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- EMDB-47570: DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islan... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47570
TitleDH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006
Map data
Sample
  • Complex: Complex of three DH726-1 Fabs with homotrimeric hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: DH726-1 Fab heavy chain
    • Protein or peptide: DH726-1 Fab light chain
Keywordsimmunoglobulin / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 speciesAlphainfluenzavirus influenzae / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsFinney J / Harrison SC / Walsh Jr RM / Kelsoe G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: IGHV3 encoded hemagglutinin stem rhesus antibodies protects against H1N1 virus by targeting a conserved epitope
Authors: Gu S / Finney J / Schmidt AG / Vandergrift NA / Luo K / Valencia SM / Mielke D / Pollara J / Zhang R / Gurley TC / Armand LC / Von Holle TA / Marshall DJ / Parks R / Sutherland LL / Scearce ...Authors: Gu S / Finney J / Schmidt AG / Vandergrift NA / Luo K / Valencia SM / Mielke D / Pollara J / Zhang R / Gurley TC / Armand LC / Von Holle TA / Marshall DJ / Parks R / Sutherland LL / Scearce RM / Wiehe K / Santra S / McGee CE / Yassine H / Graham BS / Golding H / Kepler TB / Liao H-X / Nair SK / Ferrari G / Haynes BF / Harrison SC / Moody MA
History
DepositionOct 30, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47570.png

Downloads & links

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Map

FileDownload / File: emd_47570.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 330 pix.
= 363. Å		1.1 Å/pix.
x 330 pix.
= 363. Å		1.1 Å/pix.
x 330 pix.
= 363. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.0509653 - 1.464075
Average (Standard dev.)0.00026375556 (±0.023820747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 363.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47570_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_47570_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 : Complex of three DH726-1 Fabs with homotrimeric hemagglutinin

EntireName: Complex of three DH726-1 Fabs with homotrimeric hemagglutinin
Components
  • Complex: Complex of three DH726-1 Fabs with homotrimeric hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: DH726-1 Fab heavy chain
    • Protein or peptide: DH726-1 Fab light chain

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Supramolecule #1: Complex of three DH726-1 Fabs with homotrimeric hemagglutinin

SupramoleculeName: Complex of three DH726-1 Fabs with homotrimeric hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Alphainfluenzavirus influenzae / Strain: A/Solomon Islands/3/2006

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Alphainfluenzavirus influenzae / Strain: A/Solomon Islands/3/2006
Molecular weightTheoretical: 58.436199 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPGYLLEDT ICIGYHANNS TDTVDTVLEK NVTVTHSVNL LEDSHNGKLC LLKGIAPLQL GNCSVAGWIL GNPECELLIS RESWSYIVE KPNPENGTCY PGHFADYEEL REQLSSVSSF ERFEIFPKES SWPNHTTTGV SASCSHNGES SFYKNLLWLT G KNGLYPNL ...String:
ADPGYLLEDT ICIGYHANNS TDTVDTVLEK NVTVTHSVNL LEDSHNGKLC LLKGIAPLQL GNCSVAGWIL GNPECELLIS RESWSYIVE KPNPENGTCY PGHFADYEEL REQLSSVSSF ERFEIFPKES SWPNHTTTGV SASCSHNGES SFYKNLLWLT G KNGLYPNL SKSYANNKEK EVLVLWGVHH PPNIGDQRAL YHTENAYVSV VSSHYSRKFT PEIAKRPKVR DREGRINYYW TL LEPGDTI IFEANGNLIA PRYAFALSRG FGSGIINSNA PMDECDAKCQ TPQGAINSSL PFQNVHPVTI GECPKYVRSA KLR MVTGLR NIPSIQSRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADQKSTQ NAINGITNKV NSVIEKMNTQ FTAV GKEFN KLERRMENLN KKVDDGFIDI WTYNAELLVL LENERTLDFH DSNVKNLYEK VKSQLKNNAK EIGNGCFEFY HKCND ECME SVKNGTYDYP KYSEESKLNR EKIDGVRSGA LEVLFQ

UniProtKB: Hemagglutinin

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Macromolecule #2: DH726-1 Fab heavy chain

MacromoleculeName: DH726-1 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 25.467539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCVASGFTFS NYAMYWVRQA PGKGLEWISS INSGSGSRYY ADSVKGRFTV SRDNSKNTLS LQMNSLRVE DTAVYYCAKD QSNPIFGLVI ATNSLDVWGQ GVLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVESGGG LVQPGGSLRL SCVASGFTFS NYAMYWVRQA PGKGLEWISS INSGSGSRYY ADSVKGRFTV SRDNSKNTLS LQMNSLRVE DTAVYYCAKD QSNPIFGLVI ATNSLDVWGQ GVLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK SCDKGSSLEV LF Q

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Macromolecule #3: DH726-1 Fab light chain

MacromoleculeName: DH726-1 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.205787 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ISCRASQGIS SDLAWYQQKP GKAPKLLIYK ASTLQSGVPP RFGGRGSGPD FTLTISSLQP EDFATYYCQ QHNSYPLTFG GGTKVEVKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDTVT ISCRASQGIS SDLAWYQQKP GKAPKLLIYK ASTLQSGVPP RFGGRGSGPD FTLTISSLQP EDFATYYCQ QHNSYPLTFG GGTKVEVKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.99 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ugy


Details: Hemagglutinin was modeled on PDB:5UGY. Fab was modeled on PDB:6XSK.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5ugy

source_name: PDB, initial_model_type: experimental model

6xsk

source_name: PDB, initial_model_type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.8)
Output model

PDB-9e6j:
DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006

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