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- EMDB-23254: CryoEM structure of the HCMV Trimer gHgLgO in complex with human ... -

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Basic information

Entry
Database: EMDB / ID: EMD-23254
TitleCryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth factor beta receptor type 3 and neutralizing fabs 13H11 and MSL-109
Map dataComposite map of Trimer-TGFBR3 complex bound to fabs 13H11 and Msl-109 used for model refinements
Sample
  • Complex: HCMV Trimer gHgLgO bound to human receptor TGFbR3 and neutralizing fabs 13H11 and MSL-109
    • Complex: HCMV Trimer gHgLgO
      • Protein or peptide: Envelope glycoprotein H
      • Protein or peptide: Envelope glycoprotein L
      • Protein or peptide: Envelope glycoprotein O
    • Complex: neutralizing fabs 13H11 and MSL-109
      • Protein or peptide: Transforming growth factor beta receptor type 3
      • Protein or peptide: Fab 13H11 light chain
      • Protein or peptide: Fab 13H11 heavy chain
      • Protein or peptide: Fab MSL-109 light chain
      • Protein or peptide: Fab MSL-109 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / transforming growth factor beta receptor complex assembly / : / inhibin-betaglycan-ActRII complex / definitive erythrocyte differentiation / muscular septum morphogenesis / response to follicle-stimulating hormone ...: / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / transforming growth factor beta receptor complex assembly / : / inhibin-betaglycan-ActRII complex / definitive erythrocyte differentiation / muscular septum morphogenesis / response to follicle-stimulating hormone / response to prostaglandin E / vasculogenesis involved in coronary vascular morphogenesis / transforming growth factor beta receptor activity / secondary palate development / ventricular compact myocardium morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / regulation of protein binding / heart trabecula morphogenesis / activin binding / heart trabecula formation / glycosaminoglycan binding / transforming growth factor beta binding / definitive hemopoiesis / cardiac muscle cell proliferation / ventricular cardiac muscle tissue morphogenesis / ventricular septum morphogenesis / fibroblast growth factor binding / outflow tract morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / plasma membrane => GO:0005886 / epithelial to mesenchymal transition / vasculogenesis / BMP signaling pathway / animal organ regeneration / coreceptor activity / heart morphogenesis / positive regulation of cardiac muscle cell proliferation / extracellular matrix / transforming growth factor beta receptor signaling pathway / host cell endosome membrane / HCMV Late Events / liver development / PDZ domain binding / negative regulation of transforming growth factor beta receptor signaling pathway / HCMV Early Events / negative regulation of epithelial cell proliferation / cell migration / heparin binding / host cell Golgi apparatus / angiogenesis / entry receptor-mediated virion attachment to host cell / response to hypoxia / receptor complex / intracellular signal transduction / immune response / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / external side of plasma membrane / viral envelope / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain ...Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Envelope glycoprotein L / Transforming growth factor beta receptor type 3 / Envelope glycoprotein H / Envelope glycoprotein O
Similarity search - Component
Biological speciesHuman cytomegalovirus HHV-5 / Homo sapiens (human) / Human cytomegalovirus (strain Merlin) / Human cytomegalovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKschonsak M / Rouge L / Arthur CP / Hoangdung H / Patel N / Kim I / Johnson M / Kraft E / Rohou AL / Gill A ...Kschonsak M / Rouge L / Arthur CP / Hoangdung H / Patel N / Kim I / Johnson M / Kraft E / Rohou AL / Gill A / Martinez-Martin N / Payandeh J / Ciferri C
CitationJournal: Cell / Year: 2021
Title: Structures of HCMV Trimer reveal the basis for receptor recognition and cell entry.
Authors: Marc Kschonsak / Lionel Rougé / Christopher P Arthur / Ho Hoangdung / Nidhi Patel / Ingrid Kim / Matthew C Johnson / Edward Kraft / Alexis L Rohou / Avinash Gill / Nadia Martinez-Martin / ...Authors: Marc Kschonsak / Lionel Rougé / Christopher P Arthur / Ho Hoangdung / Nidhi Patel / Ingrid Kim / Matthew C Johnson / Edward Kraft / Alexis L Rohou / Avinash Gill / Nadia Martinez-Martin / Jian Payandeh / Claudio Ciferri /
Abstract: Human cytomegalovirus (HCMV) infects the majority of the human population and represents the leading viral cause of congenital birth defects. HCMV utilizes the glycoproteins gHgLgO (Trimer) to bind ...Human cytomegalovirus (HCMV) infects the majority of the human population and represents the leading viral cause of congenital birth defects. HCMV utilizes the glycoproteins gHgLgO (Trimer) to bind to platelet-derived growth factor receptor alpha (PDGFRα) and transforming growth factor beta receptor 3 (TGFβR3) to gain entry into multiple cell types. This complex is targeted by potent neutralizing antibodies and represents an important candidate for therapeutics against HCMV. Here, we determine three cryogenic electron microscopy (cryo-EM) structures of the trimer and the details of its interactions with four binding partners: the receptor proteins PDGFRα and TGFβR3 as well as two broadly neutralizing antibodies. Trimer binding to PDGFRα and TGFβR3 is mutually exclusive, suggesting that they function as independent entry receptors. In addition, Trimer-PDGFRα interaction has an inhibitory effect on PDGFRα signaling. Our results provide a framework for understanding HCMV receptor engagement, neutralization, and the development of anti-viral strategies against HCMV.
History
DepositionJan 7, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lbg
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lbg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23254.png

Downloads & links

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Map

FileDownload / File: emd_23254.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of Trimer-TGFBR3 complex bound to fabs 13H11 and Msl-109 used for model refinements
Voxel sizeX=Y=Z: 1.1948 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-24.22022 - 47.461575
Average (Standard dev.)-0.026720036 (±0.7627732)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 353.6608 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.19480067567571.19480067567571.1948006756757
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z353.661353.661353.661
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ296296296
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS296296296
D min/max/mean-24.22047.462-0.027

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Supplemental data

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Additional map: Overall Trimer-TGFBR3-13H11-MSL109 map before focussed refinements, non-sharpened used...

Fileemd_23254_additional_1.map
AnnotationOverall Trimer-TGFBR3-13H11-MSL109 map before focussed refinements, non-sharpened used for composite map generation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focussed map on gO, gL, TGFBR3-OD2 domain, sharpened...

Fileemd_23254_additional_2.map
AnnotationFocussed map on gO, gL, TGFBR3-OD2 domain, sharpened used for composite map generation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focussed map on gH and Fv regions of...

Fileemd_23254_additional_3.map
AnnotationFocussed map on gH and Fv regions of both fabs, sharpened used for composite map generation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focussed map on gO, gL, TGFBR3-OD2 domain, non-sharpened

Fileemd_23254_additional_4.map
AnnotationFocussed map on gO, gL, TGFBR3-OD2 domain, non-sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focussed map on gH and Fv regions of both fabs, non-sharpened

Fileemd_23254_additional_5.map
AnnotationFocussed map on gH and Fv regions of both fabs, non-sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HCMV Trimer gHgLgO bound to human receptor TGFbR3 and neutralizin...

EntireName: HCMV Trimer gHgLgO bound to human receptor TGFbR3 and neutralizing fabs 13H11 and MSL-109
Components
  • Complex: HCMV Trimer gHgLgO bound to human receptor TGFbR3 and neutralizing fabs 13H11 and MSL-109
    • Complex: HCMV Trimer gHgLgO
      • Protein or peptide: Envelope glycoprotein H
      • Protein or peptide: Envelope glycoprotein L
      • Protein or peptide: Envelope glycoprotein O
    • Complex: neutralizing fabs 13H11 and MSL-109
      • Protein or peptide: Transforming growth factor beta receptor type 3
      • Protein or peptide: Fab 13H11 light chain
      • Protein or peptide: Fab 13H11 heavy chain
      • Protein or peptide: Fab MSL-109 light chain
      • Protein or peptide: Fab MSL-109 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCMV Trimer gHgLgO bound to human receptor TGFbR3 and neutralizin...

SupramoleculeName: HCMV Trimer gHgLgO bound to human receptor TGFbR3 and neutralizing fabs 13H11 and MSL-109
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 360 KDa

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Supramolecule #2: HCMV Trimer gHgLgO

SupramoleculeName: HCMV Trimer gHgLgO / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Human cytomegalovirus HHV-5
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: neutralizing fabs 13H11 and MSL-109

SupramoleculeName: neutralizing fabs 13H11 and MSL-109 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus (strain Merlin) / Strain: Merlin
Molecular weightTheoretical: 87.311273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPGLPSYLI ILAVCLFSHL LSSRYGAEAV SEPLDKAFHL LLNTYGRPIR FLRENTTQCT YNSSLRNSTV VRENAISFNF FQSYNQYYV FHMPRCLFAG PLAEQFLNQV DLTETLERYQ QRLNTYALVS KDLASYRSFS QQLKAQDSLG EQPTTVPPPI D LSIPHVWM ...String:
MRPGLPSYLI ILAVCLFSHL LSSRYGAEAV SEPLDKAFHL LLNTYGRPIR FLRENTTQCT YNSSLRNSTV VRENAISFNF FQSYNQYYV FHMPRCLFAG PLAEQFLNQV DLTETLERYQ QRLNTYALVS KDLASYRSFS QQLKAQDSLG EQPTTVPPPI D LSIPHVWM PPQTTPHGWT ESHTTSGLHR PHFNQTCILF DGHDLLFSTV TPCLHQGFYL IDELRYVKIT LTEDFFVVTV SI DDDTPML LIFGHLPRVL FKAPYQRDNF ILRQTEKHEL LVLVKKDQLN RHSYLKDPDF LDAALDFNYL DLSALLRNSF HRY AVDVLK SGRCQMLDRR TVEMAFAYAL ALFAAARQEE AGAQVSVPRA LDRQAALLQI QEFMITCLSQ TPPRTTLLLY PTAV DLAKR ALWTPNQITD ITSLVRLVYI LSKQNQQHLI PQWALRQIAD FALKLHKTHL ASFLSAFARQ ELYLMGSLVH SMLVH TTER REIFIVETGL CSLAELSHFT QLLAHPHHEY LSDLYTPCSS SGRRDHSLER LTRLFPDATV PATVPAALSI LSTMQP STL ETFPDLFCLP LGESFSALTV SEHVSYIVTN QYLIKGISYP VSTTVVGQSL IITQTDSQTK CELTRNMHTT HSITVAL NI SLENCAFCQS ALLEYDDTQG VINIMYMHDS DDVLFALDPY NEVVVSSPRT HYLMLLKNGT VLEVTDVVVD ATDGTKLG P EQKLISEEDL NSAVDGSGLN DIFEAQKIEW HENLYFQGHH HHHHHH

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Macromolecule #2: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus (strain Merlin) / Strain: Merlin
Molecular weightTheoretical: 30.846492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCRRPDCGFS FSPGPVILLW CCLLLPIVSS AAVSVAPTAA EKVPAECPEL TRRCLLGEVF EGDKYESWLR PLVNVTGRDG PLSQLIRYR PVTPEAANSV LLDEAFLDTL ALLYNNPDQL RALLTLLSSD TAPRWMTVMR GYSECGDGSP AVYTCVDDLC R GYDLTRLS ...String:
MCRRPDCGFS FSPGPVILLW CCLLLPIVSS AAVSVAPTAA EKVPAECPEL TRRCLLGEVF EGDKYESWLR PLVNVTGRDG PLSQLIRYR PVTPEAANSV LLDEAFLDTL ALLYNNPDQL RALLTLLSSD TAPRWMTVMR GYSECGDGSP AVYTCVDDLC R GYDLTRLS YGRSIFTEHV LGFELVPPSL FNVVVAIRNE ATRTNRAVRL PVSTAAAPEG ITLFYGLYNA VKEFCLRHQL DP PLLRHLD KYYAGLPPEL KQTRVNLPAH SRYGPQAVDA R

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Macromolecule #3: Envelope glycoprotein O

MacromoleculeName: Envelope glycoprotein O / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus
Molecular weightTheoretical: 58.298504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRKEDMRSI SKLFFIISLT VLLFSIINCK VVRPPGRYWL GTVLSTIGKQ KLDKFKLEIL KQLEREPYTK YFNMTRQHVK NLTMNMTQF PQYYILAGPI RNDSITYLWF DFYSTQLRKP AKYVYSQYNH TAKTITFRPP SCGTVPSMTC LSEMLNVSKR N DTGEQGCG ...String:
MGRKEDMRSI SKLFFIISLT VLLFSIINCK VVRPPGRYWL GTVLSTIGKQ KLDKFKLEIL KQLEREPYTK YFNMTRQHVK NLTMNMTQF PQYYILAGPI RNDSITYLWF DFYSTQLRKP AKYVYSQYNH TAKTITFRPP SCGTVPSMTC LSEMLNVSKR N DTGEQGCG NFTTFNPMFF NVPRWNTKLY VGPTKVNVDS QTIYFLGLTA LLLRYAQRNC THSFYLVNAM SRNLFRVPKY IN GTKLKNT MRKLKRKQAP VKEQLEKKTK KSQSTTTPYF SYTTSTALNV TTNATYRVTT SAKRIPTSTI AYRPDSSFMK SIM ATQLRD LATWVYTTLR YRNEPFCKPD RNRTAVSEFM KNTHVLIRNE TPYTIYGTLD MSSLYYNETM SVENETASDN NETT PTSPS TRFQKTFIDP LWDYLDSLLF LDKIRNFSLQ LPAYGNLTPP EHRRAVNLST LNSLWWWLQG SENLYFQGSA WSHPQ FEKG GGSGGGSGGG SAWSHPQFEK

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Macromolecule #4: Transforming growth factor beta receptor type 3

MacromoleculeName: Transforming growth factor beta receptor type 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.362203 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTSHYVIAIF ALMSSCLATA GPEPGALCEL SPVSASHPVQ ALMESFTVLS GCASRGTTGL PQEVHVLNLR TAGQGPGQLQ REVTLHLNP ISSVHIHHKS VVFLLNSPHP LVWHLKTERL ATGVSRLFLV SEGSVVQFSS ANFSLTAETE ERNFPHGNEH L LNWARKEY ...String:
MTSHYVIAIF ALMSSCLATA GPEPGALCEL SPVSASHPVQ ALMESFTVLS GCASRGTTGL PQEVHVLNLR TAGQGPGQLQ REVTLHLNP ISSVHIHHKS VVFLLNSPHP LVWHLKTERL ATGVSRLFLV SEGSVVQFSS ANFSLTAETE ERNFPHGNEH L LNWARKEY GAVTSFTELK IARNIYIKVG EDQVFPPKCN IGKNFLSLNY LAEYLQPKAA EGCVMSSQPQ NEEVHIIELI TP NSNPYSA FQVDITIDIR PSQEDLEVVK NLILILKCKK SVNWVIKSFD VKGSLKIIAP NSIGFGKESE RSMTMTKSIR DDI PSTQGN LVKWALDNGY SPITSYTMAP VANRFHLRLE NNAEEMGDEE VHTIPPELRI LLDPGALPAL QNPPIRGGEG QNGG LPFPF PDISRRVWNE EGEDGLPRPK DPVIPSIQLF PGLREPEEVQ GSVDIALSVK CDNEKMIVAV EKDSFQASGY SGMDV TLLD PTCKAKMNGT HFVLESPLNG CGTRPRWSAL DGVVYYNSIV IQVPALGDSS GWPDGYEDLE SGDNGFPGDM DEGDAS LFT RPEIVVFNCS LQQVRNPSSF QEQPHGNITF NMELYNTDLF LVPSQGVFSV PENGHVYVEV SVTKAEQELG FAIQTCF IS PYSNPDRMSH YTIIENICPK DESVKFYSPK RVHFPIPQAD MDKKRFSFVF KPVFNTSLLF LQCELTLCTK MEKHPQKL P KCVPPDEACT SLDASIIWAM MQNKKTFTKP LAVIHHEAES KEKGPSMKEP NPISPPIFHG HHHHHH

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Macromolecule #5: Fab 13H11 light chain

MacromoleculeName: Fab 13H11 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.78002 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYADIQMTQS PSSLSASVGD RVTITCRASQ GINNYLAWYQ QKPGKVPKLL IYAASTLQSG VPSRFSGSG SGTAFTLTIL SLQPEDVATY YCQKYNSAPF TFGPGTKVDI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK ...String:
MKKNIAFLLA SMFVFSIATN AYADIQMTQS PSSLSASVGD RVTITCRASQ GINNYLAWYQ QKPGKVPKLL IYAASTLQSG VPSRFSGSG SGTAFTLTIL SLQPEDVATY YCQKYNSAPF TFGPGTKVDI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #6: Fab 13H11 heavy chain

MacromoleculeName: Fab 13H11 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.600086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAQVQLVQS GAEVKKPGAS VKVSCKASGY TFTNYYIHWV RQAPGQGLEW MGIIHPSSGG TSYAQKFQG RVTMTRDTST STVSMDLSSL RSEDTAVYYC GRAFRILGLS DVFVNDWGQG TVVTVSSAST KGPSVFPLAP S SKSTSGGT ...String:
MKKNIAFLLA SMFVFSIATN AYAQVQLVQS GAEVKKPGAS VKVSCKASGY TFTNYYIHWV RQAPGQGLEW MGIIHPSSGG TSYAQKFQG RVTMTRDTST STVSMDLSSL RSEDTAVYYC GRAFRILGLS DVFVNDWGQG TVVTVSSAST KGPSVFPLAP S SKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KV DKKVEPK SCD

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Macromolecule #7: Fab MSL-109 light chain

MacromoleculeName: Fab MSL-109 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.355809 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYADIVMTQS PLSLSVTPGE PASISCRSSQ SLLHTNGYNY LDWYVQKPGQ SPQLLIYLAS NRASGVPDR FSGSGSGTDF TLKISRVETE DVGVYYCMQA LQIPRTFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS V VCLLNNFY ...String:
MKKNIAFLLA SMFVFSIATN AYADIVMTQS PLSLSVTPGE PASISCRSSQ SLLHTNGYNY LDWYVQKPGQ SPQLLIYLAS NRASGVPDR FSGSGSGTDF TLKISRVETE DVGVYYCMQA LQIPRTFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS V VCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RG ECGLNDI FEAQKIEWHE

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Macromolecule #8: Fab MSL-109 heavy chain

MacromoleculeName: Fab MSL-109 heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.547818 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAEEQVLES GGGLVKPGGS LRLSCAASGF TFSPYSVFWV RQAPGKGLEW VSSINSDSTY KYYADSVKG RFTISRDNAE NSIFLQMNSL RAEDTAVYYC ARDRSYYAFS SGSLSDYYYG LDVWGQGTLV TVSSASTKGP S VFPLAPSS ...String:
MKKNIAFLLA SMFVFSIATN AYAEEQVLES GGGLVKPGGS LRLSCAASGF TFSPYSVFWV RQAPGKGLEW VSSINSDSTY KYYADSVKG RFTISRDNAE NSIFLQMNSL RAEDTAVYYC ARDRSYYAFS SGSLSDYYYG LDVWGQGTLV TVSSASTKGP S VFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NH KPSNTKV DKKVEPKSCD

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 17 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.3 MNaClSodium chloridesodium chloride
0.025 MHEPES
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: blot for 3.5 seconds before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 19993 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in 50 frames every 0.2 s
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2780519
CTF correctionSoftware - Name: CTFFIND / Software - details: 4.1.13
Startup modelType of model: OTHER
Details: EM map of HCMV Trimer-13H11-Msl109 used as starting reference
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02)
Final 3D classificationNumber classes: 200 / Software - Name: RELION (ver. 3.1) / Details: selected 148 of 200 classes
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02)
Details: Used a score threshold of 0.25 for final 3D reconstruction. Map used for model refinements is a composite map after combining 2 focussed maps with PHENIX
Number images used: 2737199

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7lbg:
CryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth factor beta receptor type 3 and neutralizing fabs 13H11 and MSL-109

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