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- EMDB-49043: Hemagglutinin CA09 homotrimer bound to AEL31302/AEL31311 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-49043
TitleHemagglutinin CA09 homotrimer bound to AEL31302/AEL31311 Fab
Map data
Sample
  • Complex: Hemaggluinin CA09 homotrimer bound to AEL31302/AEL31311 mAb
    • Protein or peptide: Fab light chain antibody AEL31302
    • Protein or peptide: Fab heavy antibody AEL31311
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody-antigen complex / 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
Biological speciesHomo sapiens (human) / Influenza A virus (A/California/01/2009(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsFernandez-Quintero ML / Turner HL
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-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49043.png

Downloads & links

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Map

FileDownload / File: emd_49043.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 344.64 Å		0.72 Å/pix.
x 480 pix.
= 344.64 Å		0.72 Å/pix.
x 480 pix.
= 344.64 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: 0.06
Minimum - Maximum-0.2198283 - 0.38801646
Average (Standard dev.)-0.000030373174 (±0.010462199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 344.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49043_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49043_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Hemaggluinin CA09 homotrimer bound to AEL31302/AEL31311 mAb

EntireName: Hemaggluinin CA09 homotrimer bound to AEL31302/AEL31311 mAb
Components
  • Complex: Hemaggluinin CA09 homotrimer bound to AEL31302/AEL31311 mAb
    • Protein or peptide: Fab light chain antibody AEL31302
    • Protein or peptide: Fab heavy antibody AEL31311
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Hemaggluinin CA09 homotrimer bound to AEL31302/AEL31311 mAb

SupramoleculeName: Hemaggluinin CA09 homotrimer bound to AEL31302/AEL31311 mAb
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 330 KDa

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Macromolecule #1: Fab light chain antibody AEL31302

MacromoleculeName: Fab light chain antibody AEL31302 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.910879 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSD IVMTQSPDSL AVSLGERATI NCRSSQSVSS NNKNFLAWYQ EKPGQPPKVL IYWASARESG VPDRFSGSG SGTDFTLTIS GLQAEDVAVY YCQQHYRTPP TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK ...String:
MGWSCIILFL VATATGVHSD IVMTQSPDSL AVSLGERATI NCRSSQSVSS NNKNFLAWYQ EKPGQPPKVL IYWASARESG VPDRFSGSG SGTDFTLTIS GLQAEDVAVY YCQQHYRTPP TFGQGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Macromolecule #2: Fab heavy antibody AEL31311

MacromoleculeName: Fab heavy antibody AEL31311 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.024441 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSQ VQLVQSGGGV VPPGRSLRLS CAASGFTFST YGMHWVRQAP GKGLEWVAVI SYDGNYKYYA DSVRGRFTI SRDNSKNTLN LDMNSLRTED TALYYCAKDS QLRSLLYFDW LSQGYFDHWG QGTLVTVSSA STKGPSVFPL A PSSKSTSG ...String:
MGWSCIILFL VATATGVHSQ VQLVQSGGGV VPPGRSLRLS CAASGFTFST YGMHWVRQAP GKGLEWVAVI SYDGNYKYYA DSVRGRFTI SRDNSKNTLN LDMNSLRTED TALYYCAKDS QLRSLLYFDW LSQGYFDHWG QGTLVTVSSA STKGPSVFPL A PSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NT KVDKKVE PKSC

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/01/2009(H1N1))
Molecular weightTheoretical: 62.401727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDTLCIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDKHNG KLCKLRGVAP LHLGKCNIAG WILGNPECES LSTASSWSYI VETPSSDNG TCYPGDFIDY EELREQLSSV SSFERFEIFP KTSSWPNHDS NKGVTAACPH AGAKSFYKNL IWLVKKGNSY P KLSKSYIN ...String:
GDTLCIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDKHNG KLCKLRGVAP LHLGKCNIAG WILGNPECES LSTASSWSYI VETPSSDNG TCYPGDFIDY EELREQLSSV SSFERFEIFP KTSSWPNHDS NKGVTAACPH AGAKSFYKNL IWLVKKGNSY P KLSKSYIN DKGKEVLVLW GIHHPSTSAD QQSLYQNADT YVFVGSSRYS KKFKPEIAIR PKVRDQEGRM NYYWTLVEPG DK ITFEATG NLVVPRYAFA MERNAGSGII ISDTPVHDCN TTCQTPKGAI NTSLPFQNIH PITIGKCPKY VKSTKLRLAT GLR NIPSIQ SRGLFGAIAG FIEGGWTGMV DGWYGYHHQN EQGSGYAADL KSTQNAIDKI TNKVNSVIEK MNTQFTAVGK EFNH LEKRI ENLNKKVDDG FLDIWTYNAE LLVLLENERT LDYHDSNVKN LYEKVRSQLK NNAKEIGNGC FEFYHKCDNT CMESV KNGT YDYPKYSEEA KLNREEIDSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGSGL NDIFEAQKIE WHEGHHHHHH

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

Concentration1.14 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: 45.0 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 / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85692
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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