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- PDB-6idb: Crystal structure of H7 hemagglutinin mutant H7-SVTQ ( A138S, P22... -

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Basic information

Entry
Database: PDB / ID: 6idb
TitleCrystal structure of H7 hemagglutinin mutant H7-SVTQ ( A138S, P221T, L226Q) with 6'SLN
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / influenza virus / H7N9 / Hemagglutinin
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 / metal ion binding
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 A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsGao, G.F. / Xu, Y. / Qi, J.X.
CitationJournal: Cell Rep / Year: 2019
Title: Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin.
Authors: Xu, Y. / Peng, R. / Zhang, W. / Qi, J. / Song, H. / Liu, S. / Wang, H. / Wang, M. / Xiao, H. / Fu, L. / Fan, Z. / Bi, Y. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionSep 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_validate_close_contact / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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 2.1Nov 22, 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: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5885
Polymers55,4712
Non-polymers1,1173
Water2,738152
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,76415
Polymers166,4136
Non-polymers3,3519
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area38610 Å2
ΔGint-119 kcal/mol
Surface area54610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.956, 115.956, 297.050
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-996-

HOH

21A-1004-

HOH

31B-634-

HOH

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 35028.520 Da / Num. of mol.: 1 / Mutation: A138S,P221T,L226Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2 chain


Mass: 20442.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21
#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: 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 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsSequence reference R4NN21_9INFA was used according to author's suggestion. Author stated ...Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated hemagglutinin used in this studay, which was derived from AH1-H7N9 virus, was identical with R4NN21_9INFA.

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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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% w/v SOKALAN PA 25 CL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03907 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03907 Å / Relative weight: 1
ReflectionResolution: 2.5→50.032 Å / Num. obs: 26969 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 18.79
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.081 / Num. unique obs: 2320

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KOL

4kol


Resolution: 2.502→49.51 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.49
RfactorNum. reflection% reflection
Rfree0.2595 1360 5.11 %
Rwork0.199 --
obs0.202 26616 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.502→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 0 152 4044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013983
X-RAY DIFFRACTIONf_angle_d1.0695386
X-RAY DIFFRACTIONf_dihedral_angle_d19.571489
X-RAY DIFFRACTIONf_chiral_restr0.221591
X-RAY DIFFRACTIONf_plane_restr0.006707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5021-2.59150.35411200.3092200X-RAY DIFFRACTION87
2.5915-2.69520.34481460.28232515X-RAY DIFFRACTION100
2.6952-2.81790.32851480.24912508X-RAY DIFFRACTION100
2.8179-2.96640.31181170.24692559X-RAY DIFFRACTION100
2.9664-3.15230.25331220.23292542X-RAY DIFFRACTION100
3.1523-3.39560.30651300.22182548X-RAY DIFFRACTION100
3.3956-3.73720.26771450.18722554X-RAY DIFFRACTION100
3.7372-4.27780.20571420.1592568X-RAY DIFFRACTION100
4.2778-5.38850.21171310.14712580X-RAY DIFFRACTION100
5.3885-49.510.22811590.18272682X-RAY DIFFRACTION100
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)
10.49010.17490.33530.06670.14391.3140.0211-0.46010.19280.5610.1779-0.0789-0.3225-0.09880.09590.6346-0.01980.0420.5454-0.18290.32540.824117.735489.1234
21.6778-0.1528-0.15680.70430.15351.33920.13150.41360.1068-0.16760.0058-0.0927-0.11330.1135-0.05050.1713-0.01120.03850.24770.05860.333818.067715.919234.1345
31.3175-0.0620.40980.0021-0.0160.12940.31161.1215-0.5534-0.3251-0.1220.02110.15430.0125-0.01250.29030.1489-0.07030.843-0.15550.415416.41576.392215.193
40.31790.1824-0.37321.3316-0.96152.33810.03170.1785-0.0608-0.07410.17380.05670.0859-0.28640.0050.3934-0.1676-0.15450.6799-0.15390.853110.288-1.697918.0452
50.7229-0.76830.21411.3678-0.2751.39060.19910.4992-0.431-0.2111-0.1681-0.0577-0.0872-0.3795-0.01750.2429-0.0023-0.03890.54360.03140.4047.696212.852221.7228
60.5697-0.1170.09680.6061-0.08070.4410.08950.32-0.6526-0.1449-0.02260.03050.17190.0942-0.01140.25010.0196-0.03260.3892-0.12810.476520.32263.797528.7445
73.71631.7979-0.05271.29350.85731.84170.1155-0.17740.16440.0959-0.2048-0.0866-0.16610.26670.03480.1593-0.01130.0230.15830.03250.333216.541721.399154.5341
81.8828-0.1168-1.08251.244-0.22132.36860.2395-0.34830.05010.2052-0.1329-0.159-0.08320.2230.00210.1448-0.04530.01830.2010.04140.29778.225513.785960.6749
90.5422-0.2059-0.2170.41460.20830.9384-0.04-0.48980.4060.5170.03430.0299-0.3712-0.0833-0.08920.4939-0.00560.06740.3958-0.13530.27080.415617.945181.0231
100.94820.67810.92472.51981.25711.0785-0.2407-0.56580.36520.41150.1057-0.0273-0.51280.3120.05341.0307-0.04260.00450.8839-0.30.36684.332216.683199.3824
110.0126-0.07180.00920.42190.25431.7423-0.1039-0.59380.36290.5166-0.13720.0452-0.29910.1822-0.00410.7004-0.0897-0.12930.9018-0.19610.396313.110313.199893.8472
122.5833-0.9125-0.71032.48721.05021.21310.0568-0.45150.08910.6594-0.0229-0.30390.27860.75870.00850.3473-0.0465-0.04790.31330.07350.36213.77576.960759.1708
132.70862.43730.54237.73661.28130.6907-0.19170.26060.3071-0.2922-0.06680.3258-0.1829-0.21430.03090.173-0.013-0.05060.27240.06970.3763.380813.474741.3117
140.8869-0.02730.28080.8944-0.09391.7799-0.0072-0.45250.0950.47420.02770.0772-0.0976-0.0428-0.03370.3483-0.01990.02670.3699-0.0460.24771.43946.450776.8578
150.2214-0.0708-0.11290.02050.03650.0594-0.0783-0.21590.09580.2962-0.0237-0.0414-0.02520.044-0.10711.501-0.0371-0.22851.5099-0.2320.39439.652911.2404114.4585
161.84630.14321.32270.65960.62951.3750.07390.1271-0.0631-0.02390.03-0.00490.16430.1725-0.05521.5151-0.1106-0.22531.4261-0.12020.4377.92295.8756124.5822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 186 )
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 205 )
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 259 )
7X-RAY DIFFRACTION7chain 'A' and (resid 260 through 279 )
8X-RAY DIFFRACTION8chain 'A' and (resid 280 through 299 )
9X-RAY DIFFRACTION9chain 'A' and (resid 300 through 317 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 27 )
11X-RAY DIFFRACTION11chain 'B' and (resid 28 through 55 )
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 65 )
13X-RAY DIFFRACTION13chain 'B' and (resid 66 through 74 )
14X-RAY DIFFRACTION14chain 'B' and (resid 75 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 158 )
16X-RAY DIFFRACTION16chain 'B' and (resid 159 through 172 )

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