6UYN | pdb_00006uyn

Crystal structure of influenza A virus hemagglutinin from A/Ohio/09/2015 bound to the stalk-binding CR6261 antibody Fab

PDB DOI: https://doi.org/10.2210/pdb6UYN/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus, Homo sapiens
Expression System: Trichoplusia ni, Homo sapiens
Mutation(s): Yes

Deposited: 2019-11-13 Released: 2020-09-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.247 (Depositor), 0.253 (DCC)
R-Value Work:
0.209 (Depositor), 0.215 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of influenza A virus hemagglutinin from A/Ohio/09/2015 bound to the stalk-binding CR6261 antibody Fab

Edwards, T.E., Fox III, D., Horanyi, P.S., Lorimer, D.D., Calhoun, B., Conrady, D.G., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 175.42 kDa
Atom Count: 5,967
Modeled Residue Count: 790
Deposited Residue Count: 1,585
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, B	566	Influenza A virus	Mutation(s): 10 Gene Names: HA
UniProt
Find proteins for A0A6C0TB04 (Influenza A virus) Explore A0A6C0TB04 Go to UniProtKB: A0A6C0TB04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6C0TB04
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR6261 Fab heavy chain	C [auth H]	232	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CR6261 Fab light chain	D [auth L]	221	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	2		N-Glycosylation	Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.247 (Depositor), 0.253 (DCC)
R-Value Work: 0.209 (Depositor), 0.215 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.59	α = 90
b = 205.59	β = 90
c = 205.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-09-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-09-02
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary
Version 1.3: 2025-10-22
Changes: Database references, Structure summary