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- PDB-4cqp: Crystal Structure of H5 (VN1194) Ser227Asn/Gln196Arg Mutant Haema... -

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Basic information

Entry
Database: PDB / ID: 4cqp
TitleCrystal Structure of H5 (VN1194) Ser227Asn/Gln196Arg Mutant Haemagglutinin
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsXiong, 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. ...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.
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
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
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _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.id / _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 / _database_PDB_caveat.text / _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_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)58,8889
Polymers56,1052
Non-polymers2,7837
Water41423
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)176,66327
Polymers168,3156
Non-polymers8,34821
Water1086
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 area36150 Å2
ΔGint-32.9 kcal/mol
Surface area64000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.635, 100.635, 448.712
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: 37006.852 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
Mutation: S227N/Q196R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Variant: SER227ASN/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, 5 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.: 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)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 1
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)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 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

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Non-polymers , 2 types, 25 molecules

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


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→43.37 Å / Num. obs: 26069 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0046refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGW

4bgw


Resolution: 2.65→149.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 26.053 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1327 5.1 %RANDOM
Rwork0.19331 ---
obs0.19555 24721 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å21.47 Å20 Å2
2--2.94 Å20 Å2
3----9.55 Å2
Refinement stepCycle: LAST / Resolution: 2.65→149.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 182 23 4068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194156
X-RAY DIFFRACTIONr_bond_other_d0.0010.023806
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9895648
X-RAY DIFFRACTIONr_angle_other_deg0.6773.0038735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38925.099202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15915679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5421518
X-RAY DIFFRACTIONr_chiral_restr0.0590.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02950
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_it2.5216.9231932
X-RAY DIFFRACTIONr_mcbond_other2.516.9221931
X-RAY DIFFRACTIONr_mcangle_it4.09110.3842412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3077.6312223
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: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 101 -
Rwork0.307 1796 -
obs--99.84 %
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)
10.3545-0.267-0.32980.71850.76532.4414-0.0989-0.23490.06010.3027-0.13810.1080.5534-0.47490.2370.1641-0.12460.07530.471-0.1370.09233.0718-18.003-2.9123
21.0947-0.44641.14030.5549-1.27928.97230.03260.09050.0502-0.044-0.12450.1290.2298-0.32920.09190.11340.0381-0.01760.1115-0.0460.250239.8722-22.7919-53.3592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1286
2X-RAY DIFFRACTION2B1 - 1156

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