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- EMDB-25685: CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in... -

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Basic information

Entry
Database: EMDB / ID: EMD-25685
TitleCryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11
Map dataComposite map generated by combining focused refined maps. Map used for model refinements
Sample
  • Complex: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11
    • Protein or peptide: x 11 types
  • Ligand: x 1 types
KeywordsHuman Cytomegalovirus / glycoprotein complex / antibody complex / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
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
Similarity search - Domain/homology
Envelope glycoprotein H / UL128 / UL130 / Envelope glycoprotein L / UL131A
Similarity search - Component
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_25685.png

Downloads & links

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Map

FileDownload / File: emd_25685.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map generated by combining focused refined maps. Map used for model refinements
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.19 Å/pix.
x 320 pix.
= 382.336 Å		1.19 Å/pix.
x 320 pix.
= 382.336 Å		1.19 Å/pix.
x 320 pix.
= 382.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1948 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.9
Minimum - Maximum-15.368733000000001 - 30.294058
Average (Standard dev.)-0.025309997 (±0.59128356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 382.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Half map 2 of focused refinement on 2C12, 7I13, UL region.

Fileemd_25685_additional_1.map
AnnotationHalf map 2 of focused refinement on 2C12, 7I13, UL region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of focused refinement on gH and...

Fileemd_25685_additional_10.map
AnnotationSharpened map of focused refinement on gH and 13H11 region. Used for composite map generation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened map of focused refinement on gH and 13H11 region.

Fileemd_25685_additional_11.map
AnnotationNon-sharpened map of focused refinement on gH and 13H11 region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map 2 of focused refinement on gH and 13H11 region.

Fileemd_25685_additional_12.map
AnnotationHalf map 2 of focused refinement on gH and 13H11 region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map 1 of focused refinement on gH and 13H11 region.

Fileemd_25685_additional_13.map
AnnotationHalf map 1 of focused refinement on gH and 13H11 region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of focused refinement on gL region....

Fileemd_25685_additional_2.map
AnnotationSharpened map of focused refinement on gL region. Used for composite map generation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map 2 of focused refinement on gL region.

Fileemd_25685_additional_3.map
AnnotationHalf map 2 of focused refinement on gL region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of focused refinement on 2C12, 7I13,...

Fileemd_25685_additional_4.map
AnnotationSharpened map of focused refinement on 2C12, 7I13, UL region. Used for composite map generation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened map of focused refinement on gL region.

Fileemd_25685_additional_5.map
AnnotationNon-sharpened map of focused refinement on gL region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened map of overall (non-focused) refinement.

Fileemd_25685_additional_6.map
AnnotationNon-sharpened map of overall (non-focused) refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map 1 of focused refinement on gL region.

Fileemd_25685_additional_7.map
AnnotationHalf map 1 of focused refinement on gL region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened map of focused refinement on 2C12, 7I13, UL region.

Fileemd_25685_additional_8.map
AnnotationNon-sharpened map of focused refinement on 2C12, 7I13, UL region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map 1 of focused refinement on 2C12, 7I13, UL region.

Fileemd_25685_additional_9.map
AnnotationHalf map 1 of focused refinement on 2C12, 7I13, UL region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A ...

EntireName: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11
Components
  • Complex: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11
    • 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 2C12 heavy chain
    • Protein or peptide: Fab 2C12 light chain
    • Protein or peptide: Fab 7I13 light chain
    • Protein or peptide: Fab 7I13 heavy chain
    • Protein or peptide: Fab 13H11 heavy chain
    • Protein or peptide: Fab 13H11 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A ...

SupramoleculeName: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Molecular weightTheoretical: 320 KDa

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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 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 #2: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: Envelope protein UL128

MacromoleculeName: Envelope protein UL128 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: Envelope glycoprotein UL130

MacromoleculeName: Envelope glycoprotein UL130 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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 #5: Envelope protein UL131A

MacromoleculeName: Envelope protein UL131A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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 #6: Fab 2C12 heavy chain

MacromoleculeName: Fab 2C12 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.00177 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAQITLRES GPTLVKPTQT LTLTCTFSGF SLNTNGVGVG WIRQPPGKAL EWLALIYWNG NEGYSPSLK SRLTITKDTS KNQVVLTMTN MDPVDTATYY CVHWPQGLTT VTRLAFDIWG QGTMVTVSSA STKGPSVFPL A PSSKSTSG ...String:
MKKNIAFLLA SMFVFSIATN AYAQITLRES GPTLVKPTQT LTLTCTFSGF SLNTNGVGVG WIRQPPGKAL EWLALIYWNG NEGYSPSLK SRLTITKDTS KNQVVLTMTN MDPVDTATYY CVHWPQGLTT VTRLAFDIWG QGTMVTVSSA STKGPSVFPL A PSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NT KVDKKVE PKSCD

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Macromolecule #7: Fab 2C12 light chain

MacromoleculeName: Fab 2C12 light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.594654 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAQSALTQP RSVSGSPGQS VTISCTGTTS DVGRYNFVSW YQQHPGKAPK LLMYDVSQRP SGVPSRFSG SKSGNTASLT ISGLQAEDEA VFYCCSYAGG NFFSYVFGTG TKVTVLGQPK AAPSVTLFPP SSEELQANKA T LVCLISDF ...String:
MKKNIAFLLA SMFVFSIATN AYAQSALTQP RSVSGSPGQS VTISCTGTTS DVGRYNFVSW YQQHPGKAPK LLMYDVSQRP SGVPSRFSG SKSGNTASLT ISGLQAEDEA VFYCCSYAGG NFFSYVFGTG TKVTVLGQPK AAPSVTLFPP SSEELQANKA T LVCLISDF YPGAVTVAWK ADSSPVKAGV ETTTPSKQSN NKYAASSYLS LTPEQWKSHR SYSCQVTHEG STVEKTVAPT EC

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Macromolecule #8: Fab 7I13 light chain

MacromoleculeName: Fab 7I13 light chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.8449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAEIVLTQS PGTLSLSPGE RATLSCRASQ SVSSDFLAWY QQKPGQAPRL LIYGASSRAT GIPDRFSGS GSGTDFTLTI SRLEPEDFAV YYCQQYAASP PFGQGTRLEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK ...String:
MKKNIAFLLA SMFVFSIATN AYAEIVLTQS PGTLSLSPGE RATLSCRASQ SVSSDFLAWY QQKPGQAPRL LIYGASSRAT GIPDRFSGS GSGTDFTLTI SRLEPEDFAV YYCQQYAASP PFGQGTRLEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #9: Fab 7I13 heavy chain

MacromoleculeName: Fab 7I13 heavy chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.046506 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAQVQLVES GGGVVQPGRS LRLSCAASGF TFSNYGMHWV RQGPGKGLEW VAVISYDASS KYYTDSVQG RFTISRDNSK NTLFLQMNSL RGEDTAVYYC AKALRYLDWF LSDPFDYWGQ GTLVTVSSAS TKGPSVFPLA P SSKSTSGG ...String:
MKKNIAFLLA SMFVFSIATN AYAQVQLVES GGGVVQPGRS LRLSCAASGF TFSNYGMHWV RQGPGKGLEW VAVISYDASS KYYTDSVQG RFTISRDNSK NTLFLQMNSL RGEDTAVYYC AKALRYLDWF LSDPFDYWGQ GTLVTVSSAS TKGPSVFPLA P SSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TK VDKKVEP KSCD

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Macromolecule #10: Fab 13H11 heavy chain

MacromoleculeName: Fab 13H11 heavy chain / type: protein_or_peptide / ID: 10 / 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 #11: Fab 13H11 light chain

MacromoleculeName: Fab 13H11 light chain / type: protein_or_peptide / ID: 11 / 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 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 6 / 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

Concentration1.77 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.
DetailsThe sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 18326 / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2
Details: Images were collected in movie-mode at 5 frames/second.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / 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

DetailsMovie frames were corrected for motion and aligned. Images with a CTF fit resolution of 8.0 A or better were selected for particle picking.
Particle selectionNumber selected: 5128264 / Details: template-matching particle picking
Startup modelType of model: OTHER
Details: ab-initio 3D model generation from select particles within cisTEM
Final reconstructionNumber classes used: 39 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 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 using phenix combine_focused_maps
Number images used: 4792984
Initial angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.02) / Details: Auto-refine in cisTEM
Final angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.02)
Details: Manual refine in cisTEM. Map was divided in 3 sections to refine map with focused refinements.
Final 3D classificationNumber classes: 100 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

5vob


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7t4q:
CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11

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