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

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Basic information

Entry
Database: PDB / ID: 30xt
TitleStructre of ANDV spike in complex with EC1 domain of human PCDH1
Components
  • (Envelopment polyprotein) x 2
  • Protocadherin-1
KeywordsVIRAL PROTEIN / Hantavirus Andes virus PCDH1 envelope glycoprotein
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsBattini, L. / Guardado-Calvo, P.
Funding support France, United States, 2items
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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelopment polyprotein
B: Envelopment polyprotein
C: Envelopment polyprotein
D: Envelopment polyprotein
E: Envelopment polyprotein
F: Envelopment polyprotein
G: Envelopment polyprotein
H: Envelopment polyprotein
Y: Protocadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,77225
Polymers509,3879
Non-polymers9,38516
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Envelopment polyprotein


Mass: 56252.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthohantavirus andesense / Strain: Chile-9717869 / Gene: GP / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9E006
#2: Protein
Envelopment polyprotein


Mass: 57921.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthohantavirus andesense / Strain: Chile-9717869 / Gene: GP / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9E006
#3: Protein Protocadherin-1 / Cadherin-like protein 1 / Protocadherin-42 / PC42


Mass: 52688.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH1 / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q08174
#4: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1ANDV spikeCOMPLEX#1-#30RECOMBINANT
2domains EC1-4 of human PCDH1COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.456 MDaNO
210.0526 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Orthohantavirus andesense1980456
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Drosophila melanogaster (fruit fly)7227
32Drosophila melanogaster (fruit fly)7227
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium chlorideNaCl1
210 mMTrizma base2-Amino-2-(hydroxymethyl)-1,3-propanediol1
SpecimenConc.: 0.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
4cryoSPARC4.6.2CTF correction
7UCSF ChimeraX1.6.1model fitting
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC3D reconstruction
14PHENIX1.21.2model refinement
15Coot0.9.8.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267242 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
19P3I

9p3i

19P3I1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 120.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003929364
ELECTRON MICROSCOPYf_angle_d0.758539887
ELECTRON MICROSCOPYf_chiral_restr0.04954754
ELECTRON MICROSCOPYf_plane_restr0.00645014
ELECTRON MICROSCOPYf_dihedral_angle_d4.55834227

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