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- EMDB-25686: CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in... -

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Basic information

Entry
Database: EMDB / ID: EMD-25686
TitleCryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11
Map dataComposite map obtained by combining focused, sharpened maps. Map used for model building and refinements.
Sample
  • Complex: Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to 1x THBD and 2x fabs of human neutralizing antibodies MSL-109 and 13H11
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
KeywordsHuman Cytomegalovirus / glycoprotein complex / antibody complex / thrombomodulin / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


blood coagulation, common pathway / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / response to cAMP / response to X-ray ...blood coagulation, common pathway / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / response to cAMP / response to X-ray / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / female pregnancy / blood coagulation / transmembrane signaling receptor activity / signaling receptor activity / host cell endosome / response to lipopolysaccharide / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / external side of plasma membrane / viral envelope / calcium ion binding / symbiont entry into host cell / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / membrane / plasma membrane
Similarity search - Function
Cytomegalovirus UL128 protein / Thrombomodulin-like, EGF-like / : / Thrombomodulin like fifth domain, EGF-like / Thrombomodulin-like domain / Herpesvirus UL130, cytomegalovirus / HCMV glycoprotein pUL130 / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. ...Cytomegalovirus UL128 protein / Thrombomodulin-like, EGF-like / : / Thrombomodulin like fifth domain, EGF-like / Thrombomodulin-like domain / Herpesvirus UL130, cytomegalovirus / HCMV glycoprotein pUL130 / 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 / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Calcium-binding EGF domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / Coagulation Factor Xa inhibitory site / C-type lectin fold / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Envelope glycoprotein H / Thrombomodulin / UL128 / UL130 / Envelope glycoprotein L / UL131A
Similarity search - Component
Biological speciesHomo sapiens (human) / Human betaherpesvirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKschonsak M / Johnson MC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for HCMV Pentamer receptor recognition and antibody neutralization.
Authors: Marc Kschonsak / Matthew C Johnson / Rachel Schelling / Evan M Green / Lionel Rougé / Hoangdung Ho / Nidhi Patel / Cem Kilic / Edward Kraft / Christopher P Arthur / Alexis L Rohou / ...Authors: Marc Kschonsak / Matthew C Johnson / Rachel Schelling / Evan M Green / Lionel Rougé / Hoangdung Ho / Nidhi Patel / Cem Kilic / Edward Kraft / Christopher P Arthur / Alexis L Rohou / Laetitia Comps-Agrar / Nadia Martinez-Martin / Laurent Perez / Jian Payandeh / Claudio Ciferri /
Abstract: Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial ...Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV.
History
DepositionDec 10, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25686.png

Downloads & links

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Map

FileDownload / File: emd_25686.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map obtained by combining focused, sharpened maps. Map used for model building and refinements.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 429.04 Å		1.07 Å/pix.
x 400 pix.
= 429.04 Å		1.07 Å/pix.
x 400 pix.
= 429.04 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0726 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.47399116 - 3.5848255
Average (Standard dev.)0.0028422892 (±0.03619096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Non-sharpened, full map of overall map (not focused).

Fileemd_25686_additional_1.map
AnnotationNon-sharpened, full map of overall map (not focused).
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Additional map: Half map 1 of focused gH-gL (A) region.

Fileemd_25686_additional_10.map
AnnotationHalf map 1 of focused gH-gL (A) region.
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Additional map: Half map 2 of focused gH-gL (A) region.

Fileemd_25686_additional_11.map
AnnotationHalf map 2 of focused gH-gL (A) region.
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Additional map: Density modified map of focused gH-gL (A) map...

Fileemd_25686_additional_12.map
AnnotationDensity modified map of focused gH-gL (A) map used for generation of composite map.
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Additional map: Non-sharpened, full map of focused gH-gL (B) region.

Fileemd_25686_additional_13.map
AnnotationNon-sharpened, full map of focused gH-gL (B) region.
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Additional map: Half map 1 of focused gH-gL (B) region.

Fileemd_25686_additional_14.map
AnnotationHalf map 1 of focused gH-gL (B) region.
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Additional map: Half map 2 of focused gH-gL (B) region.

Fileemd_25686_additional_15.map
AnnotationHalf map 2 of focused gH-gL (B) region.
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Additional map: Density modified map of overall map (not focused)...

Fileemd_25686_additional_16.map
AnnotationDensity modified map of overall map (not focused) used for generation of composite map.
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Additional map: Half map 1 of overall map (not focused).

Fileemd_25686_additional_2.map
AnnotationHalf map 1 of overall map (not focused).
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Additional map: Density modified map of focused THBD-ULs map used...

Fileemd_25686_additional_3.map
AnnotationDensity modified map of focused THBD-ULs map used for generation of composite map.
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Additional map: Half map 2 of overall map (not focused).

Fileemd_25686_additional_4.map
AnnotationHalf map 2 of overall map (not focused).
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Additional map: Non-sharpened, full map of focused THBD-ULs region.

Fileemd_25686_additional_5.map
AnnotationNon-sharpened, full map of focused THBD-ULs region.
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Additional map: Half map 1 of focused THBD-ULs region.

Fileemd_25686_additional_6.map
AnnotationHalf map 1 of focused THBD-ULs region.
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Additional map: Half map 2 of focused THBD-ULs region.

Fileemd_25686_additional_7.map
AnnotationHalf map 2 of focused THBD-ULs region.
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AxesZYX

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Additional map: Density modified map of focused gH-gL (B) map...

Fileemd_25686_additional_8.map
AnnotationDensity modified map of focused gH-gL (B) map used for generation of composite map.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened, full map of focused gH-gL (A) region.

Fileemd_25686_additional_9.map
AnnotationNon-sharpened, full map of focused gH-gL (A) region.
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Sample components

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Entire : Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to...

EntireName: Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to 1x THBD and 2x fabs of human neutralizing antibodies MSL-109 and 13H11
Components
  • Complex: Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to 1x THBD and 2x fabs of human neutralizing antibodies MSL-109 and 13H11
    • Protein or peptide: Thrombomodulin
    • Protein or peptide: Envelope glycoprotein H
    • Protein or peptide: Envelope glycoprotein L
    • Protein or peptide: Envelope protein UL128
    • Protein or peptide: Envelope glycoprotein UL130
    • Protein or peptide: Envelope protein UL131A
    • Protein or peptide: Fab 13H11 heavy chain
    • Protein or peptide: Fab 13H11 light 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: Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to...

SupramoleculeName: Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to 1x THBD and 2x fabs of human neutralizing antibodies MSL-109 and 13H11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Molecular weightTheoretical: 590 KDa

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Macromolecule #1: Thrombomodulin

MacromoleculeName: Thrombomodulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.128371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGVLVLGAL ALAGLGFPAP AEPQPGGSQC VEHDCFALYP GPATFLNASQ ICDGLRGHLM TVRSSVAADV ISLLLNGDGG VGRRRLWIG LQLPPGCGDP KRLGPLRGFQ WVTGDNNTSY SRWARLDLNG APLCGPLCVA VSAAEATVPS EPIWEEQQCE V KADGFLCE ...String:
MLGVLVLGAL ALAGLGFPAP AEPQPGGSQC VEHDCFALYP GPATFLNASQ ICDGLRGHLM TVRSSVAADV ISLLLNGDGG VGRRRLWIG LQLPPGCGDP KRLGPLRGFQ WVTGDNNTSY SRWARLDLNG APLCGPLCVA VSAAEATVPS EPIWEEQQCE V KADGFLCE FHFPATCRPL AVEPGAAAAA VSITYGTPFA ARGADFQALP VGSSAAVAPL GLQLMCTAPP GAVQGHWARE AP GAWDCSV ENGGCEHACN AIPGAPRCQC PAGAALQADG RSCTASATQS CNDLCEHFCV PNPDQPGSYS CMCETGYRLA ADQ HRCEDV DDCILEPSPC PQRCVNTQGG FECHCYPNYD LVDGECVEPV DPCFRANCEY QCQPLNQTSY LCVCAEGFAP IPHE PHRCQ MFCNQTACPA DCDPNTQASC ECPEGYILDD GFICTDIDEC ENGGFCSGVC HNLPGTFECI CGPDSALARH IGTDC DSGK VDGGDSGSGE PPPSPTPGST LTPPAVGLVH SGGNSDYKDD DDK

UniProtKB: Thrombomodulin

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Macromolecule #2: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
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 #3: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
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 #4: Envelope protein UL128

MacromoleculeName: Envelope protein UL128 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 19.746023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSPKNLTPFL TALWLLLGHS RVPRVRAEEC CEFINVNHPP ERCYDFKMCN RFTVALRCPD GEVCYSPEKT AEIRGIVTTM THSLTRQVV HNKLTSCNYN PLYLEADGRI RCGKVNDKAQ YLLGAAGSVP YRWINLEYDK ITRIVGLDQY LESVKKHKRL D VCRAKMGY MLQ

UniProtKB: UL128

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Macromolecule #5: Envelope glycoprotein UL130

MacromoleculeName: Envelope glycoprotein UL130 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 28.866811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLRLLLRHHF HCLLLCAVWA TPCLASPWFT LTANQNPSPP WSKLTYPKPH DAATFYCPFL YPSPPRSPSQ FSGFQRVSTG PECRNETLY LLYNREGQTL VERSSTWVKK VIWYLSGRNQ TILQRMPRTA SKPSDGNVQI SVEDAKIFGA HMVPKQTKLL R FVVNDGTR ...String:
MLRLLLRHHF HCLLLCAVWA TPCLASPWFT LTANQNPSPP WSKLTYPKPH DAATFYCPFL YPSPPRSPSQ FSGFQRVSTG PECRNETLY LLYNREGQTL VERSSTWVKK VIWYLSGRNQ TILQRMPRTA SKPSDGNVQI SVEDAKIFGA HMVPKQTKLL R FVVNDGTR YQMCVMKLES WAHVFRDYSV SFQVRLTFTE ANNQTYTFCT HPNLIVGSEN LYFQGSAWSH PQFEKGGGSG GG SGGGSAW SHPQFEK

UniProtKB: UL130

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Macromolecule #6: Envelope protein UL131A

MacromoleculeName: Envelope protein UL131A / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human betaherpesvirus 5
Molecular weightTheoretical: 15.011043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MRLCRVWLSV CLCAVVLGQC QRETAEKNDY YRVPHYWDAC SRALPDQTRY KYVEQLVDLT LNYHYDASHG LDNFDVLKRI NVTEVSLLI SDFRRQNRRG GTNKRTTFNA AGSLAPHARS LEFSVRLFAN

UniProtKB: UL131A

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Macromolecule #7: Fab 13H11 heavy chain

MacromoleculeName: Fab 13H11 heavy chain / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #8: Fab 13H11 light chain

MacromoleculeName: Fab 13H11 light chain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / 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 #9: Fab MSL-109 light chain

MacromoleculeName: Fab MSL-109 light chain / type: protein_or_peptide / ID: 9 / Number of copies: 2 / 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 #10: Fab MSL-109 heavy chain

MacromoleculeName: Fab MSL-109 heavy chain / type: protein_or_peptide / ID: 10 / Number of copies: 2 / 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: 14 / 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

Concentration0.6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
25.0 mMHEPESHEPES
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300
Details: The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, ...Details: The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, Inc., Bozeman, MT)[23]. Grids were incubated with this self-assembled, monolayer (SAM) solution for 24 hours. Prior to grid freezing, grids were removed from the SAM solution and rinsed with EtOH.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP / Details: blot for 3.5s before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10926 / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 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

DetailsMovie frames were corrected for motion and aligned. Images with a CTF fit resolution of 5.0 A or better were selected for particle picking.
Particle selectionNumber selected: 10680163
Startup modelType of model: OTHER / Details: ab-initio using C2 symmetry in cisTEM
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02)
Details: A composite map was generated from the three individual focused 3D maps.
Number images used: 504492
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: OTHER
Details: Manual refine in cisTEM. Map was divided in 3 sections to refine map with focused refinements.
Final 3D classificationNumber classes: 27 / Software - Name: RELION (ver. 3.1)

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