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- PDB-3al4: Crystal structure of the swine-origin A (H1N1)-2009 influenza A v... -

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Entry
Database: PDB / ID: 3al4
TitleCrystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN/VIRAL PROTEIN / TRIMER / ENVELOPE PROTEIN / HEMAGGLUTININ / VIRAL PROTEIN-VIRAL 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 / metal ion binding / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.872 Å
AuthorsZhang, W. / Qi, J.X. / Shi, Y. / Li, Q. / Yan, J.H. / Gao, G.F.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus
Authors: Zhang, W. / Qi, J. / Shi, Y. / Li, Q. / Gao, F. / Sun, Y. / Lu, X. / Lu, Q. / Vavricka, C.J. / Liu, D. / Yan, J. / Gao, G.F.
History
DepositionJul 22, 2010Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 4, 2010ID: 3LYJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _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_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
Revision 2.1Nov 1, 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,31535
Polymers346,48112
Non-polymers6,83423
Water5,711317
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0386
Polymers57,7472
Non-polymers1,2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-41 kcal/mol
Surface area23620 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2006
Polymers57,7472
Non-polymers1,4534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-41 kcal/mol
Surface area23650 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0567
Polymers57,7472
Non-polymers1,3095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-42 kcal/mol
Surface area23700 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4105
Polymers57,7472
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-39 kcal/mol
Surface area23530 Å2
MethodPISA
5
I: Hemagglutinin
J: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7584
Polymers57,7472
Non-polymers1,0112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-41 kcal/mol
Surface area23430 Å2
MethodPISA
6
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8537
Polymers57,7472
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-42 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.020, 115.190, 114.985
Angle α, β, γ (deg.)62.31, 77.94, 81.05
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin


Mass: 36989.715 Da / Num. of mol.: 6 / Fragment: UNP residues 18-344
Source method: isolated from a genetically manipulated source
Details: HEMAGGLUTININ HA1 / Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/04/2009(H1N1) / Gene: HEMAGGLUTININ / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1
#2: Protein
Hemagglutinin


Mass: 20757.035 Da / Num. of mol.: 6 / Fragment: UNP residues 345-520
Source method: isolated from a genetically manipulated source
Details: HEMAGGLUTININ HA2 / Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/04/2009(H1N1) / Gene: HEMAGGLUTININ / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1

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Sugars , 3 types, 23 molecules

#3: 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.: 5
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
#4: 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.: 2
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
#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.: 16
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 , 1 types, 317 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 6000, 5% MPD, 0.1M MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.872→50 Å / Num. obs: 64796 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Biso Wilson estimate: 56.27 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 12.9
Reflection shellResolution: 2.87→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.501 / % possible all: 90.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(PHENIX.REFINE: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RU7

1ru7


Resolution: 2.872→24.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0.07 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 3085 5.05 %
Rwork0.246 57982 -
obs0.247 61067 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.94 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso max: 330.34 Å2 / Biso mean: 81.17 Å2 / Biso min: 16.64 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å22.924 Å2-2.521 Å2
2--0.618 Å217.083 Å2
3---4.893 Å2
Refinement stepCycle: LAST / Resolution: 2.872→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22867 0 442 317 23626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423966
X-RAY DIFFRACTIONf_angle_d0.97132453
X-RAY DIFFRACTIONf_dihedral_angle_d19.6068661
X-RAY DIFFRACTIONf_chiral_restr0.0663553
X-RAY DIFFRACTIONf_plane_restr0.0044140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8716-2.91640.3783850.32541567X-RAY DIFFRACTION57
2.9164-2.96410.36681160.31792233X-RAY DIFFRACTION77
2.9641-3.01510.35271270.31522338X-RAY DIFFRACTION80
3.0151-3.06990.32851050.3172389X-RAY DIFFRACTION84
3.0699-3.12880.33021230.29332541X-RAY DIFFRACTION86
3.1288-3.19250.32731470.29532503X-RAY DIFFRACTION88
3.1925-3.26180.31231370.29112574X-RAY DIFFRACTION90
3.2618-3.33750.31831320.2842652X-RAY DIFFRACTION91
3.3375-3.42070.30811230.28042670X-RAY DIFFRACTION92
3.4207-3.51290.30911340.27822697X-RAY DIFFRACTION93
3.5129-3.6160.30331390.25762745X-RAY DIFFRACTION96
3.616-3.73230.28771620.25682787X-RAY DIFFRACTION97
3.7323-3.86520.24881500.24842823X-RAY DIFFRACTION97
3.8652-4.01920.27721370.24522787X-RAY DIFFRACTION97
4.0192-4.20130.25461730.2342737X-RAY DIFFRACTION97
4.2013-4.42150.24941540.22472915X-RAY DIFFRACTION99
4.4215-4.69660.25431510.2052788X-RAY DIFFRACTION98
4.6966-5.05620.26181480.21962862X-RAY DIFFRACTION99
5.0562-5.55940.23041800.20892826X-RAY DIFFRACTION99
5.5594-6.35120.26471720.2392821X-RAY DIFFRACTION99
6.3512-7.95420.26021400.22982883X-RAY DIFFRACTION100
7.9542-24.1880.1941500.19962844X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -20.2272 Å / Origin y: -28.1217 Å / Origin z: -32.6646 Å
111213212223313233
T0.1288 Å20.0127 Å2-0.0565 Å2-0.1607 Å20.009 Å2--0.1165 Å2
L0.2871 °20.1286 °2-0.1928 °2-0.2431 °2-0.0709 °2--0.1527 °2
S0.0345 Å °-0.0095 Å °-0.012 Å °0.0208 Å °-0.0623 Å °-0.1407 Å °-0.0011 Å °-0.0542 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA7 - 370
2X-RAY DIFFRACTION1ALLB1 - 307
3X-RAY DIFFRACTION1ALLC7 - 371
4X-RAY DIFFRACTION1ALLD1 - 265
5X-RAY DIFFRACTION1ALLE7 - 364
6X-RAY DIFFRACTION1ALLF2 - 284
7X-RAY DIFFRACTION1ALLG7 - 378
8X-RAY DIFFRACTION1ALLH1 - 277
9X-RAY DIFFRACTION1ALLI7 - 371
10X-RAY DIFFRACTION1ALLJ1 - 319
11X-RAY DIFFRACTION1ALLK7 - 369
12X-RAY DIFFRACTION1ALLL2 - 279

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