4FQM | pdb_00004fqm

Structure of B/Brisbane/60/2008 Influenza Hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb4FQM/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza B virus (B/Brisbane/60/2008)
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-06-25 Released: 2012-08-22
Deposition Author(s): Dreyfus, C., Laursen, N.S., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free:
0.268 (Depositor), 0.226 (DCC)
R-Value Work:
0.257 (Depositor)
R-Value Observed:
0.258 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Highly conserved protective epitopes on influenza B viruses.

Dreyfus, C., Laursen, N.S., Kwaks, T., Zuijdgeest, D., Khayat, R., Ekiert, D.C., Lee, J.H., Metlagel, Z., Bujny, M.V., Jongeneelen, M., van der Vlugt, R., Lamrani, M., Korse, H.J., Geelen, E., Sahin, O., Sieuwerts, M., Brakenhoff, J.P., Vogels, R., Li, O.T., Poon, L.L., Peiris, M., Koudstaal, W., Ward, A.B., Wilson, I.A., Goudsmit, J., Friesen, R.H.

(2012) Science 337: 1343-1348

PubMed: 22878502 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1222908
Primary Citation Related Structures:
4FQH, 4FQI, 4FQJ, 4FQK, 4FQL, 4FQM, 4FQV, 4FQY

PubMed Abstract:
Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.

Organizational Affiliation

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 360.44 kDa
Atom Count: 24,446
Modeled Residue Count: 3,060
Deposited Residue Count: 3,156
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E, G, I A, C, E, G, I, K	347	Influenza B virus (B/Brisbane/60/2008)	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C0LT38 (Influenza B virus) Explore C0LT38 Go to UniProtKB: C0LT38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0LT38
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain C Focus chain E Focus chain G Focus chain I Focus chain K
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F, H, J B, D, F, H, J, L	179	Influenza B virus (B/Brisbane/60/2008)	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C0LT38 (Influenza B virus) Explore C0LT38 Go to UniProtKB: C0LT38
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0LT38
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F Focus chain H Focus chain J
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
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	AA [auth a], DA [auth d], IA [auth i], JA [auth j], KA [auth k], AA [auth a], DA [auth d], IA [auth i], JA [auth j], KA [auth k], M, NA [auth n], OA [auth o], P, Q, R, T, U, V, Y, Z	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain M Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain Q Focus chain R Focus chain T Focus chain U Focus chain V Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain M Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain Q Focus chain R Focus chain T Focus chain U Focus chain V Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	BA [auth b], CA [auth c], EA [auth e], FA [auth f], GA [auth g], BA [auth b], CA [auth c], EA [auth e], FA [auth f], GA [auth g], HA [auth h], LA [auth l], MA [auth m], N, O, S, W, X	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain O Focus chain S Focus chain W Focus chain X Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain O Focus chain S Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AB [auth G] SDF format, chain EB [auth J] SDF format, chain FB [auth K] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth D] SDF format, chain XA [auth E] SDF format, chain YA [auth F] SDF format, chain ZA [auth G] SDF format, chain WA [auth E] SDF format, chain DB [auth I] SDF format, chain CB [auth I] SDF format, chain BB [auth H] MOL2 format, chain AB [auth G] MOL2 format, chain EB [auth J] MOL2 format, chain FB [auth K] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth G] MOL2 format, chain WA [auth E] MOL2 format, chain DB [auth I] MOL2 format, chain CB [auth I] MOL2 format, chain BB [auth H] mmCIF format, chain AB [auth G] mmCIF format, chain EB [auth J] mmCIF format, chain FB [auth K] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth G] mmCIF format, chain WA [auth E] mmCIF format, chain DB [auth I] mmCIF format, chain CB [auth I] mmCIF format, chain BB [auth H]	AB [auth G] BB [auth H] CB [auth I] DB [auth I] EB [auth J] AB [auth G], BB [auth H], CB [auth I], DB [auth I], EB [auth J], FB [auth K], PA [auth A], QA [auth A], RA [auth B], SA [auth C], TA [auth C], UA [auth C], VA [auth D], WA [auth E], XA [auth E], YA [auth F], ZA [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth G] Focus chain BB [auth H] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EB [auth J] Focus chain FB [auth K] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth D] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth F] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth H] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EB [auth J] Focus chain FB [auth K] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth D] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain YA [auth F] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.268 (Depositor), 0.226 (DCC)
R-Value Work: 0.257 (Depositor)
R-Value Observed: 0.258 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.69	α = 90
b = 242.54	β = 90
c = 135.55	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Dreyfus, C.

Laursen, N.S.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2012-08-22
Type: Initial release
Version 1.1: 2012-10-03
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2018-01-31
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary

4FQM | pdb_00004fqm

Structure of B/Brisbane/60/2008 Influenza Hemagglutinin

Literature

Highly conserved protective epitopes on influenza B viruses.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2