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- EMDB-49044: Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-49044
TitleHemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 Fab
Map data
Sample
  • Complex: Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 fab
    • Protein or peptide: heavy chain antibody Fab AMB38599
    • Protein or peptide: light chain antibody Fab AMB38310
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex of antibody with influenza A antigen hemagglutinin / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus (A/California/01/2009(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFernandez-Quintero ML / Raghavan SSR / Gharpure A / Turner HL / Ward AB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Mach Intell / Year: 2025
Title: Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions.
Authors: Fabian C Spoendlin / Monica L Fernández-Quintero / Sai S R Raghavan / Hannah L Turner / Anant Gharpure / Johannes R Loeffler / Wing K Wong / Alexander Bujotzek / Guy Georges / Andrew B Ward ...Authors: Fabian C Spoendlin / Monica L Fernández-Quintero / Sai S R Raghavan / Hannah L Turner / Anant Gharpure / Johannes R Loeffler / Wing K Wong / Alexander Bujotzek / Guy Georges / Andrew B Ward / Charlotte M Deane /
Abstract: Many proteins are highly flexible and their ability to adapt their shape can be fundamental to their functional properties. For example, the flexibility of antibody complementarity-determining region ...Many proteins are highly flexible and their ability to adapt their shape can be fundamental to their functional properties. For example, the flexibility of antibody complementarity-determining region (CDR) loops influences binding affinity and specificity, making it a key factor in understanding and designing antigen interactions. With methods such as AlphaFold, it is possible to computationally predict a single, static protein structure with high accuracy. However, the reliable prediction of structural flexibility has not yet been achieved. A major factor limiting such predictions is the scarcity of suitable training data. Here we focus on predicting the structural flexibility of functionally important antibody and T cell receptor CDR3 loops. To this end, we constructed ALL-conformations by extracting CDR3s and CDR3-like loop motifs from all structures deposited in the Protein Data Bank. This dataset comprises 1.2 million loop structures representing more than 100,000 unique sequences and captures all experimentally observed conformations of these motifs. Using this dataset, we develop ITsFlexible, a deep learning tool with graph neural network architecture. We trained the model to binary classify CDR loops as 'rigid' or 'flexible' from inputs of antibody structures. ITsFlexible outperforms all alternative approaches on our crystal structure datasets and successfully generalizes to molecular dynamics simulations. We also used ITsFlexible to predict the flexibility of three CDRH3 loops with no solved structures and experimentally determined their conformations using cryogenic electron microscopy.
History
DepositionFeb 4, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49044.png

Downloads & links

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Map

FileDownload / File: emd_49044.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.5142172 - 0.8830139
Average (Standard dev.)-0.000108027016 (±0.016658578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49044_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_49044_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 : Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 fab

EntireName: Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 fab
Components
  • Complex: Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 fab
    • Protein or peptide: heavy chain antibody Fab AMB38599
    • Protein or peptide: light chain antibody Fab AMB38310
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 fab

SupramoleculeName: Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 330 KDa

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Macromolecule #1: heavy chain antibody Fab AMB38599

MacromoleculeName: heavy chain antibody Fab AMB38599 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.395014 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLLESGGG LVQPGGSLRL SCAASGFTFT HFAMTWVRQA PGKGLEWVST IDGSGGGTYS ADFVKGRFTV SRDNSKNTLF LQMNSLRAE DTALYYCAKV SPGMVDDPHL GGAFHIWGQG TMVTVSS

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Macromolecule #2: light chain antibody Fab AMB38310

MacromoleculeName: light chain antibody Fab AMB38310 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.484569 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
SYELTQPPSV SVAPGQTATI TCGGNNIGLK TVHWCQQKPG QAPVVVVYDN NDRPSGIPER FSGSNSWNTA TLTITGVEAG DEADYYCQV WDSGSHQVVF GGGTKLTFL

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/01/2009(H1N1))
Molecular weightTheoretical: 36.172762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DPGDTLCIGY HANNSTDTVD TVLEKNVTVT HSVNLLEDKH NGKLCKLRGV APLHLGKCNI AGWILGNPEC ESLSTASSWS YIVETPSSD NGTCYPGDFI DYEELREQLS SVSSFERFEI FPKTSSWPNH DSNKGVTAAC PHAGAKSFYK NLIWLVKKGN S YPKLSKSY ...String:
DPGDTLCIGY HANNSTDTVD TVLEKNVTVT HSVNLLEDKH NGKLCKLRGV APLHLGKCNI AGWILGNPEC ESLSTASSWS YIVETPSSD NGTCYPGDFI DYEELREQLS SVSSFERFEI FPKTSSWPNH DSNKGVTAAC PHAGAKSFYK NLIWLVKKGN S YPKLSKSY INDKGKEVLV LWGIHHPSTS ADQQSLYQNA DTYVFVGSSR YSKKFKPEIA IRPKVRDQEG RMNYYWTLVE PG DKITFEA TGNLVVPRYA FAMERNAGSG IIISDTPVHD CNTTCQTPKG AINTSLPFQN IHPITIGKCP KYVKSTKLRL ATG LRNIPS

UniProtKB: Hemagglutinin

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Macromolecule #4: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/01/2009(H1N1))
Molecular weightTheoretical: 19.619764 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRSQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NRE

UniProtKB: Hemagglutinin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / 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

Concentration0.6 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.84 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.5) / Number images used: 142446
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: Other, initial_model_type: in silico modelABodyBuilder2
source_name: PDB, initial_model_type: experimental model

7t3d

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9n5z:
Hemagglutinin CA09 homotrimer bound to AMB38310/AMB38599 Fab

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