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- EMDB-47201: Cryo EM structure of Hendra G ectodomain in complex with Ephrin-B... -

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Basic information

Entry
Database: EMDB / ID: EMD-47201
TitleCryo EM structure of Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270
Map data
Sample
  • Complex: Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Ephrin-B2
    • Protein or peptide: Fan HENV-270 heavy chain
    • Protein or peptide: Fan HENV-270 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
KeywordsFab / Receptor / Complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / adherens junction organization / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / adherens junction organization / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / blood vessel morphogenesis / Ephrin signaling / regulation of postsynaptic neurotransmitter receptor internalization / exo-alpha-sialidase activity / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / ephrin receptor binding / T cell costimulation / EPHB-mediated forward signaling / axon guidance / animal organ morphogenesis / adherens junction / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cell-cell signaling / negative regulation of neuron projection development / cellular response to lipopolysaccharide / virus receptor activity / presynaptic membrane / cell adhesion / host cell surface receptor binding / focal adhesion / positive regulation of cell population proliferation / viral envelope / dendrite / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / glutamatergic synapse / virion membrane / membrane / plasma membrane
Similarity search - Function
Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase ...Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / Cupredoxin
Similarity search - Domain/homology
Glycoprotein / Ephrin-B2
Similarity search - Component
Biological speciesHomo sapiens (human) / Henipavirus hendraense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: To Be Published
Title: Cryo EM structure of Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270
Authors: Binshtein E / Crowe JE
History
DepositionOct 7, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47201.png

Downloads & links

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Map

FileDownload / File: emd_47201.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 200 pix.
= 258.8 Å		1.29 Å/pix.
x 200 pix.
= 258.8 Å		1.29 Å/pix.
x 200 pix.
= 258.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0017321063 - 2.0199342
Average (Standard dev.)0.0010489804 (±0.02222079)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 258.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47201_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47201_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270

EntireName: Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270
Components
  • Complex: Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Ephrin-B2
    • Protein or peptide: Fan HENV-270 heavy chain
    • Protein or peptide: Fan HENV-270 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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Supramolecule #1: Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270

SupramoleculeName: Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus hendraense
Molecular weightTheoretical: 48.059559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ISQGVSDLVG LPNQICLQKT TSTILKPRLI SYTLPINTRE GVCITDPLLA VDNGFFAYSH LEKIGSCTRG IAKQRIIGVG EVLDRGDKV PSMFMTNVWT PPNPSTIHHC SSTYHEDFYY TLCAVSHVGD PILNSTSWTE SLSLIRLAVR PKSDSGDYNQ K YIAITKVE ...String:
ISQGVSDLVG LPNQICLQKT TSTILKPRLI SYTLPINTRE GVCITDPLLA VDNGFFAYSH LEKIGSCTRG IAKQRIIGVG EVLDRGDKV PSMFMTNVWT PPNPSTIHHC SSTYHEDFYY TLCAVSHVGD PILNSTSWTE SLSLIRLAVR PKSDSGDYNQ K YIAITKVE RGKYDKVMPY GPSGIKQGDT LYFPAVGFLP RTEFQYNDSN CPIIHCKYSK AENCRLSMGV NSKSHYILRS GL LKYNLSL GGDIILQFIE IADNRLTIGS PSKIYNSLGQ PVFYQASYSW DTMIKLGDVD TVDPLRVQWR NNSVISRPGQ SQC PRFNVC PEVCWEGTYN DAFLIDRLNW VSAGVYLNSN QTAENPVFAV FKDNEILYQV PLAEDDTNAQ KTITDCFLLE NVIW CISLV EIYDTGDSVI RPKLFAVKIP AQCS

UniProtKB: Glycoprotein

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Macromolecule #2: Ephrin-B2

MacromoleculeName: Ephrin-B2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.8031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SIVLEPIYWN SSNSKFLPGQ GLVLYPQIGD KLDIICPKVD SKTVGQYEYY KVYMVDKDQA DRCTIKKENT PLLNCAKPDQ DIKFTIKFQ EFSPNLWGLE FQKNKDYYII STSNGSLEGL DNQEGGVCQT RAMKILMKV

UniProtKB: Ephrin-B2

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Macromolecule #3: Fan HENV-270 heavy chain

MacromoleculeName: Fan HENV-270 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.946451 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGSE LKKPGASVKV SCKASGYTFT SYAVNWVRQA PGQGLEWVGW MSTNTGDPIY AQGFTGRFVF SLDTSVSTAY LQISSLKAE DSGVYYCARE GLRGRAFDIW GQGTMVTVSS A

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Macromolecule #4: Fan HENV-270 light chain

MacromoleculeName: Fan HENV-270 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.608795 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVSPGQTARI TCSGDKLGDK YAAWYQQKPG QSPVLVIYQN TKRPSGIPER FSGSSSGNTA TLTISGTQAM DEADYFCQA WDSRTNWVFG GGTKLTVLG

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #8: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 854283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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