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- PDB-5w6i: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -

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Basic information

Entry
Database: PDB / ID: 5w6i
TitleCrystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141046 (P3)
Components
  • (Hemagglutinin) x 2
  • ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
KeywordsVIRAL PROTEIN/PEPTIDE / Glycoprotein / Ectodomain / N-glycosylation / VIRAL PROTEIN / VIRAL PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / extracellular region / plasma membrane
Similarity search - Function
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 ...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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å
AuthorsWilson, I.A. / Kadam, R.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: Science / Year: 2017
Title: Potent peptidic fusion inhibitors of influenza virus.
Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Buyck, C. / Schepens, W.B.G. / Kesteleyn, B. / Stoops, B. / Vreeken, R.J. / Vermond, J. / Goutier, W. / Tang, C. / Vogels, R. / Friesen, R.H.E. ...Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Buyck, C. / Schepens, W.B.G. / Kesteleyn, B. / Stoops, B. / Vreeken, R.J. / Vermond, J. / Goutier, W. / Tang, C. / Vogels, R. / Friesen, R.H.E. / Goudsmit, J. / van Dongen, M.J.P. / Wilson, I.A.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
D: ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9778
Polymers58,2613
Non-polymers1,7165
Water00
1
A: Hemagglutinin
B: Hemagglutinin
D: ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
D: ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
D: ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,93124
Polymers174,7849
Non-polymers5,14715
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area37180 Å2
ΔGint-138 kcal/mol
Surface area65690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.305, 164.305, 164.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Hemagglutinin


Mass: 36650.293 Da / Num. of mol.: 1 / Fragment: residues 18-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452
#2: Protein Hemagglutinin


Mass: 20138.393 Da / Num. of mol.: 1 / Fragment: residues 344-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452
#3: Protein/peptide ACE-PH8-ORN-LEU-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL / cyclic peptide CP141046 (P3)


Mass: 1472.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: HA: 11 mg/ml 1M lithium chloride 10% w/v PEG 6000 0.1M sodium citrate, pH=4.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13493 / % possible obs: 99.9 % / Redundancy: 13.8 % / CC1/2: 0.98 / Rpim(I) all: 0.03 / Rsym value: 0.13 / Net I/σ(I): 43
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 4.3 / Num. unique obs: 660 / CC1/2: 0.92 / Rpim(I) all: 0.26 / Rsym value: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v712data reduction
HKL-2000v712data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU7

1ru7


Resolution: 3.104→41.076 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.04
RfactorNum. reflection% reflection
Rfree0.2553 647 4.9 %
Rwork0.208 --
obs0.2103 13205 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.104→41.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 218 0 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064259
X-RAY DIFFRACTIONf_angle_d0.8875774
X-RAY DIFFRACTIONf_dihedral_angle_d11.5091649
X-RAY DIFFRACTIONf_chiral_restr0.066629
X-RAY DIFFRACTIONf_plane_restr0.01747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.104-3.34350.39851340.32932467X-RAY DIFFRACTION98
3.3435-3.67980.34491310.2942455X-RAY DIFFRACTION96
3.6798-4.21180.24521260.23662441X-RAY DIFFRACTION96
4.2118-5.30470.2291330.1772545X-RAY DIFFRACTION99
5.3047-41.07980.2131230.1652650X-RAY DIFFRACTION100

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