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- PDB-3znl: H5 Haemagglutinin in Complex with 6-O-Sulfo-Sialyl-Lewis X (Sulfa... -

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Basic information

Entry
Database: PDB / ID: 3znl
TitleH5 Haemagglutinin in Complex with 6-O-Sulfo-Sialyl-Lewis X (Sulfated Lewis X)
Components(HAEMAGGLUTININHemagglutinin) x 2
KeywordsVIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / SULFATED SIALOSIDE / FUCOSYLATED SIALOSIDE / SULFATION / FUCOSYLATION / AVIAN FLU / SIALYLLACTOSAMINE
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: 2.5 Å
AuthorsXiong, X. / Tuzikov, A. / Coombs, P. / Martin, S.R. / Walker, P.A. / Gamblin, S.J. / Bovin, N. / Skehel, J.J.
CitationJournal: Virus Res. / Year: 2013
Title: Recognition of Sulphated and Fucosylated Receptor Sialosides by A/Vietnam/1194/2004 (H5N1) Influenza Virus.
Authors: Xiong, X. / Tuzikov, A. / Coombs, P. / Martin, S. / Walker, P.A. / Gamblin, S.J. / Bovin, N. / Skehel, J.J.
History
DepositionFeb 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
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 / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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_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: HAEMAGGLUTININ
B: HAEMAGGLUTININ
C: HAEMAGGLUTININ
D: HAEMAGGLUTININ
E: HAEMAGGLUTININ
F: HAEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,55421
Polymers168,1466
Non-polymers5,40815
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34760 Å2
ΔGint-73 kcal/mol
Surface area60720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.980, 101.600, 161.370
Angle α, β, γ (deg.)90.00, 111.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein HAEMAGGLUTININ / Hemagglutinin


Mass: 36950.766 Da / Num. of mol.: 3
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340
Source method: isolated from a natural source
Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Source: (natural) INFLUENZA A VIRUS / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: A/VIETNAM/1194/2004 (H5N1) / References: UniProt: Q6DQ34
#2: Protein HAEMAGGLUTININ / Hemagglutinin


Mass: 19097.990 Da / Num. of mol.: 3
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a natural source
Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Source: (natural) INFLUENZA A VIRUS / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: A/VIETNAM/1194/2004 (H5N1) / References: UniProt: Q6DQ34

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Sugars , 2 types, 12 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose


Type: oligosaccharide / Mass: 900.807 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpa1-4[LFucpa1-3]DGlcpNAc[6S]b1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O_6*OSO/3=O/3=O][a1221m-1a_1-5][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc6SO3]{[(3+1)][a-L-Fucp]{}[(4+1)][a-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: 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.: 9
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, 268 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 4.04 Å3/Da / Density % sol: 70 %
Description: DATA CORRECTED FOR ANISOTROPY USING UCLA MBI - DIFFRACTION ANISOTROPY SERVER RETAINING 3 SIGMA DATA.
Crystal growDetails: 0.1 M HEPES PH 7.0, 0.05 M MGCL2, 28 - 30 % PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.5→150.76 Å / Num. obs: 64504 / % possible obs: 70.4 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IBX

2ibx


Resolution: 2.5→35.7 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.869 / SU B: 20.107 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.672 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPLETENESS VS. RESOLUTION TABLE 999.99 5.39 9323 8903 5.39 4.28 9221 9089 4.28 3.74 9137 9040 3.74 3.40 9119 8419 3.40 3.15 9195 8800 3. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPLETENESS VS. RESOLUTION TABLE 999.99 5.39 9323 8903 5.39 4.28 9221 9089 4.28 3.74 9137 9040 3.74 3.40 9119 8419 3.40 3.15 9195 8800 3.15 2.97 9103 8814 2.97 2.82 9055 6258 2.82 2.70 9172 3148 2.70 2.59 9067 1560 2.59 2.50 9156 473
RfactorNum. reflection% reflectionSelection details
Rfree0.25582 3227 5 %RANDOM
Rwork0.23694 ---
obs0.23789 61277 70.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.31 Å2
2---1.01 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11595 0 351 265 12211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01912249
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211232
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.97116635
X-RAY DIFFRACTIONr_angle_other_deg0.713.00325851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2751446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16125.174603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.998152034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061551
X-RAY DIFFRACTIONr_chiral_restr0.0560.21812
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022829
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_it0.1310.6485802
X-RAY DIFFRACTIONr_mcbond_other0.1310.6485801
X-RAY DIFFRACTIONr_mcangle_it0.2440.9717242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4880.8836447
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: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 22 -
Rwork0.461 245 -
obs--3.95 %
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)
10.8433-0.0643-1.57730.2905-0.42698.4946-0.0407-0.1576-0.040.23220.00850.1735-0.3729-1.30150.03220.20790.00870.08030.5976-0.09650.27436.329157.166852.29
24.87030.1418-1.31261.5295-0.98933.5095-0.4096-0.3085-0.27750.31670.08080.25650.1677-0.97830.32870.3553-0.06650.17750.6778-0.03930.29118.3547.250481.2297
31.5707-0.47070.49463.0139-0.57342.4801-0.2907-0.49220.02280.75880.10630.1211-0.0297-0.73710.18450.646-0.06750.17310.9074-0.06830.239710.420849.800793.0866
40.69620.2094-1.33260.3793-0.006813.13460.1233-0.23840.08130.1324-0.08970.3405-0.0082-0.7394-0.03360.1210.0560.08090.4123-0.0590.34248.951756.071148.5969
51.29980.38542.49180.32880.625910.2986-0.0789-0.36080.04760.0974-0.18120.12150.3093-1.06830.26010.1233-0.03990.05310.1696-0.08660.17917.723853.348834.1109
64.5488-0.03990.82592.3942-0.087511.0618-0.10011.1055-0.411-0.4705-0.0530.20560.93380.21750.15320.1757-0.0145-0.0050.2695-0.10380.137817.057249.12751.6788
70.2464-0.08960.6560.7108-0.24386.33090.0594-0.1884-0.14780.2338-0.0486-0.11391.4660.2916-0.01070.49220.1150.04090.34220.13940.273735.785230.113556.091
81.81980.29860.07132.21081.03672.04570.1604-0.593-0.14580.8272-0.3539-0.06880.66240.29850.19360.76720.0946-0.03730.78310.18780.257940.029134.912492.8111
92.67591.03172.66960.63171.3313.6834-0.0261-0.0692-0.0060.34320.0058-0.17860.68950.82880.02030.72760.3541-0.07611.08690.29310.298947.670138.836183.775
101.0779-0.50380.12281.0398-2.021213.2052-0.1271-0.3714-0.32250.2270.1114-0.14060.46010.34990.01580.31810.04680.00390.14010.10940.306435.037631.259547.4399
110.8308-0.5374-1.70660.74491.691410.1944-0.2637-0.2068-0.1490.2428-0.05230.00530.7810.80140.3160.09850.04390.04110.20610.08030.167833.51740.517434.1038
122.4859-0.83370.20434.05210.757710.8940.25810.62710.0524-0.9732-0.4297-0.4819-0.57120.71670.17160.25040.09020.09920.21850.05620.142837.518842.03841.6598
130.55310.2062-0.17160.35070.75287.4480.0242-0.28990.16270.1291-0.0084-0.0889-0.99861.0309-0.01570.4397-0.1211-0.14460.2968-0.03080.271944.61467.767856.0888
142.4015-0.0035-0.41611.5156-0.48541.4271-0.1337-0.91880.0750.4173-0.1245-0.0824-0.6150.37050.25810.8875-0.0598-0.13930.773-0.13210.260938.727969.179593.3782
153.3647-1.5169-2.5741.86320.71362.43370.2907-0.29410.20280.404-0.22730.0934-0.98390.1652-0.06341.2703-0.0001-0.23820.5306-0.20680.203531.33872.221483.9392
160.85380.07591.56951.47361.332412.60750.0365-0.22170.30.4140.0892-0.3014-0.61860.285-0.12570.2788-0.1309-0.08510.262-0.03480.268443.99766.540847.4372
170.1540.0941-0.5311.938-2.866410.53550.0004-0.10290.06490.3785-0.2128-0.0861-1.47610.24080.21240.2467-0.0019-0.09670.13680.01370.179737.054362.543831.0837
181.35390.5594-1.4232.169-1.487711.4835-0.25480.23270.1543-0.32860.01180.0279-0.2677-0.41420.2430.1158-0.02-0.05260.04830.01470.115234.021460.720713.4726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 90
2X-RAY DIFFRACTION2A91 - 122
3X-RAY DIFFRACTION3A123 - 259
4X-RAY DIFFRACTION4A260 - 321
5X-RAY DIFFRACTION5B1 - 104
6X-RAY DIFFRACTION6B105 - 163
7X-RAY DIFFRACTION7C1 - 104
8X-RAY DIFFRACTION8C105 - 233
9X-RAY DIFFRACTION9C234 - 264
10X-RAY DIFFRACTION10C265 - 321
11X-RAY DIFFRACTION11D1 - 104
12X-RAY DIFFRACTION12D105 - 163
13X-RAY DIFFRACTION13E1 - 104
14X-RAY DIFFRACTION14E105 - 226
15X-RAY DIFFRACTION15E227 - 264
16X-RAY DIFFRACTION16E265 - 321
17X-RAY DIFFRACTION17F1 - 82
18X-RAY DIFFRACTION18F83 - 163

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