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- PDB-4juk: Crystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.2.1 -

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Basic information

Entry
Database: PDB / ID: 4juk
TitleCrystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.2.1
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: 2.7502 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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 1.2Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7196
Polymers57,9592
Non-polymers7604
Water1,00956
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,15618
Polymers173,8776
Non-polymers2,27912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area29460 Å2
ΔGint-138 kcal/mol
Surface area63140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.365, 116.365, 134.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Hemagglutinin HA1


Mass: 36978.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/common magpie/Hong Kong/5052/2007 (H5N1) / Gene: HA, hemagglutinin / Plasmid: pAcGP67B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: B7NWR4
#2: Protein Hemagglutinin HA2


Mass: 20980.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/common magpie/Hong Kong/5052/2007 (H5N1) / Gene: HA, hemagglutinin / Plasmid: pAcGP67B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: B7NWR4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 3
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 4000, 0.2M LiSO4, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 22883 / Num. obs: 27769 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.15 / Χ2: 1.29 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.853.70.53126541.2861,296.6
2.85-2.964.80.50327271.0421,299.1
2.96-3.160.45127341.1061,299.9
3.1-3.266.80.35827681.221,2100
3.26-3.467.10.26327791.3161,2100
3.46-3.737.10.227791.411,2100
3.73-4.117.10.15927681.3631,2100
4.11-4.77.10.13327941.3691,2100
4.7-5.9270.1228331.2671,299.8
5.92-506.70.08929331.3781,299.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JUM

4jum


Resolution: 2.7502→47.189 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8174 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1397 5.03 %RANDOM
Rwork0.2288 ---
all0.276 27918 --
obs0.2306 27750 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.37 Å2 / Biso mean: 39.5156 Å2 / Biso min: 2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.7502→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 47 56 4020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144090
X-RAY DIFFRACTIONf_angle_d1.3515529
X-RAY DIFFRACTIONf_chiral_restr0.103595
X-RAY DIFFRACTIONf_plane_restr0.005719
X-RAY DIFFRACTIONf_dihedral_angle_d18.0141518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7502-2.84850.30671290.26772516264596
2.8485-2.96250.28241330.2432590272399
2.9625-3.09730.28351400.236525962736100
3.0973-3.26050.29141240.231126442768100
3.2605-3.46480.24761690.216126062775100
3.4648-3.73220.27661340.204326442778100
3.7322-4.10760.25281420.206926302772100
4.1076-4.70150.21891460.196826442790100
4.7015-5.92160.26231520.230726822834100
5.9216-47.19610.29541280.27082801292999

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