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- PDB-4d00: Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in C... -

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Basic information

Entry
Database: PDB / ID: 4d00
TitleHaemagglutinin of H10N8 Influenza Virus Isolated from Humans in Complex with Human Receptor Analogue 6'SLN
Components(HAEMAGGLUTININ ...) x 2
KeywordsVIRAL PROTEIN / H10N8 / INFLUENZA / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / LSTA
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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
6'-sialyl-N-acetyllactosamine / NICKEL (II) ION / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA VIRUS A/JIANGXI- DONGHU/346/2013
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXiong, X. / Haire, L.F. / Vachieri, S.G. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Zhang, Y. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Nature / Year: 2014
Title: Receptor Binding by H10 Influenza Viruses.
Authors: Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Haire, L.F. / Zhang, Y. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J.
History
DepositionApr 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: 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 / 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_conn_angle / 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.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA1
C: HAEMAGGLUTININ HA1
D: HAEMAGGLUTININ HA1
E: HAEMAGGLUTININ HA1
F: HAEMAGGLUTININ HA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,61321
Polymers169,8136
Non-polymers4,80015
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40700 Å2
ΔGint-120.5 kcal/mol
Surface area56720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.601, 183.169, 192.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF

#1: Protein HAEMAGGLUTININ HA1


Mass: 35682.258 Da / Num. of mol.: 3
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES -2-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS A/JIANGXI- DONGHU/346/2013 (H10N8)
Description: CHINA CDC / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q0A448*PLUS
#2: Protein HAEMAGGLUTININ HA1


Mass: 20921.969 Da / Num. of mol.: 3
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS A/JIANGXI- DONGHU/346/2013 (H10N8)
Description: CHINA CDC / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P12581*PLUS

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Sugars , 3 types, 12 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.: 3
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.: 3
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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, 706 molecules

#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE GLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA (GISAID)

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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: 4.02 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 10% PEG 6000, 5% MPD AND 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 390165 / % possible obs: 92.8 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.21
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.06 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→132.58 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.829 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23474 5013 4.9 %RANDOM
Rwork0.20852 ---
obs0.20978 98018 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.987 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.21 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→132.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11564 0 309 703 12576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912136
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211117
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.95916461
X-RAY DIFFRACTIONr_angle_other_deg0.827325517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42151477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95424.643588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.037151996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4291578
X-RAY DIFFRACTIONr_chiral_restr0.060.21829
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213877
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022855
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_it0.7842.0055926
X-RAY DIFFRACTIONr_mcbond_other0.7842.0055925
X-RAY DIFFRACTIONr_mcangle_it1.4083.0047397
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2852.2896210
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 377 -
Rwork0.308 6830 -
obs--88.88 %
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)
10.16110.26840.51160.49720.7521.8822-0.035-0.04170.0153-0.0245-0.04450.0278-0.1743-0.16060.07950.0470.0384-0.00110.1849-0.02950.0328-13.420917.50455.9462
20.36830.25770.29921.2205-0.110.93130.0042-0.1288-0.06640.0391-0.0856-0.057-0.1244-0.07270.08130.11360.0067-0.02880.12650.00710.0484.741225.90688.0078
30.13540.02440.17710.57221.20092.6505-0.0567-0.055-0.0092-0.05230.00170.0312-0.1404-0.08140.0550.11530.0211-0.02880.1796-0.03610.0313-15.128115.539647.5527
41.2430.46721.10120.73780.7042.16770.1012-0.13190.12760.0075-0.19250.01190.0718-0.24110.09130.0378-0.0004-0.00630.1775-0.03480.0346-26.227-0.247123.979
50.33020.15950.34910.07770.16580.60710.00580.02230.0157-0.00090.00450.0129-0.0201-0.0053-0.01030.13390.0015-0.00950.1439-0.040.0521-5.544811.400241.688
61.3476-0.2670.34990.2620.52311.92180.0342-0.08280.0473-0.0176-0.00430.01320.0191-0.1391-0.02990.0975-0.0461-0.03170.14980.00360.0882-31.9926-14.11335.5579
70.45440.71140.77411.34971.45271.58-0.03360.1332-0.0554-0.12990.1705-0.1261-0.18070.2218-0.13690.158-0.08520.02220.1352-0.00490.01615.068121.859532.5601
80.0638-0.0535-0.09520.46640.39261.0164-0.06170.04970.0132-0.01990.063-0.0613-0.15870.014-0.00140.1433-0.0507-0.03180.0844-0.00880.064621.05140.147762.2405
90.67420.49970.69371.55812.28033.4185-0.01470.04160.0538-0.02920.0531-0.0317-0.03270.1866-0.03840.0928-0.0380.02790.1804-0.00460.047410.84289.326129.0968
100.1768-0.18780.18350.59610.56492.2066-0.07620.03290.0062-0.02790.0301-0.037-0.16640.02910.04620.1168-0.02230.02110.13960.00190.0487-1.90763.35488.7281
110.33120.38840.75250.4820.9111.74770.02390.0282-0.01360.0087-0.0153-0.01620.0346-0.0026-0.00860.0983-0.0208-0.00630.1508-0.03090.06346.44498.958836.6889
120.88291.03010.25871.4095-0.24261.54780.0010.06780.0345-0.01840.0760.0722-0.02540.0482-0.0770.11370.0134-0.01430.1561-00.0289-16.1787-8.7274-7.0008
131.40530.68141.51310.35150.81112.06960.1715-0.0905-0.06590.123-0.0438-0.06150.3209-0.0657-0.12770.15710.0316-0.07960.04370.00470.064110.7418-9.377452.9813
140.46130.11960.40710.34840.10230.54620.0879-0.0004-0.0081-0.0039-0.0401-0.07060.03480.0824-0.04780.08280.0112-0.0220.1370.00160.057929.876711.178774.5999
152.84211.98993.1091.54972.06943.54490.1007-0.1107-0.07910.1727-0.0573-0.10990.1293-0.1765-0.04340.1735-0.0325-0.02590.09010.01630.033-0.5367-8.306445.6379
160.57781.06520.53762.24441.48151.52980.14720.0315-0.04830.22110.0921-0.17450.22110.1077-0.23930.18130.0128-0.04930.078-0.01660.0466-5.6641-20.539124.7763
170.15320.10870.25320.21730.30990.53980.0524-0.0257-0.02370.0513-0.016-0.01240.0965-0.0329-0.03640.159-0.0227-0.00760.1383-0.00210.0379-4.8911-10.927628.4799
1812.6611-8.3905-0.63767.01693.65087.18960.70310.8405-0.4381-0.6157-0.70140.2786-0.3482-0.3486-0.00170.18140.0457-0.00840.1049-0.0340.0539-22.8429-27.6556-4.2948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION2A108 - 256
3X-RAY DIFFRACTION3A257 - 318
4X-RAY DIFFRACTION4B1 - 60
5X-RAY DIFFRACTION5B61 - 120
6X-RAY DIFFRACTION6B121 - 175
7X-RAY DIFFRACTION7C0 - 87
8X-RAY DIFFRACTION8C88 - 285
9X-RAY DIFFRACTION9C286 - 318
10X-RAY DIFFRACTION10D1 - 60
11X-RAY DIFFRACTION11D61 - 120
12X-RAY DIFFRACTION12D121 - 176
13X-RAY DIFFRACTION13E0 - 87
14X-RAY DIFFRACTION14E88 - 285
15X-RAY DIFFRACTION15E286 - 318
16X-RAY DIFFRACTION16F1 - 60
17X-RAY DIFFRACTION17F61 - 163
18X-RAY DIFFRACTION18F164 - 173

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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