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- EMDB-45295: Structure of the human BOS:human EMC complex in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-45295
TitleStructure of the human BOS:human EMC complex in GDN
Map dataSharpened map of human BOS:human EMC complex
Sample
  • Complex: Human BOS complex
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
Keywordsmembrane protein biogenesis / membrane protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of nodal signaling pathway / multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / determination of left/right asymmetry in lateral mesoderm ...negative regulation of nodal signaling pathway / multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / determination of left/right asymmetry in lateral mesoderm / tail-anchored membrane protein insertion into ER membrane / protein localization to nuclear inner membrane / Miscellaneous transport and binding events / cobalt ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / copper ion transport / regulation of protein complex stability / magnesium ion transmembrane transporter activity / autophagosome assembly / RHOA GTPase cycle / regulation of signal transduction / regulation of protein-containing complex assembly / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / ribosome binding / carbohydrate binding / early endosome membrane / angiogenesis / nuclear membrane / early endosome / protein stabilization / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / : / : ...: / : / : / : / : / : / : / : / : / : / BOS complex subunit NOMO1-like, first beta sandwich domain / BOS complex subunit NOMO1-like, beta sandwich domain / BOS complex subunit NOMO1-like, second beta sandwich domain / NOMO Ig-like domain / NOMO C-terminal transthyretin-like domain / NOMO third transthyretin-like domain / NOMO fifth transthyretin-like domain / NOMO sixth transthyretin-like domain / NOMO eighth prealbumin-like domain / Nicalin / Transmembrane protein 147 / Predicted membrane protein (DUF2053) / ER membrane protein complex subunit 8/9 / : / Uncharacterised protein family (UPF0172) / Carboxypeptidase regulatory-like domain / EMC2 TPR-like repeat domain / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / Carboxypeptidase-like, regulatory domain superfamily / Prealbumin-like fold domain / Prealbumin-like fold domain / Carbohydrate-binding-like fold / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamB / Peptidase M28 / Peptidase family M28 / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / MPN domain / MPN domain profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / BOS complex subunit NOMO2 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / BOS complex subunit NCLN / ER membrane protein complex subunit 6 / BOS complex subunit TMEM147 ...ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / BOS complex subunit NOMO2 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / BOS complex subunit NCLN / ER membrane protein complex subunit 6 / BOS complex subunit TMEM147 / Endoplasmic reticulum membrane protein complex subunit 7 / ER membrane protein complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsNguyen VN / Tomaleri GP / Voorhees RM
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2 GM137412 United States
Heritage Medical Research Institute United States
CitationJournal: Mol Cell / Year: 2024
Title: Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins.
Authors: Katharine R Page / Vy N Nguyen / Tino Pleiner / Giovani Pinton Tomaleri / Maxine L Wang / Alina Guna / Masami Hazu / Ting-Yu Wang / Tsui-Fen Chou / Rebecca M Voorhees /
Abstract: Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we ...Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we systematically studied the biogenesis of a panel of membrane proteins, including several G-protein-coupled receptors (GPCRs). We observed a central role for the insertase, the ER membrane protein complex (EMC), and developed a dual-guide approach to identify genetic modifiers of the EMC. We found that the back of Sec61 (BOS) complex, a component of the multipass translocon, was a physical and genetic interactor of the EMC. Functional and structural analysis of the EMC⋅BOS holocomplex showed that characteristics of a GPCR's soluble domain determine its biogenesis pathway. In contrast to prevailing models, no single insertase handles all substrates. We instead propose a unifying model for coordination between the EMC, the multipass translocon, and Sec61 for the biogenesis of diverse membrane proteins in human cells.
History
DepositionJun 11, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45295.png

Downloads & links

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Map

FileDownload / File: emd_45295.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of human BOS:human EMC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0769
Minimum - Maximum-0.14910932 - 0.41778523
Average (Standard dev.)0.00031611384 (±0.008498675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of human BOS:human EMC complex

Fileemd_45295_additional_1.map
AnnotationUnsharpened map of human BOS:human EMC complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45295_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45295_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human BOS complex

EntireName: Human BOS complex
Components
  • Complex: Human BOS complex
    • Protein or peptide: ER membrane protein complex subunit 10
    • Protein or peptide: ER membrane protein complex subunit 1
    • Protein or peptide: ER membrane protein complex subunit 2
    • Protein or peptide: ER membrane protein complex subunit 3
    • Protein or peptide: ER membrane protein complex subunit 4
    • Protein or peptide: Membrane magnesium transporter 1
    • Protein or peptide: ER membrane protein complex subunit 6
    • Protein or peptide: ER membrane protein complex subunit 7
    • Protein or peptide: ER membrane protein complex subunit 8
    • Protein or peptide: Nicalin
    • Protein or peptide: BOS complex subunit NOMO2
    • Protein or peptide: Transmembrane protein 147
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human BOS complex

SupramoleculeName: Human BOS complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12 / Details: Human BOS complex of NOMO, TMEM147, and NCLN
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ER membrane protein complex subunit 10

MacromoleculeName: ER membrane protein complex subunit 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.375797 KDa
SequenceString: MAAASAGATR LLLLLLMAVA APSRARGSGC RAGTGARGAG AEGREGEACG TVGLLLEHSF EIDDSANFRK RGSLLWNQQD GTLSLSQRQ LSEEERGRLR DVAALNGLYR VRIPRRPGAL DGLEAGGYVS SFVPACSLVE SHLSDQLTLH VDVAGNVVGV S VVTHPGGC ...String:
MAAASAGATR LLLLLLMAVA APSRARGSGC RAGTGARGAG AEGREGEACG TVGLLLEHSF EIDDSANFRK RGSLLWNQQD GTLSLSQRQ LSEEERGRLR DVAALNGLYR VRIPRRPGAL DGLEAGGYVS SFVPACSLVE SHLSDQLTLH VDVAGNVVGV S VVTHPGGC RGHEVEDVDL ELFNTSVQLQ PPTTAPGPET AAFIERLEME QAQKAKNPQE QKSFFAKYWM YIIPVVLFLM MS GAPDTGG QGGGGGGGGG GGSGR

UniProtKB: ER membrane protein complex subunit 10

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Macromolecule #2: ER membrane protein complex subunit 1

MacromoleculeName: ER membrane protein complex subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.886141 KDa
SequenceString: MAAEWASRFW LWATLLIPAA AVYEDQVGKF DWRQQYVGKV KFASLEFSPG SKKLVVATEK NVIAALNSRT GEILWRHVDK GTAEGAVDA MLLHGQDVIT VSNGGRIMRS WETNIGGLNW EITLDSGSFQ ALGLVGLQES VRYIAVLKKT TLALHHLSSG H LKWVEHLP ...String:
MAAEWASRFW LWATLLIPAA AVYEDQVGKF DWRQQYVGKV KFASLEFSPG SKKLVVATEK NVIAALNSRT GEILWRHVDK GTAEGAVDA MLLHGQDVIT VSNGGRIMRS WETNIGGLNW EITLDSGSFQ ALGLVGLQES VRYIAVLKKT TLALHHLSSG H LKWVEHLP ESDSIHYQMV YSYGSGVVWA LGVVPFSHVN IVKFNVEDGE IVQQVRVSTP WLQHLSGACG VVDEAVLVCP DP SSRSLQT LALETEWELR QIPLQSLDLE FGSGFQPRVL PTQPNPVDAS RAQFFLHLSP SHYALLQYHY GTLSLLKNFP QTA LVSFAT TGEKTVAAVM ACRNEVQKSS SSEDGSMGSF SEKSSSKDSL ACFNQTYTIN LYLVETGRRL LDTTITFSLE QSGT RPERL YIQVFLKKDD SVGYRALVQT EDHLLLFLQQ LAGKVVLWSR EESLAEVVCL EMVDLPLTGA QAELEGEFGK KADGL LGMF LKRLSSQLIL LQAWTSHLWK MFYDARKPRS QIKNEINIDT LARDEFNLQK MMVMVTASGK LFGIESSSGT ILWKQY LPN VKPDSSFKLM VQRTTAHFPH PPQCTLLVKD KESGMSSLYV FNPIFGKWSQ VAPPVLKRPI LQSLLLPVMD QDYAKVL LL IDDEYKVTAF PATRNVLRQL HELAPSIFFY LVDAEQGRLC GYRLRKDLTT ELSWELTIPP EVQRIVKVKG KRSSEHVH S QGRVMGDRSV LYKSLNPNLL AVVTESTDAH HERTFIGIFL IDGVTGRIIH SSVQKKAKGP VHIVHSENWV VYQYWNTKA RRNEFTVLEL YEGTEQYNAT AFSSLDRPQL PQVLQQSYIF PSSISAMEAT ITERGITSRH LLIGLPSGAI LSLPKALLDP RRPEIPTEQ SREENLIPYS PDVQIHAERF INYNQTVSRM RGIYTAPSGL ESTCLVVAYG LDIYQTRVYP SKQFDVLKDD Y DYVLISSV LFGLVFATMI TKRLAQVKLL NRAWR

UniProtKB: ER membrane protein complex subunit 1

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Macromolecule #3: ER membrane protein complex subunit 2

MacromoleculeName: ER membrane protein complex subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.882531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKVSELYDV TWEEMRDKMR KWREENSRNS EQIVEVGEEL INEYASKLGD DIWIIYEQVM IAALDYGRDD LALFCLQELR RQFPGSHRV KRLTGMRFEA MERYDDAIQL YDRILQEDPT NTAARKRKIA IRKAQGKNVE AIRELNEYLE QFVGDQEAWH E LAELYINE ...String:
MAKVSELYDV TWEEMRDKMR KWREENSRNS EQIVEVGEEL INEYASKLGD DIWIIYEQVM IAALDYGRDD LALFCLQELR RQFPGSHRV KRLTGMRFEA MERYDDAIQL YDRILQEDPT NTAARKRKIA IRKAQGKNVE AIRELNEYLE QFVGDQEAWH E LAELYINE HDYAKAAFCL EELMMTNPHN HLYCQQYAEV KYTQGGLENL ELSRKYFAQA LKLNNRNMRA LFGLYMSASH IA SNPKASA KTKKDNMKYA SWAASQINRA YQFAGRSKKE TKYSLKAVED MLETLQITQS

UniProtKB: ER membrane protein complex subunit 2

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Macromolecule #4: ER membrane protein complex subunit 3

MacromoleculeName: ER membrane protein complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.981924 KDa
SequenceString: MAGPELLLDS NIRLWVVLPI VIITFFVGMI RHYVSILLQS DKKLTQEQVS DSQVLIRSRV LRENGKYIPK QSFLTRKYYF NNPEDGFFK KTKRKVVPPS PMTDPTMLTD MMKGNVTNVL PMILIGGWIN MTFSGFVTTK VPFPLTLRFK PMLQQGIELL T LDASWVSS ...String:
MAGPELLLDS NIRLWVVLPI VIITFFVGMI RHYVSILLQS DKKLTQEQVS DSQVLIRSRV LRENGKYIPK QSFLTRKYYF NNPEDGFFK KTKRKVVPPS PMTDPTMLTD MMKGNVTNVL PMILIGGWIN MTFSGFVTTK VPFPLTLRFK PMLQQGIELL T LDASWVSS ASWYFLNVFG LRSIYSLILG QDNAADQSRM MQEQMTGAAM AMPADTNKAF KTEWEALELT DHQWALDDVE EE LMAKDLH FEGMFKKELQ TSIF

UniProtKB: ER membrane protein complex subunit 3

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Macromolecule #5: ER membrane protein complex subunit 4

MacromoleculeName: ER membrane protein complex subunit 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.104572 KDa
SequenceString:
MTAQGGLVAN RGRRFKWAIE LSGPGGGSRG RSDRGSGQGD SLYPVGYLDK QVPDTSVQET DRILVEKRCW DIALGPLKQI PMNLFIMYM AGNTISIFPT MMVCMMAWRP IQALMAISAT FKMLESSSQK FLQGLVYLIG NLMGLALAVY KCQSMGLLPT H ASDWLAFI EPPERMEFSG GGLLL

UniProtKB: ER membrane protein complex subunit 4

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Macromolecule #6: Membrane magnesium transporter 1

MacromoleculeName: Membrane magnesium transporter 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.706786 KDa
SequenceString:
MAPSLWKGLV GIGLFALAHA AFSAAQHRSY MRLTEKEDES LPIDIVLQTL LAFAVTCYGI VHIAGEFKDM DATSELKNKT FDTLRNHPS FYVFNHRGRV LFRPSDTANS SNQDALSSNT SLKLRKLESL RR

UniProtKB: ER membrane protein complex subunit 5

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Macromolecule #7: ER membrane protein complex subunit 6

MacromoleculeName: ER membrane protein complex subunit 6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.029248 KDa
SequenceString:
MAAVVAKREG PPFISEAAVR GNAAVLDYCR TSVSALSGAT AGILGLTGLY GFIFYLLASV LLSLLLILKA GRRWNKYFKS RRPLFTGGL IGGLFTYVLF WTFLYGMVHV Y

UniProtKB: ER membrane protein complex subunit 6

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Macromolecule #8: ER membrane protein complex subunit 7

MacromoleculeName: ER membrane protein complex subunit 7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.501586 KDa
SequenceString: MAAALWGFFP VLLLLLLSGD VQSSEVPGAA AEGSGGSGVG IGDRFKIEGR AVVPGVKPQD WISAARVLVD GEEHVGFLKT DGSFVVHDI PSGSYVVEVV SPAYRFDPVR VDITSKGKMR ARYVNYIKTS EVVRLPYPLQ MKSSGPPSYF IKRESWGWTD F LMNPMVMM ...String:
MAAALWGFFP VLLLLLLSGD VQSSEVPGAA AEGSGGSGVG IGDRFKIEGR AVVPGVKPQD WISAARVLVD GEEHVGFLKT DGSFVVHDI PSGSYVVEVV SPAYRFDPVR VDITSKGKMR ARYVNYIKTS EVVRLPYPLQ MKSSGPPSYF IKRESWGWTD F LMNPMVMM MVLPLLIFVL LPKVVNTSDP DMRREMEQSM NMLNSNHELP DVSEFMTRLF SSKSSGKSSS GSSKTGKSGA GK RR

UniProtKB: Endoplasmic reticulum membrane protein complex subunit 7

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Macromolecule #9: ER membrane protein complex subunit 8

MacromoleculeName: ER membrane protein complex subunit 8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.807076 KDa
SequenceString: MPGVKLTTQA YCKMVLHGAK YPHCAVNGLL VAEKQKPRKE HLPLGGPGAH HTLFVDCIPL FHGTLALAPM LEVALTLIDS WCKDHSYVI AGYYQANERV KDASPNQVAE KVASRIAEGF SDTALIMVDN TKFTMDCVAP TIHVYEHHEN RWRCRDPHHD Y CEDWPEAQ ...String:
MPGVKLTTQA YCKMVLHGAK YPHCAVNGLL VAEKQKPRKE HLPLGGPGAH HTLFVDCIPL FHGTLALAPM LEVALTLIDS WCKDHSYVI AGYYQANERV KDASPNQVAE KVASRIAEGF SDTALIMVDN TKFTMDCVAP TIHVYEHHEN RWRCRDPHHD Y CEDWPEAQ RISASLLDSR SYETLVDFDN HLDDIRNDWT NPEINKAVLH LC

UniProtKB: ER membrane protein complex subunit 8

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Macromolecule #10: Nicalin

MacromoleculeName: Nicalin / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.047145 KDa
SequenceString: MLEEAGEVLE NMLKASCLPL GFIVFLPAVL LLVAPPLPAA DAAHEFTVYR MQQYDLQGQP YGTRNAVLNT EARTMAAEVL SRRCVLMRL LDFSYEQYQK ALRQSAGAVV IILPRAMAAV PQDVVRQFME IEPEMLAMET AVPVYFAVED EALLSIYKQT Q AASASQGS ...String:
MLEEAGEVLE NMLKASCLPL GFIVFLPAVL LLVAPPLPAA DAAHEFTVYR MQQYDLQGQP YGTRNAVLNT EARTMAAEVL SRRCVLMRL LDFSYEQYQK ALRQSAGAVV IILPRAMAAV PQDVVRQFME IEPEMLAMET AVPVYFAVED EALLSIYKQT Q AASASQGS ASAAEVLLRT ATANGFQMVT SGVQSKAVSD WLIASVEGRL TGLGGEDLPT IVIVAHYDAF GVAPWLSLGA DS NGSGVSV LLELARLFSR LYTYKRTHAA YNLLFFASGG GKFNYQGTKR WLEDNLDHTD SSLLQDNVAF VLCLDTVGRG SSL HLHVSK PPREGTLQHA FLRELETVAA HQFPEVRFSM VHKRINLAED VLAWEHERFA IRRLPAFTLS HLESHRDGQR SSIM DVRSR VDSKTLTRNT RIIAEALTRV IYNLTEKGTP PDMPVFTEQM QIQQEQLDSV MDWLTNQPRA AQLVDKDSTF LSTLE HHLS RYLKDVKQHH VKADKRDPEF VFYDQLKQVM NAYRVKPAVF DLLLAVGIAA YLGMAYVAVQ HFSLLYKTVQ RLLVKA KTQ

UniProtKB: BOS complex subunit NCLN

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Macromolecule #11: BOS complex subunit NOMO2

MacromoleculeName: BOS complex subunit NOMO2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.580234 KDa
SequenceString: MLVGQGAGLL GPAVVTAAVV LLLSGVGPAH GSEDIVVGCG GFVKSDVEIN YSLIEIKLYT KHGTLKYQTD CAPNNGYFMI PLYDKGDFI LKIEPPLGWS FEPTTVELHV DGVSDICTKG GDINFVFTGF SVNGKVLSKG QPLGPAGVQV SLRNTGTEAK I QSTVTQPG ...String:
MLVGQGAGLL GPAVVTAAVV LLLSGVGPAH GSEDIVVGCG GFVKSDVEIN YSLIEIKLYT KHGTLKYQTD CAPNNGYFMI PLYDKGDFI LKIEPPLGWS FEPTTVELHV DGVSDICTKG GDINFVFTGF SVNGKVLSKG QPLGPAGVQV SLRNTGTEAK I QSTVTQPG GKFAFFKVLP GDYEILATHP TWALKEASTT VRVTNSNANA ASPLIVAGYN VSGSVRSDGE PMKGVKFLLF SS LVTKEDV LGCNVSPVPG FQPQDESLVY LCYTVSREDG SFSFYSLPSG GYTVIPFYRG ERITFDVAPS RLDFTVEHDS LKI EPVFHV MGFSVTGRVL NGPEGDGVPE AVVTLNNQIK VKTKADGSFR LENITTGTYT IHAQKEHLYF ETVTIKIAPN TPQL ADIVA TGFSVCGRIS IIRFPDTVKQ MNKYKVVLSS QDKDKSLVTV ETDAHGSFCF KAKPGTYKVQ VMVPEAETRA GLTLK PQTF PLTVTDRPVM DVAFVQFLAS VSGKVSCLDT CGDLLVTLQS LSRQGEKRSL QLSGKVNAMT FTFDNVLPGK YKISIM HED WCWKNKSLEV EVLEDDVSAV EFRQTGYMLR CSLSHAITLE FYQDGNGREN VGIYNLSKGV NRFCLSKPGV YKVTPRS CH RFEQAFYTYD TSSPSILTLT AIRHHVLGTI TTDKMMDVTV TIKSSIDSEP ALVLGPLKSV QELRREQQLA EIEARRQE R EKNGNEEGEE RMTKPPVQEM VDELQGPFSY DFSYWARSGE KITVTPSSKE LLFYPPSMEA VVSGESCPGK LIEIHGKAG LFLEGQIHPE LEGVEIVISE KGASSPLITV FTDDKGAYSV GPLHSDLEYT VTSQKEGYVL TAVEGTIGDF KAYALAGVSF EIKAEDDQP LPGVLLSLSG GLFRSNLLTQ DNGILTFSNL SPGQYYFKPM MKEFRFEPSS QMIEVQEGQN LKITITGYRT A YSCYGTVS SLNGEPEQGV AMEAVGQNDC SIYGEDTVTD EEGKFRLRGL LPGCVYHVQL KAEGNDHIER ALPHHRVIEV GN NDIDDVN IIVFRQINQF DLSGNVITSS EYLPTLWVKL YKSENLDNPI QTVSLGQSLF FHFPPLLRDG ENYVVLLDST LPR SQYDYI LPQVSFTAVG YHKHITLIFN PTRKLPEQDI AQGSYIALPL TLLVLLAGYN HDKLIPLLLQ LTSRLQGVGA LGQA ASDNS GPEDAKRQAK KQKTRRTLRL QEEFQLMWCL VPWRGTLGIH LFSSLPFASE ILLETTATCI HY

UniProtKB: BOS complex subunit NOMO2

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Macromolecule #12: Transmembrane protein 147

MacromoleculeName: Transmembrane protein 147 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.279848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTLFHFGNCF ALAYFPYFIT YKCSGLSEYN AFWKCVQAGV TYLFVQLCKM LFLATFFPTW EGGIYDFIGE FMKASVDVAD LIGLNLVMS RNAGKGEYKI MVAALGWATA ELIMSRCIPL WVGARGIEFD WKYIQMSIDS NISLVHYIVA SAQVWMITRY D LYHTFRPA ...String:
MTLFHFGNCF ALAYFPYFIT YKCSGLSEYN AFWKCVQAGV TYLFVQLCKM LFLATFFPTW EGGIYDFIGE FMKASVDVAD LIGLNLVMS RNAGKGEYKI MVAALGWATA ELIMSRCIPL WVGARGIEFD WKYIQMSIDS NISLVHYIVA SAQVWMITRY D LYHTFRPA VLLLMFLSVY KAFVMETFVH LCSLGSWAAL LARAVVTGLL ALSTLALYVA VVNVHS

UniProtKB: BOS complex subunit TMEM147

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration2.53 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMsodium chlorideNaCl
2.0 mMmagnesium acetate
1.0 mMdithiothreitol
0.0105 % (w/v)glyco-diosgenin
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
DetailsSample solubilized and purified in GDN.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 17978 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 45703
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)

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Atomic model buiding 1

Initial model
PDB IDChain

8s9s

source_name: PDB, initial_model_type: experimental model

9c7u

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9c7v:
Structure of the human BOS:human EMC complex in GDN

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