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- EMDB-61145: Complex structure of influenza hemagglutinin HA stem with CR9114 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61145
TitleComplex structure of influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
Map dataThis is an EM map.
Sample
  • Complex: Complex of influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
    • Protein or peptide: Designed influenza hemagglutinin stem #219 HA2
    • Protein or peptide: CR9114 light chain
    • Protein or peptide: CR9114 heavy chain
    • Protein or peptide: FISW84 light chain
    • Protein or peptide: FISW84 heavy chain
    • Protein or peptide: Designed influenza hemagglutinin stem #219 HA1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantigen / complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsRu YX / Liu DJ / Deng L / Li YW
Funding support1 items
OrganizationGrant numberCountry
Other governmentK22227503
CitationJournal: To Be Published
Title: Structure-based design of a broadly protective influenza hemagglutinin stem immunogen
Authors: Ru YX / Liu DJ / Deng L / Li YW
History
DepositionAug 12, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61145.png

Downloads & links

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Map

FileDownload / File: emd_61145.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an EM map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.5449735 - 1.6315739
Average (Standard dev.)0.0004957446 (±0.027860116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: This is half map B.

Fileemd_61145_half_map_1.map
AnnotationThis is half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is half map A.

Fileemd_61145_half_map_2.map
AnnotationThis is half map A.
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 influenza hemagglutinin HA stem with CR9114 Fab and FI...

EntireName: Complex of influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
Components
  • Complex: Complex of influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
    • Protein or peptide: Designed influenza hemagglutinin stem #219 HA2
    • Protein or peptide: CR9114 light chain
    • Protein or peptide: CR9114 heavy chain
    • Protein or peptide: FISW84 light chain
    • Protein or peptide: FISW84 heavy chain
    • Protein or peptide: Designed influenza hemagglutinin stem #219 HA1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of influenza hemagglutinin HA stem with CR9114 Fab and FI...

SupramoleculeName: Complex of influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Designed influenza hemagglutinin stem #219 HA2

MacromoleculeName: Designed influenza hemagglutinin stem #219 HA2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 22.529188 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: CLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINCITN KVNSVIEKMN TQYTAIGKEF NKSERRIENL NKKVDDGFL DIWCYIAELL VLLENERTLD FHDSNVKNLY EKVKCQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY P KYSEESKL ...String:
CLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINCITN KVNSVIEKMN TQYTAIGKEF NKSERRIENL NKKVDDGFL DIWCYIAELL VLLENERTLD FHDSNVKNLY EKVKCQLKNN AKEIGNGCFE FYHKCNNECM ESVKNGTYDY P KYSEESKL NREKIDGVKL ESMGVYQIEG RHHHHHH

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Macromolecule #2: CR9114 light chain

MacromoleculeName: CR9114 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.840172 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QSALTQPPAV SGTPGQRVTI SCSGSDSNIG RRSVNWYQQF PGTAPKLLIY SNDQRPSVVP DRFSGSKSGT SASLAISGLQ SEDEAEYYC AAWDDSLKGA VFGGGTQLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPPAV SGTPGQRVTI SCSGSDSNIG RRSVNWYQQF PGTAPKLLIY SNDQRPSVVP DRFSGSKSGT SASLAISGLQ SEDEAEYYC AAWDDSLKGA VFGGGTQLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #3: CR9114 heavy chain

MacromoleculeName: CR9114 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.157125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKSSGGTSN NYAISWVRQA PGQGLDWMGG ISPIFGSTAY AQKFQGRVTI SADIFSNTAY MELNSLTSE DTAVYFCARH GNYYYYSGMD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGAE VKKPGSSVKV SCKSSGGTSN NYAISWVRQA PGQGLDWMGG ISPIFGSTAY AQKFQGRVTI SADIFSNTAY MELNSLTSE DTAVYFCARH GNYYYYSGMD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKTH TCPPCPAPEL LG GPSVFLF PPKPKDTLMI SRTPEVTCVV VDVSHEDPEV KFNWYVDGVE VHNAKTKPRE EQYNSTYRVV SVLTVLHQDW LNG KEYKCK VSNKALPAPI EKTISKAKGQ PREPQVYTLP PSRDELTKNQ VSLTCLVKGF YPSDIAVEWE SNGQPENNYK TTPP VLDSD GSFFLYSKLT VDKSRWQQGN VFSCSVMHEA LHNHYTQKSL SLSPGK

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Macromolecule #4: FISW84 light chain

MacromoleculeName: FISW84 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.38091 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EVVMTQSPAT LSVSPGEGAT LSCRASQSVN TNVAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDFAVYYCQ QYSNWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EVVMTQSPAT LSVSPGEGAT LSCRASQSVN TNVAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDFAVYYCQ QYSNWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: FISW84 heavy chain

MacromoleculeName: FISW84 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.808098 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYGMAWVRQA PGKGLEWVSF ISATGLSTYF ADSVKGRFTI SRDTTKNTLY LQMNSLRAD DTAVYFCARM RRTMIAFGGN DFWGQGTLVT VSSASTKGPS VFPLAPSGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYGMAWVRQA PGKGLEWVSF ISATGLSTYF ADSVKGRFTI SRDTTKNTLY LQMNSLRAD DTAVYFCARM RRTMIAFGGN DFWGQGTLVT VSSASTKGPS VFPLAPSGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CDKTHTCPPC PAPELLGGPS VF LFPPKPK DTLMISRTPE VTCVVVDVSH EDPEVKFNWY VDGVEVHNAK TKPREEQYNS TYRVVSVLTV LHQDWLNGKE YKC KVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSRDE LTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSD GSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPG K

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Macromolecule #6: Designed influenza hemagglutinin stem #219 HA1

MacromoleculeName: Designed influenza hemagglutinin stem #219 HA1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.535295 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
DTICIGYHAN NSTDTVDTVC EKNVTVTHSV NLLEDGGGGY VCSAKLRMVT GLRNKPSKQS Q

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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: 3 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242713
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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