3R2X | pdb_00003r2x

Crystal structure of the de novo designed binding protein HB36.3 in complex the the 1918 influenza virus hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb3R2X/pdb

Classification: VIRAL PROTEIN/DE NOVO PROTEIN
Organism(s): Influenza A virus (A/Brevig Mission/1/1918(H1N1)), synthetic construct
Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-14 Released: 2011-05-11
Deposition Author(s): Ekiert, D.C., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.249 (Depositor), 0.230 (DCC)
R-Value Work:
0.223 (Depositor), 0.212 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.

Fleishman, S.J., Whitehead, T.A., Ekiert, D.C., Dreyfus, C., Corn, J.E., Strauch, E.M., Wilson, I.A., Baker, D.

(2011) Science 332: 816-821

PubMed: 21566186 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1202617
Primary Citation Related Structures:
3R2X

PubMed Abstract:
We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.

Organizational Affiliation

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content

Total Structure Weight: 68.42 kDa
Atom Count: 4,608
Modeled Residue Count: 575
Deposited Residue Count: 603
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	331	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3 Go to UniProtKB: Q9WFX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WFX3
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	179	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3 Go to UniProtKB: Q9WFX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WFX3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HB36.3, designed hemagglutinin binding protein	C	93	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

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

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 E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.249 (Depositor), 0.230 (DCC)
R-Value Work: 0.223 (Depositor), 0.212 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.054	α = 90
b = 130.054	β = 90
c = 313.735	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
XPREP	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-05-11

Deposition Author(s):

Ekiert, D.C.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2011-05-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-11-27
Changes: Data collection, Database references, Structure summary