8TX3 | pdb_00008tx3

Fab 3864-6 in complex with influenza HA H3-VIC11

PDB DOI: https://doi.org/10.2210/pdb8TX3/pdb
EM Map EMD-41676: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Influenza A virus (A/Victoria/361/2011(H3N2)), Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-22 Released: 2024-09-11
Deposition Author(s): Morano, N.C., Shapiro, L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody

Rawi, R., Morano, N.C., Cheung, C.S.F., Du, H., Gorman, J., Prabhakaran, M., Becker, J.E., Bylund, T., Charaf, S., Chen, X., Lee, M., Harris, D.R., Olia, A.S., Ou, L., Wang, L., Wang, S., Zhang, B., Kanekiyo, M., McDermott, A.B., Zhou, T., Shapiro, L., Kwong, P.D.

(2025) Structure

DOI: https://doi.org/10.1016/j.str.2025.07.015

Macromolecule Content

Total Structure Weight: 352.01 kDa
Atom Count: 17,923
Modeled Residue Count: 2,172
Deposited Residue Count: 3,048
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E [auth G]	350	Influenza A virus (A/Victoria/361/2011(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for L0HR89 (Influenza A virus) Explore L0HR89 Go to UniProtKB: L0HR89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0HR89
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain C Focus chain E [auth G]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F [auth I]	222	Influenza A virus (A/Victoria/361/2011(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for L0HR89 (Influenza A virus) Explore L0HR89 Go to UniProtKB: L0HR89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0HR89
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 3864-6 Heavy Chain	G [auth H], I [auth E], K [auth F]	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 3864-6 Light Chain	H [auth L], J, L [auth K]	214	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
alpha-D-mannopyranose-(1-3)-[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	M, N, O, Q, R M, N, O, Q, R, S, U, V, W	5		N-Glycosylation	Interactions Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain U Focus chain V Focus chain W Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain U Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
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	P, T, X	3		N-Glycosylation	Interactions Focus chain P Focus chain T Focus chain X Interactions & Density Focus chain P Focus chain T Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain LA [auth G] SDF format, chain KA [auth G] SDF format, chain JA [auth G] SDF format, chain IA [auth G] SDF format, chain HA [auth D] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth B] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth B] DA [auth C] EA [auth C] AA [auth A], BA [auth A], CA [auth B], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth D], IA [auth G], JA [auth G], KA [auth G], LA [auth G], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth D] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth D] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Morano, N.C.

Shapiro, L.

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	FNIH SHAP19IUFV

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Structure summary
Version 1.2: 2025-09-24
Changes: Data collection, Database references

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 8TX3 | pdb_00008tx3

Fab 3864-6 in complex with influenza HA H3-VIC11

The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

8TX3 | pdb_00008tx3