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- PDB-3znm: H5 Haemagglutinin in Complex with Sialyl-Lewis X -

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Basic information

Entry
Database: PDB / ID: 3znm
TitleH5 Haemagglutinin in Complex with Sialyl-Lewis X
Components(HAEMAGGLUTININ) x 2
KeywordsVIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / SULFATED SIALOSIDE / FUCOSYLATED SIALOSIDE / SULFATION / FUCOSYLATION / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / SULFATED LEWIS X
Function / homology
Function and homology information


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 / 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: 2.4 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 1.2Jan 21, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description
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_struct_special_symmetry / 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_struct_special_symmetry.label_asym_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
Revision 2.2Nov 13, 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: HAEMAGGLUTININ
B: HAEMAGGLUTININ
C: HAEMAGGLUTININ
D: HAEMAGGLUTININ
E: HAEMAGGLUTININ
F: HAEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,31421
Polymers168,1466
Non-polymers5,16815
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34390 Å2
ΔGint-70.6 kcal/mol
Surface area60540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.560, 101.360, 161.200
Angle α, β, γ (deg.)90.00, 111.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-2017-

HOH

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein HAEMAGGLUTININ


Mass: 36950.766 Da / Num. of mol.: 3
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
Source method: isolated from a natural source
Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
Source: (natural) INFLUENZA A VIRUS / Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: VIETNAM/1194/2004 (H5N1) / References: UniProt: Q6DQ34
#2: Protein HAEMAGGLUTININ


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: VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: 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-beta-D-glucopyranose


Type: oligosaccharide / Mass: 820.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpa1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/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-GlcpNAc]{[(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


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, 306 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 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: 2.4→150.76 Å / Num. obs: 77719 / % possible obs: 75.6 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2

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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: 2.4→37.15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.891 / SU B: 18.031 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. 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 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. 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
Rfree0.25632 3882 5 %RANDOM
Rwork0.23777 ---
obs0.2387 73837 75.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.21 Å2
2---0.65 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11595 0 339 303 12237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01912237
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211232
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9716614
X-RAY DIFFRACTIONr_angle_other_deg0.723.00325851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22551446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91225.174603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.569152034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0251551
X-RAY DIFFRACTIONr_chiral_restr0.0550.21809
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_it0.1540.5515802
X-RAY DIFFRACTIONr_mcbond_other0.1540.5515801
X-RAY DIFFRACTIONr_mcangle_it0.2870.8267242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5940.8196435
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: 2.403→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.546 18 -
Rwork0.382 361 -
obs--4.98 %
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)
10.2987-0.10780.95690.4519-0.48446.80260.063-0.1673-0.15570.181-0.0345-0.06361.28340.384-0.02840.5820.1510.05040.40150.11380.344335.853128.721352.2625
21.99-1.04492.09654.0864-0.6354.9221-0.0055-0.1073-0.10860.4288-0.2552-0.41320.82520.80160.26070.5180.1889-0.02880.57340.17570.361743.416935.424481.1968
32.19910.680.93912.21150.87622.08040.1092-0.5725-0.09470.6881-0.28290.0050.69140.33020.17360.74430.1336-0.02480.77780.15050.327840.197635.921593.0471
40.7137-0.38830.53470.4072-1.144411.5261-0.049-0.291-0.32140.07050.1468-0.00910.70940.3752-0.09780.5040.07110.01080.27710.10420.410835.474231.513148.5969
50.8011-0.3825-1.31890.48631.60038.4083-0.2077-0.1883-0.13260.17240.00030.00530.63670.75020.20740.23480.04110.03360.2190.06520.241433.448240.441234.0859
62.4665-0.68640.46293.36520.740210.07990.21460.70450.0473-0.9256-0.2774-0.4086-0.41940.79320.06280.2680.06830.07220.25130.03550.259637.440841.96811.6881
70.34920.0473-0.5070.31050.35766.02770.0076-0.24810.16170.17570.0164-0.1156-0.99830.9751-0.0240.4694-0.1485-0.11640.4011-0.02390.348344.511467.650556.089
82.6884-0.0677-0.91411.7020.04622.3645-0.1333-0.90340.15880.4162-0.0704-0.1324-0.5940.48850.20370.8441-0.0869-0.12460.656-0.09730.347738.206768.908892.775
93.1253-0.821-2.96241.37290.64243.16160.1527-0.19360.22510.1851-0.08850.1479-0.77230.023-0.06421.150.0477-0.20420.5434-0.18630.372231.034573.553383.7345
100.47010.09541.4221.38640.925613.3573-0.0197-0.18440.26380.33460.0917-0.1783-0.72970.4527-0.0720.3095-0.1598-0.09620.4052-0.04380.380843.899366.432347.4468
110.20190.1298-0.57261.0719-2.01529.1391-0.0629-0.10180.07310.2376-0.144-0.0992-0.93580.19250.20690.215-0.0369-0.07970.20880.00690.247336.645860.49434.0929
122.45560.8175-0.94762.9961-0.118910.3836-0.28650.63920.3459-0.88390.17010.2164-0.5218-0.70950.11640.3009-0.045-0.07030.20560.03270.257333.315363.18661.693
130.3622-0.0878-0.13210.2105-0.58265.667-0.033-0.1507-0.01560.1840.06310.1725-0.4065-1.34-0.030.29380.00940.090.6238-0.0980.35827.568756.473456.067
141.5696-0.44960.53841.8076-0.74442.0829-0.3191-0.46540.02410.72640.12270.1531-0.0965-0.75450.19640.6554-0.03750.1650.9405-0.05220.38049.299450.668393.3255
150.7838-0.3129-0.07983.4512-2.3894.317-0.1285-0.2401-0.24570.31460.08770.21380.704-1.06840.04080.4589-0.23050.18030.8858-0.06480.332510.343342.798883.8854
161.13270.1801-1.94420.64010.835413.17810.0953-0.28240.04070.283-0.03670.31530.0345-0.715-0.05860.20920.0860.06470.4601-0.060.35668.922656.550347.4227
171.31230.62862.5770.45970.79489.8632-0.0188-0.36410.06130.0467-0.15930.11990.526-1.34610.17820.1795-0.00210.04320.3223-0.09390.272415.857752.560131.0476
182.04210.04511.78451.1024-0.478511.2148-0.05290.408-0.1067-0.1824-0.06550.09320.44840.01520.11840.0529-0.00640.02060.1232-0.00870.213318.935450.826113.4716
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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