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- EMDB-23253: CryoEM structure of the HCMV Trimer gHgLgO in complex with human ... -

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Basic information

Entry
Database: EMDB / ID: EMD-23253
TitleCryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109
Map dataComposite map of HCMV Trimer-PDGFRa with fabs 13H11 and Msl-109 used for model building
Sample
  • Complex: HCMV Trimer gHgLgO bound to human receptor PDGFRa 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: PDGFRa and neutralizing fabs 13H11 and MSL-109
      • Protein or peptide: Isoform 3 of Platelet-derived growth factor receptor alpha
      • 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
Keywordsvirus / receptor / complex / neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / platelet-derived growth factor receptor-ligand complex / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization ...Imatinib-resistant PDGFR mutants / Sunitinib-resistant PDGFR mutants / Regorafenib-resistant PDGFR mutants / Sorafenib-resistant PDGFR mutants / PDGFR mutants bind TKIs / platelet-derived growth factor receptor-alpha signaling pathway / platelet-derived growth factor receptor-ligand complex / metanephric glomerular capillary formation / regulation of mesenchymal stem cell differentiation / luteinization / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / vascular endothelial growth factor binding / embryonic skeletal system morphogenesis / retina vasculature development in camera-type eye / embryonic digestive tract morphogenesis / Leydig cell differentiation / cardiac myofibril assembly / Signaling by PDGF / cell activation / male genitalia development / positive regulation of chemotaxis / phospholipase C activator activity / embryonic cranial skeleton morphogenesis / platelet-derived growth factor receptor binding / signal transduction involved in regulation of gene expression / face morphogenesis / estrogen metabolic process / adrenal gland development / odontogenesis of dentin-containing tooth / roof of mouth development / microvillus / platelet-derived growth factor receptor signaling pathway / white fat cell differentiation / negative regulation of platelet activation / hematopoietic progenitor cell differentiation / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / transmembrane receptor protein tyrosine kinase activity / extracellular matrix organization / Downstream signal transduction / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / host cell endosome membrane / HCMV Late Events / cell chemotaxis / cellular response to reactive oxygen species / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / lung development / wound healing / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / platelet aggregation / HCMV Early Events / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / cell junction / cell migration / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein autophosphorylation / host cell Golgi apparatus / in utero embryonic development / entry receptor-mediated virion attachment to host cell / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / nuclear body / cilium / positive regulation of cell migration / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / positive regulation of cell population proliferation / viral envelope / endoplasmic reticulum membrane / protein-containing complex binding / host cell plasma membrane / virion membrane / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Platelet-derived growth factor receptor alpha / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily ...Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Platelet-derived growth factor receptor alpha / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / 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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Envelope glycoprotein L / Platelet-derived growth factor receptor alpha / Envelope glycoprotein H / Envelope glycoprotein O
Similarity search - Component
Biological speciesHuman cytomegalovirus / Homo sapiens (human) / Human cytomegalovirus (strain Merlin)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKschonsak M / Rouge L
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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lbf
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lbf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23253.png

Downloads & links

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Map

FileDownload / File: emd_23253.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of HCMV Trimer-PDGFRa with fabs 13H11 and Msl-109 used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.35 Å/pix.
x 264 pix.
= 356.77 Å		1.35 Å/pix.
x 264 pix.
= 356.77 Å		1.35 Å/pix.
x 264 pix.
= 356.77 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3514 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2 / Movie #1: 3.2
Minimum - Maximum-21.646014999999998 - 52.082053999999999
Average (Standard dev.)-0.032921784 (±0.6735747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 356.7696 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.35140151515151.35140151515151.3514015151515
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z356.770356.770356.770
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ264264264
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-21.64652.082-0.033

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Supplemental data

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Additional map: Focussed map of gL and part. gH region,...

Fileemd_23253_additional_1.map
AnnotationFocussed map of gL and part. gH region, 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 of PDGFRa and gO region, sharpened...

Fileemd_23253_additional_2.map
AnnotationFocussed map of PDGFRa and gO region, 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: Overall map of Trimer-PDGFRa bound to 2 fabs...

Fileemd_23253_additional_3.map
AnnotationOverall map of Trimer-PDGFRa bound to 2 fabs 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 of part. gH and Fv regions...

Fileemd_23253_additional_4.map
AnnotationFocussed map of part. 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 of part. gH and Fv regions of both fabs, non-sharpened

Fileemd_23253_additional_5.map
AnnotationFocussed map of part. 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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Additional map: Focussed map of gL and part. gH region, non-sharpened

Fileemd_23253_additional_6.map
AnnotationFocussed map of gL and part. gH region, non-sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focussed map of PDGFRa and gO region, non-sharpened

Fileemd_23253_additional_7.map
AnnotationFocussed map of PDGFRa and gO region, 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 PDGFRa and neutralizin...

EntireName: HCMV Trimer gHgLgO bound to human receptor PDGFRa and neutralizing fabs 13H11 and MSL-109
Components
  • Complex: HCMV Trimer gHgLgO bound to human receptor PDGFRa 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: PDGFRa and neutralizing fabs 13H11 and MSL-109
      • Protein or peptide: Isoform 3 of Platelet-derived growth factor receptor alpha
      • 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 PDGFRa and neutralizin...

SupramoleculeName: HCMV Trimer gHgLgO bound to human receptor PDGFRa and neutralizing fabs 13H11 and MSL-109
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 335 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

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

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

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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

UniProtKB: Envelope glycoprotein H

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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

UniProtKB: Envelope glycoprotein L

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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

UniProtKB: Envelope glycoprotein O

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Macromolecule #4: Isoform 3 of Platelet-derived growth factor receptor alpha

MacromoleculeName: Isoform 3 of Platelet-derived growth factor receptor alpha
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.15466 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSS ASAAHTGLYT CYYNHTQTEE NELEGRHIYI YVPDPDVAFV PLGMTDYLVI VEDDDSAIIP CRTTDPETPV T LHNSEGVV ...String:
MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSS ASAAHTGLYT CYYNHTQTEE NELEGRHIYI YVPDPDVAFV PLGMTDYLVI VEDDDSAIIP CRTTDPETPV T LHNSEGVV PASYDSRQGF NGTFTVGPYI CEATVKGKKF QTIPFNVYAL KATSELDLEM EALKTVYKSG ETIVVTCAVF NN EVVDLQW TYPGEVKGKG ITMLEEIKVP SIKLVYTLTV PEATVKDSGD YECAARQATR EVKEMKKVTI SVHEKGFIEI KPT FSQLEA VNLHEVKHFV VEVRAYPPPR ISWLKNNLTL IENLTEITTD VEKIQEIRYR SKLKLIRAKE EDSGHYTIVA QNED AVKSY TFELLTQVPS SILDLVDDHH GSTGGQTVRC TAEGTPLPDI EWMICKDIKK CNNETSWTIL ANNVSNIITE IHSRD RSTV EGRVTFAKVE ETIAVRCLAK NLLGAENREL KLVAPTLRSE DDDDK

UniProtKB: Platelet-derived growth factor receptor alpha

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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: 18 / 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 state2D array

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.3 MNaClsodium chloride
0.025 MHEPES

Details: The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5
GridModel: C-flat-1.2/1.3 / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Details: The grid was coated with Au/Pd 80/20 prior use.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.5 seconds before plunging.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 2 / Number real images: 34829 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in 50 frames every 0.2 s
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
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

Particle selectionNumber selected: 4151085
Startup modelType of model: OTHER
Details: EM map of HCMV Trimer-13H11-Msl109 used as starting reference
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02)
Details: Used score threshold of 0.25 for final 3D reconstruction. Map used for model refinements is a composite map after combining 3 focussed maps with PHENIX
Number images used: 3560620
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.02)
Final 3D classificationNumber classes: 100 / Software - Name: RELION (ver. 3.1) / Details: selected 50 of 100 classes

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7lbf:
CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109

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