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- PDB-4jul: Crystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.4 -

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Basic information

Entry
Database: PDB / ID: 4jul
TitleCrystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.4
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN / hemagglutinin / viral envelope protein / viral fusion protein / sialic acid / glycosylation
Function / homology
Function and homology information


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
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 / molecular replacement / Resolution: 2.7927 Å
AuthorsDuBois, R.M. / Zaraket, H. / Reddivari, M. / Coop, T. / Heath, R.J. / White, S.W. / Russell, C.J.
CitationJournal: To be Published
Title: To be published
Authors: DuBois, R.M. / Zaraket, H. / Reddivari, M. / Coop, T. / Heath, R.J. / White, S.W. / Russell, C.J.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_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_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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
H: Hemagglutinin HA1
I: Hemagglutinin HA2
J: Hemagglutinin HA1
K: Hemagglutinin HA2
L: Hemagglutinin HA1
M: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,56024
Polymers347,09312
Non-polymers3,46712
Water00
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,28012
Polymers173,5466
Non-polymers1,7346
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29500 Å2
ΔGint-110 kcal/mol
Surface area60780 Å2
MethodPISA
2
H: Hemagglutinin HA1
I: Hemagglutinin HA2
J: Hemagglutinin HA1
K: Hemagglutinin HA2
L: Hemagglutinin HA1
M: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,28012
Polymers173,5466
Non-polymers1,7346
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29260 Å2
ΔGint-124 kcal/mol
Surface area60510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.584, 71.557, 247.054
Angle α, β, γ (deg.)83.94, 85.46, 60.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hemagglutinin HA1


Mass: 36868.527 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/duck/Laos/3295/2006 (H5N1) / Gene: HA, hemagglutinin / Plasmid: pAcGP67B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q00G25
#2: Protein
Hemagglutinin HA2


Mass: 20980.234 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/duck/Laos/3295/2006 (H5N1) / Gene: HA, hemagglutinin / Plasmid: pAcGP67B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q00G25
#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.: 4
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: 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.: 8
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% PEG 6000, 0.2M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7927→50 Å / Num. all: 105080 / Num. obs: 85955 / % possible obs: 81.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7927-2.91.90.379168
2.9-3.022.20.362172.7
3.02-3.152.40.29174.2
3.15-3.322.50.232175.2
3.32-3.532.70.182176.4
3.53-3.82.70.129180
3.8-4.182.70.093185.6
4.18-4.792.60.067191
4.79-6.032.70.061195.7
6.03-503.20.042199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JUM

4jum


Resolution: 2.7927→48.873 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 1.96 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 4347 5.06 %
Rwork0.1959 --
obs0.1989 85835 81.36 %
all-105500 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.1419 Å2
Refinement stepCycle: LAST / Resolution: 2.7927→48.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23528 0 224 0 23752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124317
X-RAY DIFFRACTIONf_angle_d1.43932877
X-RAY DIFFRACTIONf_dihedral_angle_d18.2878926
X-RAY DIFFRACTIONf_chiral_restr0.0993531
X-RAY DIFFRACTIONf_plane_restr0.0064296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7927-2.82440.4071140.3271938X-RAY DIFFRACTION58
2.8244-2.85770.36521280.29342283X-RAY DIFFRACTION67
2.8577-2.89250.42371240.28052333X-RAY DIFFRACTION70
2.8925-2.92910.32281230.26272402X-RAY DIFFRACTION74
2.9291-2.96770.3141090.25572489X-RAY DIFFRACTION72
2.9677-3.00830.29561290.24352427X-RAY DIFFRACTION73
3.0083-3.05130.33851270.24842441X-RAY DIFFRACTION75
3.0513-3.09680.29171330.23192479X-RAY DIFFRACTION73
3.0968-3.14520.34681270.24312476X-RAY DIFFRACTION73
3.1452-3.19670.36691400.23162447X-RAY DIFFRACTION75
3.1967-3.25190.30791370.23122501X-RAY DIFFRACTION73
3.2519-3.3110.27021320.22792503X-RAY DIFFRACTION77
3.311-3.37460.30161430.23372518X-RAY DIFFRACTION75
3.3746-3.44350.32381140.23752563X-RAY DIFFRACTION76
3.4435-3.51840.27711250.22172568X-RAY DIFFRACTION78
3.5184-3.60020.27651410.20452647X-RAY DIFFRACTION78
3.6002-3.69020.25611460.19542623X-RAY DIFFRACTION81
3.6902-3.78990.23071580.18942769X-RAY DIFFRACTION81
3.7899-3.90140.26431550.19222726X-RAY DIFFRACTION84
3.9014-4.02730.22841920.1862843X-RAY DIFFRACTION85
4.0273-4.17110.231700.18192881X-RAY DIFFRACTION87
4.1711-4.3380.23661290.1712991X-RAY DIFFRACTION90
4.338-4.53530.19871730.16113026X-RAY DIFFRACTION90
4.5353-4.77430.20181590.1623137X-RAY DIFFRACTION93
4.7743-5.07310.23011640.17073109X-RAY DIFFRACTION95
5.0731-5.46430.22281550.16553202X-RAY DIFFRACTION95
5.4643-6.01330.22531920.18023233X-RAY DIFFRACTION97
6.0133-6.88140.24021740.17833262X-RAY DIFFRACTION99
6.8814-8.6620.22691640.17833359X-RAY DIFFRACTION100
8.662-48.88060.2181700.17793312X-RAY DIFFRACTION99

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