[English] 日本語
Yorodumi
- EMDB-45424: PN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45424
TitlePN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin
Map dataPN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin
Sample
  • Complex: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
    • Protein or peptide: Y2 COBRA HA
    • Protein or peptide: PN-SIA49 Fab heavy chain
    • Protein or peptide: PN-SIA49 Fab light chain
KeywordsAntibody / influenza / Fab / VIRAL PROTEIN
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsNagashima KA / Mousa JJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: To Be Published
Title: Cryo-EM map of the PN-SIA49 Fab in complex with the Y2 H1 influenza hemagglutinin
Authors: Nagashima KA / Mousa JJ
History
DepositionJun 19, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45424.png

Downloads & links

-
Map

FileDownload / File: emd_45424.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 384 pix.
= 468.48 Å		1.22 Å/pix.
x 384 pix.
= 468.48 Å		1.22 Å/pix.
x 384 pix.
= 468.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.02569748 - 2.297837
Average (Standard dev.)0.0005001541 (±0.013976184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 468.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional Map

Fileemd_45424_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_45424_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_45424_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin

EntireName: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
Components
  • Complex: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
    • Protein or peptide: Y2 COBRA HA
    • Protein or peptide: PN-SIA49 Fab heavy chain
    • Protein or peptide: PN-SIA49 Fab light chain

-
Supramolecule #1: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin

SupramoleculeName: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus

-
Macromolecule #1: Y2 COBRA HA

MacromoleculeName: Y2 COBRA HA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAILVVLLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETS NSDNGTCYPG DFINYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK ...String:
MKAILVVLLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETS NSDNGTCYPG DFINYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK KGNSYPKLSQ SYINDKGKEV LVLWGIHHPS TTADQQSLYQ NADAYVFVGT SRYSKKFKPE IAIRPKVRDQ EGRMNYYWTL VEPGDKITFE ATGNLVVPRY AFTMERNAGS GIIISDTPVH DCNTTCQTPE GAINTSLPFQ NVHPITIGKC PKYVKSTKLR LATGLRNVPS IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID KITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRNQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREKIDGV GTGYIPEAPR DGQAYVRKDG EWVLLSTFLG SGLNDIFEAQ KIEWHEGHHH HHH

-
Macromolecule #2: PN-SIA49 Fab heavy chain

MacromoleculeName: PN-SIA49 Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVKLLESGGG LVQPGGSLRL SCAASGITFS SYAMSWVRQA PGKGLEWVST VNSGGGSTYY GDSVRGRFTI SRDNSKSTLY LQLNSLRAED TAIYYCAKDK GRPIFGLVTP SYYMDVWGNG TTVTVSS

-
Macromolecule #3: PN-SIA49 Fab light chain

MacromoleculeName: PN-SIA49 Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ELTQSPSSLS ASVGDSVTIT CRTSERISTY LNWYQQKPGK APRLLVSGAS TLQGGVPSRF SGSGSGTAFT LTINSLQPED FATYYCQQSY STPLTFGGGT KVEIK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 110499
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110499
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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