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- PDB-4bse: Human H7N9 Influenza Virus Haemagglutinin in Complex with Human R... -

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Basic information

Entry
Database: PDB / ID: 4bse
TitleHuman H7N9 Influenza Virus Haemagglutinin in Complex with Human Receptor Analogue LSTc
Components(HAEMAGGLUTININ ...Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / H7N3 / H7N9 / H5N1 / FOWL PLAGUE VIRUS / GLYCOPROTEIN / VIRUS RECEPTOR / BIRD FLU / SIALYLLACTOSAMINE / LSTC
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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
6'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA VIRUS A/ANHUI/1/2013
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsXiong, X. / Haire, L.F. / Martin, S.R. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / McCauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 2013
Title: Receptor Binding by an H7N9 Influenza Virus from Humans
Authors: Xiong, X. / Martin, S.R. / Haire, L.F. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / Mccauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J.
History
DepositionJun 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,64022
Polymers55,4362
Non-polymers3,20420
Water1,54986
1
A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules

A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules

A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,91966
Polymers166,3086
Non-polymers9,61160
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 area46780 Å2
ΔGint-717.3 kcal/mol
Surface area58790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.890, 115.890, 296.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2047-

HOH

31B-2015-

HOH

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Components

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HAEMAGGLUTININ ... , 2 types, 2 molecules AB

#1: Protein HAEMAGGLUTININ HA1


Mass: 34993.559 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 19-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS A/ANHUI/1/2013 (H7N9) / Description: WHO CHINESE NATIONAL INFLUENZA CENTER / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: M4YV75
#2: Protein HAEMAGGLUTININ HA2


Mass: 20442.463 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 340-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS A/ANHUI/1/2013 (H7N9) / Description: WHO CHINESE NATIONAL INFLUENZA CENTER / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: M4YV75

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Sugars , 3 types, 5 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-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/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}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.: 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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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, 101 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA (GISAID) M4YV75 IS THE CLOSEST MATCH IN UNIPROT.

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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: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 291 K
Details: 291 K, 0.1 M PIPES PH 7.0, 2.2 M AMMONIUM SULFATE, 1% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.55→41.55 Å / Num. obs: 25386 / % possible obs: 99.9 % / Observed criterion σ(I): 2.86 / Redundancy: 9.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.23
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.86 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TI8
Resolution: 2.55→41.58 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.223 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27891 1292 5.1 %RANDOM
Rwork0.23274 ---
obs0.23508 24090 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.27 Å20 Å2
2--0.27 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 191 86 4069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194051
X-RAY DIFFRACTIONr_bond_other_d0.0010.023676
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9895493
X-RAY DIFFRACTIONr_angle_other_deg0.7183.0038424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95524.513195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7115663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9981528
X-RAY DIFFRACTIONr_chiral_restr0.0610.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02933
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_it0.4731.5821942
X-RAY DIFFRACTIONr_mcbond_other0.4731.5811941
X-RAY DIFFRACTIONr_mcangle_it0.8452.3712424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5582.2382107
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: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 82 -
Rwork0.319 1762 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.20780.089-0.99061.4205-0.16652.38210.19350.15010.14890.0128-0.00050.4138-0.355-0.1056-0.19310.0951-0.0334-0.0010.1278-0.02340.361137.2084-34.824-5.5663
20.5011-0.16261.22030.4227-2.157415.2260.2779-0.4060.01030.24880.02120.0026-0.09190.3966-0.29910.6416-0.1471-0.01570.5386-0.07310.367338.9441-49.906126.2351
33.44920.78280.37322.3550.66024.66470.3779-0.7422-0.18851.0338-0.0254-0.0233-0.03570.1901-0.35240.7199-0.20010.00110.4175-0.03540.349240.5966-44.132331.9508
41.4304-0.4596-2.65980.18460.757211.7673-0.94070.3508-0.330.38140.13720.08020.18940.54740.80351.2438-0.46660.13771.0314-0.29890.647947.6902-36.711433.0652
52.12221.7932-0.29243.36591.08991.45650.351-0.0974-0.23190.95520.0819-0.50380.11350.6088-0.43280.4706-0.2437-0.0240.4919-0.19020.328641.818-44.912617.8937
61.72850.0211-2.34532.0808-1.62525.93410.01880.34450.1081-0.30150.08770.39780.0191-0.4764-0.10650.0922-0.0287-0.06130.15030.03760.303740.9015-31.0161-17.3137
70.9421-0.44640.60081.07991.44924.68650.12980.61930.1196-0.52-0.47870.27480.0127-0.40830.34891.1151-0.1263-0.43611.08530.27740.426140.4961-29.0753-51.9268
84.872-0.69962.4154.7255-3.042612.1787-0.11870.0672-0.3587-0.31030.05210.44050.5364-1.01170.06660.3931-0.1484-0.10730.5225-0.08060.467341.5075-39.2061-36.7956
92.27771.3596-0.44582.3539-0.54826.34980.0715-0.05930.04560.1206-0.24920.1375-0.1206-0.29650.17770.02810.00480.01780.0584-0.00790.275150.5892-30.8499-5.6239
101.86010.785-0.76433.40873.32755.0285-0.29271.09420.0392-0.91730.4667-0.149-0.3962-0.0816-0.1740.98170.1781-0.13081.01270.04310.318449.6184-34.4206-53.285
116.62242.8012-7.14424.3536-4.69968.7561-0.24611.1646-0.3789-0.3390.13460.6159-0.0431-0.81720.11151.5517-0.0662-0.47571.6952-0.18040.335343.434-38.1185-68.9356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2A103 - 124
3X-RAY DIFFRACTION3A125 - 183
4X-RAY DIFFRACTION4A184 - 217
5X-RAY DIFFRACTION5A218 - 268
6X-RAY DIFFRACTION6A269 - 316
7X-RAY DIFFRACTION7B1 - 31
8X-RAY DIFFRACTION8B32 - 59
9X-RAY DIFFRACTION9B60 - 104
10X-RAY DIFFRACTION10B105 - 136
11X-RAY DIFFRACTION11B137 - 170

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