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- PDB-3vun: Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) he... -

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Basic information

Entry
Database: PDB / ID: 3vun
TitleCrystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group.
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / VIRAL ENVELOPE PROTEIN / MEMBRANE FUSION / Glycosilation
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
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYasutake, Y. / Suzuki, T. / Kawaguchi, A. / Nobusawa, E.
CitationJournal: To be Published
Title: Crystal structure of a influenza A virus (A/Aichi/2/1968 H3N2) hemagglutinin in C2 space group
Authors: Yasutake, Y. / Suzuki, T. / Kawaguchi, A. / Nobusawa, E.
History
DepositionJul 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: 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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,03421
Polymers169,3116
Non-polymers9,72315
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44980 Å2
ΔGint35 kcal/mol
Surface area59500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.016, 98.130, 144.776
Angle α, β, γ (deg.)90.00, 113.11, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA10 - 32510 - 325
21THRTHRGLUGLUCC10 - 32510 - 325
31THRTHRGLUGLUEE10 - 32510 - 325
12GLYGLYILEILEBB1 - 1731 - 173
22GLYGLYILEILEDD1 - 1731 - 173
32GLYGLYILEILEFF1 - 1731 - 173

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.499445, 0.866345, -0.000776), (-0.866344, -0.499446, -0.001241), (-0.001462, 5.3E-5, 0.999999)30.90738, 44.67792, 0.0693
3given(-0.499619, -0.866245, -0.000964), (0.866244, -0.499619, 0.000947), (-0.001302, -0.000362, 0.999999)54.11747, -4.45502, 0.02657

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 36238.652 Da / Num. of mol.: 3 / Mutation: G144S, I182V / Source method: isolated from a natural source
Details: Mutations (G144S and I182V) occurred during laboratory passage
Source: (natural) Influenza A virus / Strain: A/Aichi/2/1968 H3N2 / References: UniProt: P03437
#2: Protein Hemagglutinin HA2 chain


Mass: 20198.324 Da / Num. of mol.: 3 / Mutation: E132D / Source method: isolated from a natural source
Details: Mutations (E132D) occurred during laboratory passage
Source: (natural) Influenza A virus / Strain: A/Aichi/2/1968 H3N2 / References: UniProt: P03437

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Sugars , 4 types, 15 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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: 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: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 6
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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Details

Sequence detailsTHE SEQUENCE CONFLICTS IN THIS STRUCTURE WERE NATURALLY OCCURRENCE.

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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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 0.2M imidazole (pH 7.0), 27% Jeffamine ED-2001 (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 43601 / Num. obs: 43601 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3HMG

3hmg


Resolution: 3→30.59 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 39.396 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27513 2197 5 %RANDOM
Rwork0.21591 ---
obs0.21877 41388 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.656 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å2-3.49 Å2
2--3.53 Å2-0 Å2
3----8.04 Å2
Refinement stepCycle: LAST / Resolution: 3→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11607 0 648 0 12255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.99917124
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27551470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97224.769585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.105151998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9361572
X-RAY DIFFRACTIONr_chiral_restr0.080.22007
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1264MEDIUM POSITIONAL0.070.5
12C1264MEDIUM POSITIONAL0.080.5
13E1264MEDIUM POSITIONAL0.080.5
11A1177LOOSE POSITIONAL0.165
12C1177LOOSE POSITIONAL0.145
13E1177LOOSE POSITIONAL0.165
11A1264MEDIUM THERMAL1.512
12C1264MEDIUM THERMAL1.62
13E1264MEDIUM THERMAL1.542
11A1177LOOSE THERMAL1.8110
12C1177LOOSE THERMAL1.8410
13E1177LOOSE THERMAL1.8210
21B692MEDIUM POSITIONAL0.080.5
22D692MEDIUM POSITIONAL0.070.5
23F692MEDIUM POSITIONAL0.070.5
21B714LOOSE POSITIONAL0.255
22D714LOOSE POSITIONAL0.195
23F714LOOSE POSITIONAL0.165
21B692MEDIUM THERMAL1.52
22D692MEDIUM THERMAL1.512
23F692MEDIUM THERMAL1.622
21B714LOOSE THERMAL1.9810
22D714LOOSE THERMAL1.9710
23F714LOOSE THERMAL1.9710
LS refinement shellResolution: 3.003→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 152 -
Rwork0.308 2784 -
obs--91.98 %
Refinement TLS params.Method: refined / Origin x: 28.3353 Å / Origin y: 13.3963 Å / Origin z: 13.1834 Å
111213212223313233
T0.0045 Å20 Å2-0.0091 Å2-0.0351 Å20.0018 Å2--0.2034 Å2
L0.7259 °20.0048 °20.0104 °2-0.7578 °20.0069 °2--0.3378 °2
S0.0373 Å °0.0521 Å °-0.0041 Å °-0.0396 Å °0.042 Å °-0.0003 Å °-0.0008 Å °0.0077 Å °-0.0793 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 38
2X-RAY DIFFRACTION1A39 - 325
3X-RAY DIFFRACTION1B1 - 62
4X-RAY DIFFRACTION1B63 - 173
5X-RAY DIFFRACTION1C7 - 38
6X-RAY DIFFRACTION1C39 - 325
7X-RAY DIFFRACTION1D1 - 62
8X-RAY DIFFRACTION1D63 - 173
9X-RAY DIFFRACTION1E7 - 38
10X-RAY DIFFRACTION1E39 - 325
11X-RAY DIFFRACTION1F1 - 62
12X-RAY DIFFRACTION1F63 - 173

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