[English] 日本語
Yorodumi
- EMDB-25687: CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25687
TitleCryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11
Map dataComposite map of combined focused refinement maps. Used for model refinements.
Sample
  • Complex: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to Neuropilin 2 and fabs of human neutralizing antibodies 8I21 and 13H11
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
Keywordsglycoprotein complex / antibody complex / Neuropilin 2 / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus ...vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / axon extension involved in axon guidance / sympathetic neuron projection extension / NrCAM interactions / Neurophilin interactions with VEGF and VEGFR / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / vascular endothelial growth factor receptor activity / nerve development / semaphorin receptor complex / semaphorin receptor activity / outflow tract septum morphogenesis / regulation of postsynapse organization / negative chemotaxis / growth factor binding / cytokine binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / axon guidance / cellular response to leukemia inhibitory factor / signaling receptor activity / heparin binding / angiogenesis / host cell endosome / host cell Golgi apparatus / postsynaptic membrane / entry receptor-mediated virion attachment to host cell / cell adhesion / axon / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / glutamatergic synapse / virion membrane / extracellular region / metal ion binding / identical protein binding / membrane / plasma 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 ...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 / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Envelope glycoprotein H / Neuropilin-2 / UL128 / UL130 / Envelope glycoprotein L / UL131A
Similarity search - Component
Biological speciesHuman betaherpesvirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25687.png

Downloads & links

-
Map

FileDownload / File: emd_25687.map.gz / Format: CCP4 / Size: 87.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of combined focused refinement maps. Used for model refinements.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 284 pix.
= 383.798 Å		1.35 Å/pix.
x 284 pix.
= 383.798 Å		1.35 Å/pix.
x 284 pix.
= 383.798 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: 0.8
Minimum - Maximum0.0 - 15.305042
Average (Standard dev.)0.011590637 (±0.18164654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions284284284
Spacing284284284
CellA=B=C: 383.7976 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Additional map: Non-sharpened, full map of overall (non-focused)refinement

Fileemd_25687_additional_1.map
AnnotationNon-sharpened, full map of overall (non-focused)refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Non-sharpened, full map of focused refinement on 8I21-UL128 region

Fileemd_25687_additional_10.map
AnnotationNon-sharpened, full map of focused refinement on 8I21-UL128 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Half map 1 of focused refinement on 8I21-UL128 region

Fileemd_25687_additional_11.map
AnnotationHalf map 1 of focused refinement on 8I21-UL128 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Density modified map of focused refined 8I12-UL128 region....

Fileemd_25687_additional_12.map
AnnotationDensity modified map of focused refined 8I12-UL128 region. Map used for composite map generation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Density modified map of focused refined NRP2-UL region....

Fileemd_25687_additional_13.map
AnnotationDensity modified map of focused refined NRP2-UL region. Map used for composite map generation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Non-sharpened, full map of focused refinement on NRP2-UL region

Fileemd_25687_additional_2.map
AnnotationNon-sharpened, full map of focused refinement on NRP2-UL region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Half map 1 of focused refinement on NRP2-UL region

Fileemd_25687_additional_3.map
AnnotationHalf map 1 of focused refinement on NRP2-UL region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Half map 2 of focused refinement on NRP2-UL region

Fileemd_25687_additional_4.map
AnnotationHalf map 2 of focused refinement on NRP2-UL region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Half map 2 of focused refinement on 8I21-UL128 region

Fileemd_25687_additional_5.map
AnnotationHalf map 2 of focused refinement on 8I21-UL128 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Non-sharpened, full map of focused refinement on 13H11-gH region

Fileemd_25687_additional_6.map
AnnotationNon-sharpened, full map of focused refinement on 13H11-gH region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Half map 1 of focused refinement on 13H11-gH region

Fileemd_25687_additional_7.map
AnnotationHalf map 1 of focused refinement on 13H11-gH region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Half map 2 of focused refinement on 13H11-gH region

Fileemd_25687_additional_8.map
AnnotationHalf map 2 of focused refinement on 13H11-gH region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Density modified map of focused refined 13H11-gH region....

Fileemd_25687_additional_9.map
AnnotationDensity modified map of focused refined 13H11-gH region. Map used for composite map generation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

EntireName: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to Neuropilin 2 and fabs of human neutralizing antibodies 8I21 and 13H11
Components
  • Complex: Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to Neuropilin 2 and fabs of human neutralizing antibodies 8I21 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: Neuropilin-2
    • Protein or peptide: Fab 8I21 heavy chain
    • Protein or peptide: Fab 13H11 heavy chain
    • Protein or peptide: Fab 13H11 light chain
    • Protein or peptide: Fab 8I21 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

+
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 Neuropilin 2 and fabs of human neutralizing antibodies 8I21 and 13H11
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Molecular weightTheoretical: 360 KDa

+
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

+
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

+
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

+
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

+
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

+
Macromolecule #6: Neuropilin-2

MacromoleculeName: Neuropilin-2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.923211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMFPLTWVF LALYFSRHQV RGQPDPPCGG RLNSKDAGYI TSPGYPQDYP SHQNCEWIVY APEPNQKIVL NFNPHFEIEK HDCKYDFIE IRDGDSESAD LLGKHCGNIA PPTIISSGSM LYIKFTSDYA RQGAGFSLRY EIFKTGSEDC SKNFTSPNGT I ESPGFPEK ...String:
MDMFPLTWVF LALYFSRHQV RGQPDPPCGG RLNSKDAGYI TSPGYPQDYP SHQNCEWIVY APEPNQKIVL NFNPHFEIEK HDCKYDFIE IRDGDSESAD LLGKHCGNIA PPTIISSGSM LYIKFTSDYA RQGAGFSLRY EIFKTGSEDC SKNFTSPNGT I ESPGFPEK YPHNLDCTFT ILAKPKMEII LQFLIFDLEH DPLQVGEGDC KYDWLDIWDG IPHVGPLIGK YCGTKTPSEL RS STGILSL TFHTDMAVAK DGFSARYYLV HQEPLENFQC NVPLGMESGR IANEQISASS TYSDGRWTPQ QSRLHGDDNG WTP NLDSNK EYLQVDLRFL TMLTAIATQG AISRETQNGY YVKSYKLEVS TNGEDWMVYR HGKNHKVFQA NNDATEVVLN KLHA PLLTR FVRIRPQTWH SGIALRLELF GCRVTDAPCS NMLGMLSGLI ADSQISASST QEYLWSPSAA RLVSSRSGWF PRIPQ AQPG EEWLQVDLGT PKTVKGVIIQ GARGGDSITA VEARAFVRKF KVSYSLNGKD WEYIQDPRTQ QPKLFEGNMH YDTPDI RRF DPIPAQYVRV YPERWSPAGI GMRLEVLGCD WTDSKPTVET LGPTVKSEET TTPYPTEEEA TECGENCSFE DDKDLQL PS GFNCNFDFLE EPCGWMYDHA KWLRTTWASS SSPNDRTFPD DRNFLRLQSD SQREGQYARL ISPPVHLPRS PVCMEFQY Q ATGGRGVALQ VVREASQESK LLWVIREDQG GEWKHGRIIL PSYDMEYQIV FEGVIGKGRS GEIAIDDIRI STDVPLENC MEPISAFAGE NFKVDIPEIH EREGYEDEID DEYEVDWSNS SSATSGSGAP STDKEKSWLY TLDPGNSDYK DDDDK

UniProtKB: Neuropilin-2

+
Macromolecule #7: Fab 8I21 heavy chain

MacromoleculeName: Fab 8I21 heavy chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.816311 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYALVELVES GGGVVQPGRS LRLSCAASGF TFSSDGMHWV RQSPGRGLEW VAFISSDGST PYYADSVKG RFTISRDNSK NTLYLQMNSL RAEDTAMYFC AKDWALFRWL RTFDHWGQGT LVTVSSASTK GPSVFPLAPS S KSTSGGTA ...String:
MKKNIAFLLA SMFVFSIATN AYALVELVES GGGVVQPGRS LRLSCAASGF TFSSDGMHWV RQSPGRGLEW VAFISSDGST PYYADSVKG RFTISRDNSK NTLYLQMNSL RAEDTAMYFC AKDWALFRWL RTFDHWGQGT LVTVSSASTK GPSVFPLAPS S KSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VD KKVEPKS CD

+
Macromolecule #8: Fab 13H11 heavy chain

MacromoleculeName: Fab 13H11 heavy chain / type: protein_or_peptide / ID: 8 / 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

+
Macromolecule #9: Fab 13H11 light chain

MacromoleculeName: Fab 13H11 light chain / type: protein_or_peptide / ID: 9 / 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

+
Macromolecule #10: Fab 8I21 light chain

MacromoleculeName: Fab 8I21 light chain / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.99508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAETVMTQS PATLSVSPGG RATLSCRASQ SVGINLAWYQ QKPGQAPRLL IYGASTRASG FPARFSGSG SGTEFTLTIT SLQSEDFAVY YCQQYNDWPP WTFGQGTKVE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL L NNFYPREA ...String:
MKKNIAFLLA SMFVFSIATN AYAETVMTQS PATLSVSPGG RATLSCRASQ SVGINLAWYQ QKPGQAPRLL IYGASTRASG FPARFSGSG SGTEFTLTIT SLQSEDFAVY YCQQYNDWPP WTFGQGTKVE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL L NNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

+
Macromolecule #12: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
25.0 mMHEPESHEPES
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP / Details: blot for 3.5 seconds before plunging.
DetailsSample was mildly crosslinked with 0.025% glutaraldehyde, incubated for 10 min at room temperature and quenched with 9 mM TRIS pH 7.5

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 21357 / Average exposure time: 10.0 sec. / Average electron dose: 52.0 e/Å2
Details: Images were collected in movie-mode at 4 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

+
Image processing

DetailsMovie frames were corrected for motion and aligned. Images with a CTF fit resolution of 6.0 A or better were selected for particle picking.
Particle selectionNumber selected: 2532206 / 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: 44 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 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: 2252924
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)

-
Atomic model buiding 1

Initial model
PDB IDChain

2qqo

source_name: PDB, initial_model_type: experimental model

5vob

source_name: PDB, initial_model_type: experimental model
Output model

PDB-7t4s:
CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more