RALLTPIVIP KLPRGARTGA VKKAWEAYGV DAKWKETNWA KKQLQQERRQ SLTDFDRFKV MRLKKQRRFE ERKALAKIKA AA

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Macromolecule #18: uL30

MacromoleculeName: uL30 / type: protein_or_peptide / ID: 18 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MSSTTVPTQN DILVPETLLK KRKSQEKARA ERAAALEKRK QANKEKRQVI FKRAEKYVKE YREQEREKIR LARIAKQQGS FHIPAEAKLV FVIRIKGINK IPPKPRKILQ LLRLRQINNG VFVKVTKATA EMIKIVEPWV AYGYPNLKSV RELIYKRGYG KVNGQRIPLT ...String:
MSSTTVPTQN DILVPETLLK KRKSQEKARA ERAAALEKRK QANKEKRQVI FKRAEKYVKE YREQEREKIR LARIAKQQGS FHIPAEAKLV FVIRIKGINK IPPKPRKILQ LLRLRQINNG VFVKVTKATA EMIKIVEPWV AYGYPNLKSV RELIYKRGYG KVNGQRIPLT DNAIIEENLG KYGIICIEDL IHEIFTVGPN FKQAANFLWP FKLSNPNGGF RPRKFKHFIE GGDLGNREEH INALIRAMN

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Macromolecule #19: eL33

MacromoleculeName: eL33 / type: protein_or_peptide / ID: 19 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MPSEAGHRLY VKGRHLSYQR GRRNTHPKTS LIKIEGVDDT AAANFYLGKR VAYVYRAQKE VRGTKIRVIW GKITRPHGNS GVVRAKFTHP LPARSFGASV RIMLYPSSI

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Macromolecule #20: uL24

MacromoleculeName: uL24 / type: protein_or_peptide / ID: 20 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString:
MKVRPTVSSS RRKARKAHFS APSSVRRVIM SAPLSKELRE KYNVRSIPIR KGDEVQIVRG AHKDKEGKVT SVYRLKYVIH VERVTREKAT GQTVPIGIHP SNVVITKLHL DKDRENILAR IKAGREQVAK AKGKKTAA

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Macromolecule #21: uL4

MacromoleculeName: uL4 / type: protein_or_peptide / ID: 21 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
SequenceString: MASRPTVTVF GADGKPTGAT EVLPKVFSAP IRPDIVKHVH TGMAKNKRQP YAVSEKAGHQ TSAESWGTGR AVARIPRVSG GGTHRAGQGA FGNMCRSGRM FAPTKIWRKW HVKINQGQKR FATASALAAS AVAPLLMARG HQVSTVPEVP LVVDSAAVAG DAVAKTAAAY ...String:
MASRPTVTVF GADGKPTGAT EVLPKVFSAP IRPDIVKHVH TGMAKNKRQP YAVSEKAGHQ TSAESWGTGR AVARIPRVSG GGTHRAGQGA FGNMCRSGRM FAPTKIWRKW HVKINQGQKR FATASALAAS AVAPLLMARG HQVSTVPEVP LVVDSAAVAG DAVAKTAAAY KLLKAIGAGP DVEKVKKSKK LRAGKGKMRG RRHRQRRGPL IVYSPEHDGK ELVKGFRNIP GVETCPVDAL NLLQLAPGGH LGRFIVWTSA AIKQLDAVYE SKKGFFLPAN IVSQADLSRL INSTEIQSVL RAPKGEARTK RACVQKKNPL RNKQIMLRLN PYASTFAKEK LGEVKAEEGK PPKVPASFKE LLHEA

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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

Concentration0.3 mg/mL
BufferpH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: NH4CH2COOH / Component - Name: Ammonium acetate
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: For plunging, blot force 0 and blotting time of 4 sec were applied..

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.15 K / Max: 103.15 K
Alignment procedureComa free - Residual tilt: 14.7 mrad
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2808 / Average electron dose: 30.0 e/Å2

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Image processing

Particle selectionNumber selected: 276399
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1) / Software - details: Patch CTF
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7bgj

Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 256 / Avg.num./class: 1000 / Software - Name: cryoSPARC (ver. 3.1) / Software - details: 2D Classification
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Software - details: Local Refinement / Number images used: 20279
FSC plot (resolution estimation)

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