7JIX | pdb_00007jix

Murine antibody that engages the influenza hemagglutinin receptor binding site

PDB DOI: https://doi.org/10.2210/pdb7JIX/pdb

Classification: Viral protein/IMMUNE SYSTEM
Organism(s): Influenza A virus (A/Solomon Islands/3/2006 (Egg passage)(H1N1)), Influenza A virus (A/Mexico/UASLP-006/2008(H1N1)), Mus musculus
Expression System: Trichoplusia ni, Homo sapiens
Mutation(s): No

Deposited: 2020-07-23 Released: 2021-07-28
Deposition Author(s): Bajic, G., Schmidt, A.G.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free:
0.255 (Depositor), 0.254 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Murine antibody that engages the influenza hemagglutinin receptor binding site

Bajic, G., Schmidt, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 107.9 kDa
Atom Count: 7,365
Modeled Residue Count: 931
Deposited Residue Count: 958
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A	334	Influenza A virus (A/Solomon Islands/3/2006 (Egg passage)(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7Y8A6 (Influenza A virus) Explore A7Y8A6 Go to UniProtKB: A7Y8A6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7Y8A6
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B	177	Influenza A virus (A/Mexico/UASLP-006/2008(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for G2TTT7 (Influenza A virus) Explore G2TTT7 Go to UniProtKB: G2TTT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2TTT7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	C [auth L]	220	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	D [auth H]	227	Mus musculus	Mutation(s): 0

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	5		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G78750JU GlyCosmos: G78750JU GlyGen: G78750JU

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], G [auth E]	3		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain G [auth E] Interactions & Density Focus chain F [auth D] Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.255 (Depositor), 0.254 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.507	α = 90
b = 198.507	β = 90
c = 198.507	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Bajic, G.

Schmidt, A.G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI089618

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary