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- PDB-4kdn: Crystal structure of the hemagglutinin of ferret-transmissible H5... -

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Basic information

Entry
Database: PDB / ID: 4kdn
TitleCrystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with avian receptor analog LSTa
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / homotrimer / virus attachment and 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 / identical protein binding
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
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.483 Å
AuthorsLu, X. / Shi, Y. / Zhang, W. / Zhang, Y. / Qi, J. / Gao, G.F.
CitationJournal: Protein Cell / Year: 2013
Title: Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut).
Authors: Lu, X. / Shi, Y. / Zhang, W. / Zhang, Y. / Qi, J. / Gao, G.F.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 29, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_src_gen / 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_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_seq_id_1 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,40814
Polymers169,8536
Non-polymers2,5558
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34450 Å2
ΔGint-142 kcal/mol
Surface area61500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.680, 245.156, 68.557
Angle α, β, γ (deg.)90.00, 113.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin /


Mass: 36447.383 Da / Num. of mol.: 3 / Fragment: Residues 17-337 / Mutation: N170D, N236K, Q238L, T331I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: (A/Viet Nam/1203/2004(H5N1)) / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6DQ33
#2: Protein Hemagglutinin /


Mass: 20170.232 Da / Num. of mol.: 3 / Fragment: Residues 347-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: (A/Viet Nam/1203/2004(H5N1)) / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6DQ33

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Sugars , 3 types, 8 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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) influenza virus / Production host: Spodoptera frugiperda (fall armyworm)
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-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) influenza virus / Production host: Spodoptera frugiperda (fall armyworm)
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: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 176 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium cacodylate pH6.0 15% w/v PEG 4,000, 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: Jan 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.483→50 Å / Num. all: 68678 / Num. obs: 68678 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.4

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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 / Resolution: 2.483→35.369 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 30.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 3467 5.05 %RANDOM
Rwork0.2229 ---
all0.2248 68621 --
obs0.2248 68621 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.483→35.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11925 0 168 176 12269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512387
X-RAY DIFFRACTIONf_angle_d1.10316745
X-RAY DIFFRACTIONf_dihedral_angle_d18.4414608
X-RAY DIFFRACTIONf_chiral_restr0.0721803
X-RAY DIFFRACTIONf_plane_restr0.0042173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4832-2.51720.32781100.31142256X-RAY DIFFRACTION84
2.5172-2.55320.32921370.31322721X-RAY DIFFRACTION99
2.5532-2.59130.35611380.28842596X-RAY DIFFRACTION99
2.5913-2.63180.3681530.29772719X-RAY DIFFRACTION100
2.6318-2.67490.3561320.29492636X-RAY DIFFRACTION99
2.6749-2.7210.30661360.29272663X-RAY DIFFRACTION99
2.721-2.77050.33651350.2852672X-RAY DIFFRACTION99
2.7705-2.82370.31881640.2762628X-RAY DIFFRACTION99
2.8237-2.88130.33851420.25982655X-RAY DIFFRACTION99
2.8813-2.9440.31111380.26582647X-RAY DIFFRACTION99
2.944-3.01240.29781340.2682683X-RAY DIFFRACTION99
3.0124-3.08770.29281550.26512641X-RAY DIFFRACTION99
3.0877-3.17110.32491270.25512646X-RAY DIFFRACTION98
3.1711-3.26440.26931410.25772668X-RAY DIFFRACTION99
3.2644-3.36970.29661380.23792645X-RAY DIFFRACTION99
3.3697-3.490.26021260.23362646X-RAY DIFFRACTION98
3.49-3.62960.24721420.22212623X-RAY DIFFRACTION98
3.6296-3.79460.27891190.21262610X-RAY DIFFRACTION97
3.7946-3.99440.27661730.20712579X-RAY DIFFRACTION97
3.9944-4.24430.20731300.19232598X-RAY DIFFRACTION96
4.2443-4.57140.19351510.17962537X-RAY DIFFRACTION95
4.5714-5.03020.22291300.17872506X-RAY DIFFRACTION94
5.0302-5.75540.21961430.18592555X-RAY DIFFRACTION94
5.7554-7.2410.22791360.21332590X-RAY DIFFRACTION96
7.241-35.3730.23171370.1972434X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 6.5696 Å / Origin y: 26.2147 Å / Origin z: 14.4105 Å
111213212223313233
T0.2086 Å20.0119 Å2-0.0155 Å2-0.1996 Å2-0.0089 Å2--0.1396 Å2
L0.4572 °2-0.0647 °2-0.0523 °2-0.5073 °2-0.1533 °2--0.3415 °2
S0.0017 Å °0.0982 Å °-0.0431 Å °-0.069 Å °0.0204 Å °0.0032 Å °0.1721 Å °-0.0075 Å °0.0025 Å °
Refinement TLS groupSelection details: all

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