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- PDB-6mym: Crystal structure of hemagglutinin from influenza virus A/Phillip... -

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Basic information

Entry
Database: PDB / ID: 6mym
TitleCrystal structure of hemagglutinin from influenza virus A/Phillipines/2/1982 (H3N2)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza hemagglutinin crystal structure / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsDai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be published
Title: Crystal structure of hemagglutinin from influenza virus A/Phillipines/2/1982 (H3N2)
Authors: Dai, Y.N. / Fremont, D.H.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,31725
Polymers167,4703
Non-polymers8,84622
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24690 Å2
ΔGint87 kcal/mol
Surface area61680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.780, 187.580, 107.730
Angle α, β, γ (deg.)90.000, 109.820, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and (resid 8 through 324 or resid 334 through 502))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA8 - 712
211chain BB8 - 713
311(chain C and (resid 8 through 324 or resid 334 through 502))C8 - 324
321(chain C and (resid 8 through 324 or resid 334 through 502))C334 - 502

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Components

#1: Protein Hemagglutinin /


Mass: 55823.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Philippines/2/1982(H3N2))
Strain: A/Philippines/2/1982 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: D8KS88
#2: 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.: 7
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
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 5.56 Å3/Da / Density % sol: 77.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 2.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 16, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.45→48.58 Å / Num. obs: 133433 / % possible obs: 99.7 % / Redundancy: 13.8 % / Biso Wilson estimate: 58.17 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.8
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 12.6 % / Num. unique obs: 6553 / CC1/2: 0.718 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP5

2yp5


Resolution: 2.45→48.58 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.19
RfactorNum. reflection% reflection
Rfree0.2542 6555 4.93 %
Rwork0.227 --
obs0.2283 132930 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 252.24 Å2 / Biso mean: 84.6909 Å2 / Biso min: 37.78 Å2
Refinement stepCycle: final / Resolution: 2.45→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11515 0 581 171 12267
Biso mean--132.26 73.06 -
Num. residues----1459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612394
X-RAY DIFFRACTIONf_angle_d0.89916865
X-RAY DIFFRACTIONf_chiral_restr0.0541946
X-RAY DIFFRACTIONf_plane_restr0.0062141
X-RAY DIFFRACTIONf_dihedral_angle_d13.1867355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7139X-RAY DIFFRACTION9.5TORSIONAL
12B7139X-RAY DIFFRACTION9.5TORSIONAL
13C7139X-RAY DIFFRACTION9.5TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.47780.45692320.42153910414294
2.4778-2.5070.43552020.41884241444399
2.507-2.53760.39142180.3964125434399
2.5376-2.56970.41332240.370342734497100
2.5697-2.60350.36142310.34141984429100
2.6035-2.63920.35512310.324641984429100
2.6392-2.67690.35342070.333942014408100
2.6769-2.71680.35212120.333342164428100
2.7168-2.75930.33262150.301542574472100
2.7593-2.80450.31242300.289541864416100
2.8045-2.85290.3412290.286742254454100
2.8529-2.90470.3182260.293942074433100
2.9047-2.96060.30642210.29542574478100
2.9606-3.0210.32081990.274242204419100
3.021-3.08670.29432120.253442514463100
3.0867-3.15850.27032200.24642294449100
3.1585-3.23740.24992060.234542194425100
3.2374-3.3250.29212130.23542294442100
3.325-3.42280.23292300.21442184448100
3.4228-3.53320.23822280.224542024430100
3.5332-3.65950.2532350.219142314466100
3.6595-3.80590.24172230.2154211443499
3.8059-3.97910.22762470.20474201444899
3.9791-4.18870.21132150.18914223443899
4.1887-4.4510.20521990.17094225442499
4.451-4.79440.19852140.167742154429100
4.7944-5.27640.19672070.176942634470100
5.2764-6.03860.22772130.206542844497100
6.0386-7.60330.26132150.23142694484100
7.6033-48.59120.22842010.2134191439296
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)
12.3749-1.8286-4.662.03073.29227.54070.02550.5512-0.2534-0.3713-0.45730.3203-0.0361-0.91790.38650.52040.0475-0.12930.73430.02630.4626-18.421260.4165122.3728
22.4835-0.3298-2.28951.459-0.01823.67470.17160.3124-0.0144-0.6795-0.2965-0.25570.1050.02870.11910.870.17050.0340.59950.10760.41535.647554.8102104.1264
35.4921-4.5762-3.77354.49492.88322.78210.3440.47210.0587-0.2945-0.27420.1173-0.1694-0.3642-0.05280.3033-0.0224-0.10060.5021-0.00080.4782-31.366575.2654150.2693
42.1016-2.6048-2.2683.91582.79152.7008-0.3581-0.4125-0.12310.38820.2781-0.12020.50680.42960.08810.59220.1045-0.00890.50440.1170.52264.221738.6412144.2135
51.1983-0.9804-1.47243.33832.28282.897-0.1569-0.0512-0.0771-0.3642-0.0048-0.2060.34460.21370.15880.70250.19660.04620.46740.16820.55311.144834.2397127.0794
65.6195-2.056-6.07631.81722.18987.2137-0.5595-0.385-0.37810.53670.13870.08780.75280.49560.41490.51120.019-0.05890.47490.08280.4198-21.10266.7589167.2032
74.0483-2.2448-2.7372.04991.6242.74120.3289-0.24490.4609-0.31590.089-0.8987-0.08760.6924-0.40380.5851-0.01240.09650.7173-0.02670.976221.786566.8883130.8135
82.8635-3.7343-4.05866.00975.76267.06710.0443-0.40960.49350.08840.4809-0.659-0.06150.8021-0.54850.5202-0.0926-0.0530.46850.00330.479-14.7385.6379160.0124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 104 )A8 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 308 )A105 - 308
3X-RAY DIFFRACTION3chain 'A' and (resid 309 through 502 )A309 - 502
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 146 )B8 - 146
5X-RAY DIFFRACTION5chain 'B' and (resid 147 through 314 )B147 - 314
6X-RAY DIFFRACTION6chain 'B' and (resid 315 through 502 )B315 - 502
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 340 )C8 - 340
8X-RAY DIFFRACTION8chain 'C' and (resid 341 through 502 )C341 - 502

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