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- PDB-5w5u: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -

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Basic information

Entry
Database: PDB / ID: 5w5u
TitleCrystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141037 (P4)
Components
  • (Hemagglutinin) x 2
  • ACE-PH8-ORN-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
KeywordsVIRAL PROTEIN / Glycoprotein / Ectodomain / N-glycosylation
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: 2.461 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 15, 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 / 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 / pdbx_struct_special_symmetry / 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_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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,65610
Polymers58,2753
Non-polymers1,3807
Water1,02757
1
A: Hemagglutinin
B: Hemagglutinin
D: ACE-PH8-ORN-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)178,96730
Polymers174,8269
Non-polymers4,14021
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area36930 Å2
ΔGint-200 kcal/mol
Surface area65010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.362, 161.362, 161.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-322-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide ACE-PH8-ORN-MLE-GLU-TYR-PHE-GLU-TRP-LEU-SER-BAL / cyclic peptide CP141037 (P4)


Mass: 1486.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 5 molecules

#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.: 1
Source method: isolated from a genetically manipulated source
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.: 4
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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Non-polymers , 2 types, 59 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: HA conc. 11 mg/ml 1M lithium chloride 10% w/v PEG 6000 0.1M sodium citrate, pH= 5.0

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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: 2.46→50 Å / Num. obs: 25055 / % possible obs: 98.4 % / Redundancy: 4.4 % / CC1/2: 0.93 / Rpim(I) all: 0.04 / Rsym value: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1249 / CC1/2: 0.65 / Rpim(I) all: 0.44 / Rsym value: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000v712data reduction
HKL-2000v712data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU7

1ru7


Resolution: 2.461→31.646 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.251 1273 5.08 %
Rwork0.2098 --
obs0.2119 25047 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.461→31.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 0 86 57 4172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074223
X-RAY DIFFRACTIONf_angle_d0.9645721
X-RAY DIFFRACTIONf_dihedral_angle_d12.0681642
X-RAY DIFFRACTIONf_chiral_restr0.048618
X-RAY DIFFRACTIONf_plane_restr0.01743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4607-2.55920.39281430.32522651X-RAY DIFFRACTION100
2.5592-2.67560.36221350.29682673X-RAY DIFFRACTION100
2.6756-2.81660.3321330.29032671X-RAY DIFFRACTION100
2.8166-2.9930.30741450.27432638X-RAY DIFFRACTION100
2.993-3.22390.32161590.2682667X-RAY DIFFRACTION100
3.2239-3.54790.32171420.25172642X-RAY DIFFRACTION99
3.5479-4.06040.2431340.19682652X-RAY DIFFRACTION98
4.0604-5.11220.19291450.1632611X-RAY DIFFRACTION97
5.1122-31.64830.18941370.16072569X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -21.091 Å / Origin y: -35.4558 Å / Origin z: -9.9274 Å
111213212223313233
T0.3719 Å20.0631 Å20.0444 Å2-0.3341 Å20.0177 Å2--0.3066 Å2
L0.6666 °20.5034 °20.3873 °2-0.6755 °20.3104 °2--0.3933 °2
S0.0052 Å °-0.0741 Å °-0.0015 Å °0.1183 Å °-0.0183 Å °0.0198 Å °0.115 Å °0.0137 Å °-0 Å °
Refinement TLS groupSelection details: all

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