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- PDB-4k65: Structure of an airborne transmissible avian influenza H5 hemaggl... -

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Basic information

Entry
Database: PDB / ID: 4k65
TitleStructure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the influenza virus A/Indonesia/5/2005
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / virus attachment / membrane fusion
Function / homology
Function and homology information


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 / 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: 2.9 Å
AuthorsZhang, W. / Shi, Y. / Lu, X. / Shu, Y. / Qi, J. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: An airborne transmissible avian influenza H5 hemagglutinin seen at the atomic level.
Authors: Zhang, W. / Shi, Y. / Lu, X. / Shu, Y. / Qi, J. / Gao, G.F.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Refinement description
Revision 1.2Jul 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,90210
Polymers220,4598
Non-polymers4422
Water00
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0089
Polymers165,3446
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area28460 Å2
ΔGint-132 kcal/mol
Surface area58470 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0089
Polymers165,3446
Non-polymers6643
Water0
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 area28340 Å2
ΔGint-134 kcal/mol
Surface area58800 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin

E: Hemagglutinin
F: Hemagglutinin

E: Hemagglutinin
F: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)165,3446
Polymers165,3446
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area27450 Å2
ΔGint-154 kcal/mol
Surface area59350 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin

G: Hemagglutinin
H: Hemagglutinin

G: Hemagglutinin
H: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)165,3446
Polymers165,3446
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area27730 Å2
ΔGint-152 kcal/mol
Surface area59530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.637, 70.637, 487.656
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Hemagglutinin


Mass: 36203.953 Da / Num. of mol.: 4 / Fragment: UNP residues 17-326 / Mutation: H107Y, T160A, Q226L, G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Indonesia/5/2005(H5N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8HWY8
#2: Protein
Hemagglutinin


Mass: 18910.838 Da / Num. of mol.: 4 / Fragment: UNP residues 347-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Indonesia/5/2005(H5N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8HWY8
#3: 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.: 2
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
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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 1500, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: -h,-k,l / Fraction: 0.431
ReflectionResolution: 2.9→50 Å / Num. all: 56188 / Num. obs: 56188 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→3 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FK0

2fk0


Resolution: 2.9→48.876 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8088 / SU ML: 0.34 / σ(F): 1.97 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 2833 5.05 %RANDOM
Rwork0.2081 ---
all0.2106 56153 --
obs0.2106 56153 92.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.66 Å2 / Biso mean: 61.2666 Å2 / Biso min: 2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15480 0 28 0 15508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515890
X-RAY DIFFRACTIONf_angle_d0.98721490
X-RAY DIFFRACTIONf_dihedral_angle_d16.4865848
X-RAY DIFFRACTIONf_chiral_restr0.0682292
X-RAY DIFFRACTIONf_plane_restr0.0052810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8945-2.94440.37251290.2983257287
2.9444-2.99790.27781370.2593259292
2.9979-3.05560.28951540.259272792
3.0556-3.1180.31951460.2547258492
3.118-3.18570.28461420.2534268393
3.1857-3.25980.33771370.2472263793
3.2598-3.34130.28881490.2471271092
3.3413-3.43170.28961350.235261794
3.4317-3.53260.31261580.2284270191
3.5326-3.64660.26261450.204255992
3.6466-3.77690.24051210.2139261390
3.7769-3.9280.23181410.1967270991
3.928-4.10670.23691430.1823266794
4.1067-4.32310.22371400.1737263792
4.3231-4.59380.20381440.1661262392
4.5938-4.94820.23361380.169268692
4.9482-5.44550.24081410.1854264691
5.4455-6.23210.23241320.2062268093
6.2321-7.84660.24561470.209284097
7.8466-48.88310.24961540.2073283798
Refinement TLS params.Method: refined / Origin x: 24.5671 Å / Origin y: -2.3255 Å / Origin z: -174.9651 Å
111213212223313233
T0.03 Å20.0016 Å2-0.0005 Å2-0.0254 Å20.0029 Å2--0.0313 Å2
L-0.0016 °20.0001 °2-0.0006 °2--0.0008 °2-0.001 °2--0.0002 °2
S-0.0026 Å °-0.003 Å °-0.0077 Å °0.0007 Å °-0.0044 Å °-0.0026 Å °-0.0022 Å °0.0045 Å °0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 324
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allB335 - 498
4X-RAY DIFFRACTION1allC4 - 324
5X-RAY DIFFRACTION1allC601
6X-RAY DIFFRACTION1allD335 - 498
7X-RAY DIFFRACTION1allE4 - 324
8X-RAY DIFFRACTION1allF335 - 498
9X-RAY DIFFRACTION1allG4 - 324
10X-RAY DIFFRACTION1allH335 - 498

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