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- PDB-3r2x: Crystal structure of the de novo designed binding protein HB36.3 ... -

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Basic information

Entry
Database: PDB / ID: 3r2x
TitleCrystal structure of the de novo designed binding protein HB36.3 in complex the the 1918 influenza virus hemagglutinin
Components
  • (Hemagglutinin) x 2
  • HB36.3, designed hemagglutinin binding protein
KeywordsVIRAL PROTEIN/DE NOVO PROTEIN / hemagglutinin / glycoprotein / VIRAL PROTEIN-DE NOVO PROTEIN complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Apc36109-like domain / Endonuclease III; domain 1 / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily ...Apc36109-like domain / Endonuclease III; domain 1 / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
artificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: Science / Year: 2011
Title: Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.
Authors: Fleishman, S.J. / Whitehead, T.A. / Ekiert, D.C. / Dreyfus, C. / Corn, J.E. / Strauch, E.M. / Wilson, I.A. / Baker, D.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: HB36.3, designed hemagglutinin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4225
Polymers67,4523
Non-polymers9702
Water0
1
A: Hemagglutinin
B: Hemagglutinin
C: HB36.3, designed hemagglutinin binding protein
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
C: HB36.3, designed hemagglutinin binding protein
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
C: HB36.3, designed hemagglutinin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,26715
Polymers202,3579
Non-polymers2,9106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area36240 Å2
ΔGint-149 kcal/mol
Surface area70580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.054, 130.054, 313.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin / / 1918 hemagglutinin receptor binding domain


Mass: 36452.797 Da / Num. of mol.: 1 / Fragment: HA1 chain (UNP residues 18-344)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918 (H1N1) / Gene: HA, hemagglutinin / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin / / 1918 hemagglutinin fusion subunit


Mass: 20394.445 Da / Num. of mol.: 1 / Fragment: HA2 chain (UNP residues 345-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918 (H1N1) / Gene: HA, hemagglutinin / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q9WFX3
#3: Protein HB36.3, designed hemagglutinin binding protein


Mass: 10605.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (BL21/DE3)
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG8000, 200 mM magnesium chloride, 100mM Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 19261 / Num. obs: 19208 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 118 Å2 / Rsym value: 0.22 / Net I/σ(I): 19.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.19 / Rsym value: 0.84 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.745 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 955 5.07 %RANDOM
Rwork0.2233 ---
obs0.2245 18838 99.55 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.87 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.7226 Å20 Å20 Å2
2---6.7226 Å20 Å2
3---13.4451 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 64 0 4608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144728
X-RAY DIFFRACTIONf_angle_d1.7956413
X-RAY DIFFRACTIONf_dihedral_angle_d17.1761730
X-RAY DIFFRACTIONf_chiral_restr0.093700
X-RAY DIFFRACTIONf_plane_restr0.009824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.26350.42731500.39992483X-RAY DIFFRACTION99
3.2635-3.46790.36581320.36452515X-RAY DIFFRACTION100
3.4679-3.73550.32121360.292521X-RAY DIFFRACTION100
3.7355-4.11120.27941230.22012550X-RAY DIFFRACTION100
4.1112-4.70560.18861540.16952536X-RAY DIFFRACTION100
4.7056-5.92650.23241320.18332599X-RAY DIFFRACTION100
5.9265-45.750.23181280.21822679X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61240.3233-0.49312.03990.61875.6349-0.28540.23760.0786-0.34860.1534-0.43130.08510.6758-1.39120.7605-0.09490.03541.05770.11621.2831-45.6744.67765.0683
21.11840.02470.89340.6397-0.41760.9767-0.1511-0.80210.25940.6663-0.2352-0.2837-0.2224-0.10670.14841.5328-0.0355-0.30371.6502-0.04151.2727-52.957240.699257.532
31.4391-0.4835-0.44861.48610.11562.1105-0.6859-0.41310.04630.02120.2848-0.73930.42451.00880.30551.38140.1295-0.37721.97230.33561.8548-31.337740.576246.8611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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