8T1G

The crystal structure of hemagglutinin form a h7n9 influenza virus (a/shanghai/1/2013) in complex with antibody 1E11

PDB DOI: https://doi.org/10.2210/pdb8T1G/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Influenza A virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-06-02 Released: 2024-05-29
Deposition Author(s): Zhou, T., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.215
R-Value Work: 0.182
R-Value Observed: 0.182

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of hemagglutinin form a h7n9 influenza virus (a/shanghai/1/2013) in complex with antibody 1E11

Zhou, T., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 328.82 kDa
Atom Count: 22,809
Modelled Residue Count: 2,914
Deposited Residue Count: 2,946
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	321	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21 Go to UniProtKB: R4NN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4NN21
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	210	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21 Go to UniProtKB: R4NN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4NN21
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D Focus chain F
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1E11 Fab Heavy chain	G, H, J	232	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
1E11 Fab Light chain	I, K, L	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O, Q	3		N-Glycosylation	Interactions Focus chain M Focus chain O Focus chain Q Interactions & Density Focus chain M Focus chain O Focus chain Q
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	N, R	4		N-Glycosylation	Interactions Focus chain N Focus chain R Interactions & Density Focus chain N Focus chain R
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	4		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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 U [auth B] SDF format, chain W [auth C] SDF format, chain AA [auth F] SDF format, chain T [auth A] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain T [auth A] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain U [auth B] mmCIF format, chain W [auth C] mmCIF format, chain AA [auth F] mmCIF format, chain T [auth A] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth F] T [auth A] U [auth B] W [auth C] X [auth D] AA [auth F], T [auth A], U [auth B], W [auth C], X [auth D], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain T [auth A] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain T [auth A] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Z [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain V [auth C] SDF format, chain Y [auth E] MOL2 format, chain S [auth A] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth E] mmCIF format, chain S [auth A] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth E]	S [auth A], V [auth C], Y [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain V [auth C] Focus chain Y [auth E] Interactions & Density Focus chain S [auth A] Focus chain V [auth C] Focus chain Y [auth E]