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- PDB-4cqz: Crystal Structure of H5 (VN1194) Gln196Arg Mutant Haemagglutinin -

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Basic information

Entry
Database: PDB / ID: 4cqz
TitleCrystal Structure of H5 (VN1194) Gln196Arg Mutant Haemagglutinin
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / HAEMAGGLUTININ MUTANT / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiu, J. / Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Liu, J. / Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Virology / Year: 2014
Title: Enhanced Human Receptor Binding by H5 Haemagglutinins.
Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J.
History
DepositionFeb 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Nov 7, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_chiral / struct_asym / struct_conn / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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)58,0327
Polymers56,0782
Non-polymers1,9545
Water1,56787
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)174,09521
Polymers168,2336
Non-polymers5,86215
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area35160 Å2
ΔGint-63.6 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.149, 101.149, 447.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1


Mass: 36979.828 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340
Mutation: Q196R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Variant: GLN196ARG MUTANT / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34
#2: Protein Hemagglutinin HA2


Mass: 19097.990 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34

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Sugars , 4 types, 4 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-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/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 1
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)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 1
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

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Non-polymers , 2 types, 88 molecules

#7: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMULTIBASIC SITE REMOVED

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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: 3.74 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 0.1 M HEPES/MOPS PH 7.0, 0.05 M MGCL2, 28-30% PEG 550 MME, SEEDED WITH CRUSHED WILD-TYPE VN1194 HA CRYSTALS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→74.65 Å / Num. obs: 24883 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0046refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGW

4bgw


Resolution: 2.7→149.3 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 26.609 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25225 1261 5.1 %RANDOM
Rwork0.21721 ---
obs0.21899 23515 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.888 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.66 Å20 Å2
2--1.33 Å20 Å2
3----4.31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→149.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 129 87 4077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194096
X-RAY DIFFRACTIONr_bond_other_d0.0010.023760
X-RAY DIFFRACTIONr_angle_refined_deg0.9821.9745563
X-RAY DIFFRACTIONr_angle_other_deg0.6573.0038644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2965483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89525.075201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62615679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4251518
X-RAY DIFFRACTIONr_chiral_restr0.0540.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02947
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4544.7481932
X-RAY DIFFRACTIONr_mcbond_other1.4394.7461931
X-RAY DIFFRACTIONr_mcangle_it2.4967.1172412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8225.2732164
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 68 -
Rwork0.343 1723 -
obs--98.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10190.04570.21120.16250.01193.5818-0.05160.04550.04430.0687-0.0855-0.0906-0.3220.74150.13710.216-0.1279-0.06730.36680.03840.1328-29.312535.678256.0648
21.5747-0.5444-0.64081.28130.44532.0177-0.2861-0.49710.04210.13990.2186-0.007-0.34930.39220.06750.4493-0.0784-0.0960.4412-0.02030.0316-34.794641.33791.3109
30.2450.11151.22290.64830.51927.65110.01770.1216-0.0040.0597-0.1115-0.111-0.24830.25740.09380.2041-0.0706-0.06790.34980.02330.1196-30.467635.007747.9598
42.64440.6226-1.83380.2467-0.66246.4143-0.1311-0.10760.1606-0.04370.0206-0.0372-0.73180.62160.11050.2146-0.0741-0.00380.22110.04930.1686-36.181437.539416.3212
51.2158-0.0174-1.09793.5563-4.637314.9885-0.22280.04420.18810.1524-0.0614-0.12250.17790.7120.28420.1794-0.0135-0.01080.25540.0430.1431-43.589928.103564.4692
61.02740.5834-2.18450.3805-1.170710.4564-0.24760.14090.0004-0.0689-0.01060.0059-0.0184-0.64530.25820.2704-0.05550.00150.32740.04280.1698-42.865631.761518.2408
711.95643.97482.40345.4460.02730.6578-0.86140.921.0878-0.88550.65710.454-0.15680.19460.20440.5337-0.2437-0.03680.47560.2310.183-38.124844.0166-5.7018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 262
3X-RAY DIFFRACTION3A263 - 321
4X-RAY DIFFRACTION4B1 - 60
5X-RAY DIFFRACTION5B61 - 84
6X-RAY DIFFRACTION6B85 - 141
7X-RAY DIFFRACTION7B142 - 163

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