[English] 日本語
Yorodumi
- EMDB-70234: Cryo-EM structure of NI06063_d30_103 Fab in complex with influenz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70234
TitleCryo-EM structure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
Map datastructure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
Sample
  • Complex: Cryo-EM structure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: NI06063_d30_103 Fab heavy chain
    • Protein or peptide: NI06063_d30_103 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza / Hemagglutinin / Antibody complex / 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 speciesInfluenza A virus (A/Hong Kong/485197/2014(H3N2)) / Influenza A virus (A/Michigan/45/2015(H1N1)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsJo G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: To Be Published
Title: A single amino acid substitution in hemagglutinin stalk drives heterosubtypic imprinting of cross-group reactive B cells in children
Authors: Jo G / Ward AB
History
DepositionApr 16, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70234.png

Downloads & links

-
Map

FileDownload / File: emd_70234.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.8948018 - 1.0302343
Average (Standard dev.)-0.00019701247 (±0.02193842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_70234_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_70234_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of NI06063_d30_103 Fab in complex with influenz...

EntireName: Cryo-EM structure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
Components
  • Complex: Cryo-EM structure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: NI06063_d30_103 Fab heavy chain
    • Protein or peptide: NI06063_d30_103 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Cryo-EM structure of NI06063_d30_103 Fab in complex with influenz...

SupramoleculeName: Cryo-EM structure of NI06063_d30_103 Fab in complex with influenza virus hemagglutinin from A/Michigan/45/2015 (H1N1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (A/Hong Kong/485197/2014(H3N2))

-
Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Michigan/45/2015(H1N1))
Molecular weightTheoretical: 38.285199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAILVVLLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ASSWSYIVET SNSDNGTCYP GDFINYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK S FYKNLIWL ...String:
MKAILVVLLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ASSWSYIVET SNSDNGTCYP GDFINYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK S FYKNLIWL VKKGNSYPKL NQSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADAYVFV GTSRYSKKFK PEIATRPKVR DQ EGRMNYY WTLVEPGDKI TFEATGNLVV PRYAFTMERN AGSGIIISDT PVHDCNTTCQ TPEGAINTSL PFQNIHPITI GKC PKYVKS TKLRLATGLR NVPSIQSR

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Michigan/45/2015(H1N1))
Molecular weightTheoretical: 26.852693 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREKIDGGYI PEAPRDGQAY VRKDGEWVLL STFLGSENLY FQGSHHHHHH GLNDIFEAQK IEWHE

UniProtKB: Hemagglutinin

-
Macromolecule #3: NI06063_d30_103 Fab heavy chain

MacromoleculeName: NI06063_d30_103 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.519073 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVHLVESGGG VVQPGRSLRL SCAASGFTFS NYGMHWVRQA PGKGLEWVAF ISYDGSNEYY ADSVKGRFTI SRDYSKYTLY LQMNSLRAE DTAVYYCAKD GQWLVRGAFD FWGQGTMVTV SS

-
Macromolecule #4: NI06063_d30_103 Fab light chain

MacromoleculeName: NI06063_d30_103 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.21243 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCSGTGSDVG SSHLVSWYQH HPGKAPKLMI FEVSKRPLGV SNRFSGSKSG NTASLTISGL QTEDEADYY CCSYAGGRGV FGGGTKLTVL

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4107 / Average exposure time: 4.48 sec. / Average electron dose: 44.87 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 276374
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more