[English] 日本語
Yorodumi
- EMDB-71420: KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71420
TitleKL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Map datasharpened map
Sample
  • Complex: KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: KL-15-6H4 heavy chain Fv
    • Protein or peptide: KL-15-6H4 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza virus / hemagglutinin / avian influenza virus / antibody Fab complex / glycoprotein / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Biological speciesInfluenza A virus (A/shearwater/West Australia/2576/79(H15N9)) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsLeon AN / Ferguson JA / Han JH / 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: Characterization of the antigenicity of influenza A virus hemagglutinin subtype H15
Authors: Bhavsar D / Leon AN
History
DepositionJun 24, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71420.png

Downloads & links

-
Map

FileDownload / File: emd_71420.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-1.3005456 - 2.0485198
Average (Standard dev.)-0.00019581421 (±0.0468754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_71420_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_71420_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_71420_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/...

EntireName: KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Components
  • Complex: KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: KL-15-6H4 heavy chain Fv
    • Protein or peptide: KL-15-6H4 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/...

SupramoleculeName: KL-H15-6H4 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))

-
Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))
Molecular weightTheoretical: 35.870426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKICLGHHAV ANGTKVNTLT ERGVEVVNAT ETVEITGIDK VCTKGKKAVD LGSCGILGTI IGPPQCDLHL EFKADLIIER RNSSDICYP GRFTNEEALR QIIRESGGID KESMGFRYSG IRTDGATSAC KRTVSSFYSE MKWLSSSMNN QVFPQLNQTY R NTRKEPAL ...String:
DKICLGHHAV ANGTKVNTLT ERGVEVVNAT ETVEITGIDK VCTKGKKAVD LGSCGILGTI IGPPQCDLHL EFKADLIIER RNSSDICYP GRFTNEEALR QIIRESGGID KESMGFRYSG IRTDGATSAC KRTVSSFYSE MKWLSSSMNN QVFPQLNQTY R NTRKEPAL IVWGVHHSSS LDEQNKLYGT GNKLITVGSS KYQQSFSPSP GARPKVNGQA GRIDFHWMLL DPGDTVTFTF NG AFIAPDR ATFLRSNAPS GIEYNGKSLG IQSDAQIDES CEGECFYSGG TINSPLPFQN IDSRAVGKCP RYVKQSSLPL ALG MKNVPE KI

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))
Molecular weightTheoretical: 19.678582 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GAIAGFIENG WEGLIDGWYG FRHQNAQGQG TAADYKSTQA AIDQITGKLN RLIEKTNKQF ELIDNEFTEV EQQIGNVINW TRDSLTEIW SYNAELLVAM ENQHTIDLAD SEMNKLYERV RRQLRENAEE DGTGCFEIFH RCDDQCMESI RNNTYNHTEY R QEALQNRI M

UniProtKB: Hemagglutinin

-
Macromolecule #3: KL-15-6H4 heavy chain Fv

MacromoleculeName: KL-15-6H4 heavy chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.665913 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
QLQQSGTVLA RPGASVKMSC KASGYSFTSY WMHWVKQRPG QGLEWIGAIY PGNSDASNNQ KFTGKANLTA VTSASTAYME LSSLTNEDS AVYYCTRGDY DGYYFDYWGQ GTTLTV

-
Macromolecule #4: KL-15-6H4 light chain Fv

MacromoleculeName: KL-15-6H4 light chain Fv / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.486975 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIVMTQSPSS LSVSAGEKVT MSCKSSQSLL NSGNQKNYLA WYQQKPGQPP KLLIFGASTR ESGVPDRFTG SGSGTDFTLT IHPVQGEDR AVYYCQNYHK YPFTFGWGTK LEIK

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 12 / 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

Concentration0.70 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: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1895 / Average exposure time: 1.4 sec. / Average electron dose: 49.77 e/Å2
Electron beamAcceleration voltage: 300 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: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95746
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