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- EMDB-58134: Structre of ANDV spike in complex with EC1 domain of human PCDH1 -

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Basic information

Entry
Database: EMDB / ID: EMD-58134
TitleStructre of ANDV spike in complex with EC1 domain of human PCDH1
Map dataCryoEM map of the complex of Andes virus spike with EC1 domain of human PCDH1.
Sample
  • Complex: ANDV spike
    • Complex: domains EC1-4 of human PCDH1
      • Protein or peptide: Protocadherin-1
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein
KeywordsHantavirus Andes virus PCDH1 envelope glycoprotein / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / homophilic cell-cell adhesion / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / cell adhesion molecule binding / cell junction / cell-cell junction / nervous system development / cell-cell signaling ...symbiont-mediated suppression of host TRAF-mediated signal transduction / homophilic cell-cell adhesion / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / cell adhesion molecule binding / cell junction / cell-cell junction / nervous system development / cell-cell signaling / host cell surface / cell adhesion / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope / calcium ion binding / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / plasma membrane
Similarity search - Function
Protocadherin / Protocadherin / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Cadherin, N-terminal ...Protocadherin / Protocadherin / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Cadherin, N-terminal / Cadherin-like / : / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Protocadherin-1 / Envelopment polyprotein
Similarity search - Component
Biological speciesOrthohantavirus andesense / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsBattini L / Guardado-Calvo P
Funding support France, United States, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI181977 United States
CitationJournal: To Be Published
Title: Structre of ANDV spike in complex with EC1 domain of human PCDH1
Authors: Battini L / Guardado-Calvo P
History
DepositionMay 17, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58134.png

Downloads & links

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Map

FileDownload / File: emd_58134.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the complex of Andes virus spike with EC1 domain of human PCDH1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 416 pix.
= 310.128 Å		0.75 Å/pix.
x 416 pix.
= 310.128 Å		0.75 Å/pix.
x 416 pix.
= 310.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7455 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2283988 - 0.4975486
Average (Standard dev.)0.0007000259 (±0.013955489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 310.12802 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer cryoEM map of the complex of Andes...

Fileemd_58134_additional_1.map
AnnotationDeepEMhancer cryoEM map of the complex of Andes virus spike with EC1 domain of human PCDH1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the complex of Andes virus...

Fileemd_58134_half_map_1.map
AnnotationHalf map of the complex of Andes virus spike with EC1 domain of human PCDH1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the complex of Andes virus...

Fileemd_58134_half_map_2.map
AnnotationHalf map of the complex of Andes virus spike with EC1 domain of human PCDH1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ANDV spike

EntireName: ANDV spike
Components
  • Complex: ANDV spike
    • Complex: domains EC1-4 of human PCDH1
      • Protein or peptide: Protocadherin-1
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein

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Supramolecule #1: ANDV spike

SupramoleculeName: ANDV spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Orthohantavirus andesense
Molecular weightTheoretical: 52.6 KDa

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Supramolecule #2: domains EC1-4 of human PCDH1

SupramoleculeName: domains EC1-4 of human PCDH1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Orthohantavirus andesense / Strain: Chile-9717869
Molecular weightTheoretical: 56.252641 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: KTIYELKMEC PHTVGLGQGY IIGSTELGLI SIEAASDIKL ESSCNFDLHT TSMAQKSFTQ VEWRKKSDTT DTTNAASTTF EAQTKTVNL RGTCILAPEL YDTLKKVKKT VLCYDLTCNQ THCQPTVYLI APVLTCMSIR SCMASVFTSR IQVIYEKTHC V TGQLIEGQ ...String:
KTIYELKMEC PHTVGLGQGY IIGSTELGLI SIEAASDIKL ESSCNFDLHT TSMAQKSFTQ VEWRKKSDTT DTTNAASTTF EAQTKTVNL RGTCILAPEL YDTLKKVKKT VLCYDLTCNQ THCQPTVYLI APVLTCMSIR SCMASVFTSR IQVIYEKTHC V TGQLIEGQ CFNPAHTLTL SQPAHTYDTV TLPISCFFTP KKSEQLKVIK TFEGILTKTG CTENALQGYY VCFLGSHSEP LI VPSLEDI RSAEVVSRML VHPRGEDHDA IQNSQSHLRI VGPITAKVPS TSSTDTLKGT AFAGVPMYSS LSTLVRNADP EFV FSPGIV PESNHSTCDK KTVPITWTGY LPISGEMEKV TGCTVFCTLA GPGASCEAYS ENGIFNISSP TCLVNKVQRF RGSE QKINF ICQRVDQDVV VYCNGQKKVI LTKTLVIGQC IYTFTSLFSL MPDVAHSLAV ELCVPGLHGG GGSGMSPYKK AIEIT KRLL ELLLSNPELA KKNLGGIATL ISLLALISAL DGC

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Orthohantavirus andesense / Strain: Chile-9717869
Molecular weightTheoretical: 57.921977 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: ETPLMESGWS DTAHGVGEIP MKTDLELDFS LPSSSSYSYR RKLTNPANKE ESIPFHFQME KQVIHAEIQP LGHWMDATFN IKTAFHCYG ACQKYSYPWQ TSKCFFEKDY QYETGWGCNP GDCPGVGTGC TACGVYLDKL KSVGKAYKII SLKYTRKVCI Q LGTEQTCK ...String:
ETPLMESGWS DTAHGVGEIP MKTDLELDFS LPSSSSYSYR RKLTNPANKE ESIPFHFQME KQVIHAEIQP LGHWMDATFN IKTAFHCYG ACQKYSYPWQ TSKCFFEKDY QYETGWGCNP GDCPGVGTGC TACGVYLDKL KSVGKAYKII SLKYTRKVCI Q LGTEQTCK HIDANDCLVT PSVKVCIVGT VSKLQPSDTL LFLGPLEQGG IILKQWCTTS CAFGDPGDIM STPSGMRCPE HT GSFRKIC GFATTPVCEY QGNTISGYKR MMATKDSFQS FNLTEPHITT NKLEWIDPDG NTRDHVNLVL NRDVSFQDLS DNP CKVDLH TQAIEGAWGS GVGFTLTCTV GLTECPSFMT SIKACDLAMC YGSTVTNLAR GSNTVKVVGK GGHSGSSFKC CHDT DCSSE GLLASAPHLE RVTGFNQIDS DKVYDDGAPP CTAKCWATKS GEWALGIANG NGGGSCTLDE KDIEPYIKKL EESLG SGGG SLVPRGSGSG SAWSHPQFEK GSGSAWSHPQ FEKGLNDIFE AQKIEWHE

UniProtKB: Envelopment polyprotein

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Macromolecule #3: Protocadherin-1

MacromoleculeName: Protocadherin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.688906 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: RSTRVVYKVP EEQPPNTLIG SLAADYGFPD VGHLYKLEVG APYLRVDGKT GDIFTTETSI DREGLRECQN QLPGDPCILE FEVSITDLV QNGSPRLLEG QIEVQDINDN TPNFASPVIT LAIPENTNIG SLFPIPLASD RDAGPNGVAS YELQAGPEAQ E LFGLQVAE ...String:
RSTRVVYKVP EEQPPNTLIG SLAADYGFPD VGHLYKLEVG APYLRVDGKT GDIFTTETSI DREGLRECQN QLPGDPCILE FEVSITDLV QNGSPRLLEG QIEVQDINDN TPNFASPVIT LAIPENTNIG SLFPIPLASD RDAGPNGVAS YELQAGPEAQ E LFGLQVAE DQEEKQPQLI VMGNLDRERW DSYDLTIKVQ DGGSPPRASS ALLRVTVLDT NDNAPKFERP SYEAELSENS PI GHSVIQV KANDSDQGAN AEIEYTFHQA PEVVRRLLRL DRNTGLITVQ GPVDREDLST LRFSVLAKDR GTNPKSARAQ VVV TVKDMN DNAPTIEIRG IGLVTHQDGM ANISEDVAEE TAVALVQVSD RDEGENAAVT CVVAGDVPFQ LRQASETGSD SKKK YFLQT TTPLDYEKVK DYTIEIVAVD SGNPPLSSTN SLKVQVVDVN DNAGPGGGSH HHHHHHHGGG SGGSLVPRGS GGTWS HPQF EK

UniProtKB: Protocadherin-1

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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

Concentration0.34 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
10.0 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTrizma base
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 267242
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 5 / Avg.num./class: 67000 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9p3i

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-30xt:
Structre of ANDV spike in complex with EC1 domain of human PCDH1

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