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- PDB-4k67: Structure of an airborne transmissible avian influenza H5 hemaggl... -

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Basic information

Entry
Database: PDB / ID: 4k67
TitleStructure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the influenza virus A/Indonesia/5/2005 complexed with human receptor analog LSTc
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 / 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
6'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, W. / Shi, Y. / Lu, X. / Shu, Y. / 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 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 / entity_name_com / 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_molecule_features / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 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 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 2.3Oct 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)223,63616
Polymers220,4598
Non-polymers3,1778
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)167,42212
Polymers165,3446
Non-polymers2,0786
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 area31550 Å2
ΔGint-123 kcal/mol
Surface area58310 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)167,42212
Polymers165,3446
Non-polymers2,0786
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 area31360 Å2
ΔGint-121 kcal/mol
Surface area58620 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,03212
Polymers165,3446
Non-polymers2,6876
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 area32180 Å2
ΔGint-113 kcal/mol
Surface area58940 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,03212
Polymers165,3446
Non-polymers2,6876
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 area32220 Å2
ΔGint-108 kcal/mol
Surface area58950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.626, 70.626, 494.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 4:324 )
21chain C and (resseq 4:324 )
31chain E and (resseq 4:324 )
41chain G and (resseq 4:324 )
12chain B and (resseq 335:498 )
22chain D and (resseq 335:498 )
32chain F and (resseq 335:498 )
42chain H and (resseq 335:498 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSERchain 'A' and (resseq 4:324 )AA4 - 3241 - 321
21GLNGLNSERSERchain 'C' and (resseq 4:324 )CC4 - 3241 - 321
31GLNGLNSERSERchain 'E' and (resseq 4:324 )EE4 - 3241 - 321
41GLNGLNSERSERchain 'G' and (resseq 4:324 )GG4 - 3241 - 321
12GLYGLYGLUGLUchain 'B' and (resseq 335:498 )BB335 - 4981 - 164
22GLYGLYGLUGLUchain 'D' and (resseq 335:498 )DD335 - 4981 - 164
32GLYGLYGLUGLUchain 'F' and (resseq 335:498 )FF335 - 4981 - 164
42GLYGLYGLUGLUchain 'H' and (resseq 335:498 )HH335 - 4981 - 164

NCS ensembles :
ID
1
2

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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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}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.: 4
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: 3.23 Å3/Da / Density % sol: 61.92 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 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: 0.2206
ReflectionResolution: 2.7→50 Å / Num. all: 72276 / Num. obs: 72276 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 51 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FK0

2fk0


Resolution: 2.7→49.117 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7704 / SU ML: 0.39 / σ(F): 1.97 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 3629 5.02 %RANDOM
Rwork0.2273 ---
all0.2287 72239 --
obs0.2287 72239 95.24 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.182 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 276.75 Å2 / Biso mean: 77.8937 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1--8.6607 Å20 Å2-0 Å2
2---8.6607 Å20 Å2
3---17.3213 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15480 0 212 0 15692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516082
X-RAY DIFFRACTIONf_angle_d1.0821772
X-RAY DIFFRACTIONf_dihedral_angle_d18.7675926
X-RAY DIFFRACTIONf_chiral_restr0.1362358
X-RAY DIFFRACTIONf_plane_restr0.0032822
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2542X-RAY DIFFRACTIONPOSITIONAL0.051
12C2542X-RAY DIFFRACTIONPOSITIONAL0.051
13E2542X-RAY DIFFRACTIONPOSITIONAL0.156
14G2542X-RAY DIFFRACTIONPOSITIONAL0.171
21B1328X-RAY DIFFRACTIONPOSITIONAL0.102
22D1328X-RAY DIFFRACTIONPOSITIONAL0.102
23F1328X-RAY DIFFRACTIONPOSITIONAL0.175
24H1328X-RAY DIFFRACTIONPOSITIONAL0.153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6999-2.73540.36261020.351257794
2.7354-2.77290.3691440.3206267396
2.7729-2.81250.32941410.2998266997
2.8125-2.85450.33711380.3051264995
2.8545-2.89910.31891500.2824264097
2.8991-2.94660.32131510.2986265794
2.9466-2.99740.33221420.2829261296
2.9974-3.05190.31111190.2624272495
3.0519-3.11060.26831310.2508260695
3.1106-3.17410.23641500.2282260095
3.1741-3.24310.25171350.2341260494
3.2431-3.31850.29211310.252265496
3.3185-3.40150.30331470.2526259493
3.4015-3.49340.28071420.2349264495
3.4934-3.59620.24251390.2311257893
3.5962-3.71220.26871360.2394261193
3.7122-3.84490.29091250.2345260297
3.8449-3.99870.22571510.2113261294
3.9987-4.18060.25121460.2083264695
4.1806-4.40090.2341510.205267996
4.4009-4.67650.20191550.1944264596
4.6765-5.03720.23141470.1927266696
5.0372-5.54350.221490.2011260696
5.5435-6.34420.23041450.2014274799
6.3442-7.98750.21061250.1984277599
7.9875-49.12480.24451370.2124254091
Refinement TLS params.Method: refined / Origin x: 25.2967 Å / Origin y: 0.8509 Å / Origin z: 178.8035 Å
111213212223313233
T0.1105 Å2-0.0104 Å20.012 Å2-0.1146 Å2-0.0004 Å2--0.1061 Å2
L0 °2-0.0015 °20.0002 °2--0.0015 °20.0034 °2--0.0039 °2
S0.0081 Å °-0.0032 Å °-0.0052 Å °0.0039 Å °0.0026 Å °-0.0081 Å °0.0023 Å °0.0018 Å °-0.0042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 324
2X-RAY DIFFRACTION1allA601 - 603
3X-RAY DIFFRACTION1allB335 - 498
4X-RAY DIFFRACTION1allC4 - 324
5X-RAY DIFFRACTION1allC601 - 603
6X-RAY DIFFRACTION1allD335 - 498
7X-RAY DIFFRACTION1allE4 - 324
8X-RAY DIFFRACTION1allE601 - 604
9X-RAY DIFFRACTION1allF335 - 498
10X-RAY DIFFRACTION1allG4 - 324
11X-RAY DIFFRACTION1allG601 - 604
12X-RAY DIFFRACTION1allH335 - 498

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