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- PDB-4n5z: Crystal structure of aerosol transmissible influenza H5 hemagglut... -

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Basic information

Entry
Database: PDB / ID: 4n5z
TitleCrystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D, N224K, Q226L and T318I) from the influenza virus A/Viet Nam/1203/2004 (H5N1)
Components
  • Hemagglutinin
  • Hemagglutinin HA1 chain
KeywordsVIRAL PROTEIN / H5N1 / Influenza Virus / hemagglutinin / Ferret transmissible
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane / identical protein binding / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9537 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2014
Title: Hemagglutinin Receptor Specificity and Structural Analyses of Respiratory Droplet-Transmissible H5N1 Viruses.
Authors: de Vries, R.P. / Zhu, X. / McBride, R. / Rigter, A. / Hanson, A. / Zhong, G. / Hatta, M. / Xu, R. / Yu, W. / Kawaoka, Y. / de Haan, C.A. / Wilson, I.A. / Paulson, J.C.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_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
Revision 2.2Nov 6, 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 HA1 chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA1 chain
K: Hemagglutinin HA1 chain
M: Hemagglutinin HA1 chain
O: Hemagglutinin HA1 chain
Q: Hemagglutinin HA1 chain
S: Hemagglutinin HA1 chain
U: Hemagglutinin HA1 chain
W: Hemagglutinin HA1 chain
Y: Hemagglutinin HA1 chain
a: Hemagglutinin HA1 chain
c: Hemagglutinin HA1 chain
B: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
H: Hemagglutinin
J: Hemagglutinin
L: Hemagglutinin
N: Hemagglutinin
P: Hemagglutinin
R: Hemagglutinin
T: Hemagglutinin
V: Hemagglutinin
X: Hemagglutinin
Z: Hemagglutinin
b: Hemagglutinin
d: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)895,88960
Polymers882,63430
Non-polymers13,25530
Water00
1
A: Hemagglutinin HA1 chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA1 chain
B: Hemagglutinin
H: Hemagglutinin
J: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,56012
Polymers176,5276
Non-polymers3,0336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28280 Å2
ΔGint-136 kcal/mol
Surface area62700 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
K: Hemagglutinin HA1 chain
D: Hemagglutinin
F: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,15312
Polymers176,5276
Non-polymers2,6266
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28700 Å2
ΔGint-150 kcal/mol
Surface area62550 Å2
MethodPISA
3
M: Hemagglutinin HA1 chain
O: Hemagglutinin HA1 chain
Q: Hemagglutinin HA1 chain
N: Hemagglutinin
P: Hemagglutinin
R: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,57813
Polymers176,5276
Non-polymers3,0517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28640 Å2
ΔGint-144 kcal/mol
Surface area62460 Å2
MethodPISA
4
S: Hemagglutinin HA1 chain
U: Hemagglutinin HA1 chain
W: Hemagglutinin HA1 chain
T: Hemagglutinin
V: Hemagglutinin
X: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,56012
Polymers176,5276
Non-polymers3,0336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28780 Å2
ΔGint-141 kcal/mol
Surface area62890 Å2
MethodPISA
5
Y: Hemagglutinin HA1 chain
a: Hemagglutinin HA1 chain
c: Hemagglutinin HA1 chain
Z: Hemagglutinin
b: Hemagglutinin
d: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,03911
Polymers176,5276
Non-polymers1,5125
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28590 Å2
ΔGint-134 kcal/mol
Surface area62810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.240, 118.943, 273.410
Angle α, β, γ (deg.)88.43, 89.68, 60.26
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Hemagglutinin HA1 chain


Mass: 37961.168 Da / Num. of mol.: 15 / Fragment: receptor binding domain, HA1 / Mutation: N158D, N224K, Q226L, T318I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/VIET NAM/1203/2004 / Gene: HA / Plasmid: PFASTBAC-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6DQ33, UniProt: Q5EP31*PLUS
#2: Protein
Hemagglutinin


Mass: 20881.104 Da / Num. of mol.: 15 / Fragment: membrane fusion domain, HA2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/VIET NAM/1203/2004 / Gene: HA / Plasmid: PFASTBAC-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6DQ33
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 11
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
#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.: 7
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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M tris, pH 8.0, 0.2 M KF, 20% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.05876 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05876 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 236232 / % possible obs: 89.7 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.13 / Net I/σ(I): 8.5
Reflection shellResolution: 2.95→3.02 Å / % possible all: 77.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N5Y

4n5y


Resolution: 2.9537→47.749 Å / SU ML: 0.47 / Cross valid method: throughtout / σ(F): 1.96 / Phase error: 32.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 11846 5.02 %RANDOM
Rwork0.233 ---
obs0.2354 235905 87.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9537→47.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60030 0 874 0 60904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01162611
X-RAY DIFFRACTIONf_angle_d1.45584691
X-RAY DIFFRACTIONf_dihedral_angle_d18.33623380
X-RAY DIFFRACTIONf_chiral_restr0.0659153
X-RAY DIFFRACTIONf_plane_restr0.00810979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9537-2.98720.43661130.37072214X-RAY DIFFRACTION26
2.9872-3.02240.43133510.37366398X-RAY DIFFRACTION76
3.0224-3.05920.43233350.36797075X-RAY DIFFRACTION82
3.0592-3.0980.40073830.34967010X-RAY DIFFRACTION83
3.098-3.13870.36523890.32427320X-RAY DIFFRACTION85
3.1387-3.18170.38594090.31287076X-RAY DIFFRACTION84
3.1817-3.22710.34823670.30347325X-RAY DIFFRACTION86
3.2271-3.27530.35233370.2997146X-RAY DIFFRACTION83
3.2753-3.32650.35993880.30167258X-RAY DIFFRACTION86
3.3265-3.3810.34533980.30277355X-RAY DIFFRACTION86
3.381-3.43930.32943610.31827347X-RAY DIFFRACTION86
3.4393-3.50180.37953840.28777051X-RAY DIFFRACTION83
3.5018-3.56910.31014160.26937365X-RAY DIFFRACTION87
3.5691-3.6420.31284050.26597556X-RAY DIFFRACTION89
3.642-3.72110.35944040.28337129X-RAY DIFFRACTION84
3.7211-3.80760.28794000.2617654X-RAY DIFFRACTION90
3.8076-3.90280.32554160.25887768X-RAY DIFFRACTION91
3.9028-4.00830.33353730.26227322X-RAY DIFFRACTION87
4.0083-4.12620.26434530.21037999X-RAY DIFFRACTION94
4.1262-4.25930.25994150.19988122X-RAY DIFFRACTION95
4.2593-4.41140.23433920.19178192X-RAY DIFFRACTION96
4.4114-4.58790.23854170.19058135X-RAY DIFFRACTION96
4.5879-4.79650.22934410.18248185X-RAY DIFFRACTION96
4.7965-5.04910.24764560.18868211X-RAY DIFFRACTION97
5.0491-5.36510.24333980.18128392X-RAY DIFFRACTION97
5.3651-5.77870.21774680.18668257X-RAY DIFFRACTION98
5.7787-6.3590.2494600.1978387X-RAY DIFFRACTION99
6.359-7.27640.23184510.19798390X-RAY DIFFRACTION99
7.2764-9.15690.22864340.19278407X-RAY DIFFRACTION98
9.1569-47.75480.2464320.22438013X-RAY DIFFRACTION95

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