8U44

CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06

PDB DOI: https://doi.org/10.2210/pdb8U44/pdb
EM Map EMD-41874: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Expression System: Cricetulus griseus, Trichoplusia ni
Mutation(s): No

Deposited: 2023-09-08 Released: 2024-06-26
Deposition Author(s): Moore, N., Han, J., Ward, A.B., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.41 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Persistence of germinal center B cell responses after influenza virus vaccination in humans

McIntire, K.M., Meng, H., Lin, T.H., Kim, W., Moore, N.E., Han, J., McMahon, M., Wang, M., Malladi, S.K., Mohammed, B.M., Zhou, J.Q., Schmitz, A.J., Hoehn, K., Suessen, T., Middleton, W.D., Teefey, S.A., Presti, R.M., Krammer, F., Turner, J.S., Ward, A.B., Wilson, I.A., Kleinstein, S.H., Ellebedy, A.H.

To be published.

Macromolecule Content

Total Structure Weight: 359.9 kDa
Atom Count: 17,028
Modelled Residue Count: 2,169
Deposited Residue Count: 3,255
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
05.GC.w2.3C10-H1_SI06 Heavy chain	A [auth V], E [auth S], I [auth U]	245	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
05.GC.w2.3C10-H1_SI06 Light chain	B [auth X], F [auth T], J [auth W]	235	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	C [auth A], G, K [auth H]	368	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus) Explore A7Y8I1 Go to UniProtKB: A7Y8I1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7Y8I1
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C [auth A] Focus chain G Focus chain K [auth H]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	D [auth B], H [auth I], L [auth J]	237	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7Y8I1 (Influenza A virus) Explore A7Y8I1 Go to UniProtKB: A7Y8I1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7Y8I1
Sequence Annotations Expand
Reference Sequence

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 P [auth G] SDF format, chain Q [auth G] SDF format, chain T [auth H] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth G] SDF format, chain S [auth H] SDF format, chain U [auth H] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth H] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] MOL2 format, chain U [auth H] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth H] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth G] mmCIF format, chain S [auth H] mmCIF format, chain U [auth H]	M [auth A] N [auth A] O [auth A] P [auth G] Q [auth G] M [auth A], N [auth A], O [auth A], P [auth G], Q [auth G], R [auth G], S [auth H], T [auth H], U [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H]