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- PDB-4fiu: The structure of hemagglutinin of H16 subtype influenza virus wit... -

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Basic information

Entry
Database: PDB / ID: 4fiu
TitleThe structure of hemagglutinin of H16 subtype influenza virus with V327G mutation
Componentshemagglutinin
KeywordsVIRAL PROTEIN / membrane glycoprotein / receptor binding / virus fusion / 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
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsLu, X. / Shi, Y. / Gao, F. / Xiao, H. / Wang, M. / Qi, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2012
Title: Insights into Avian Influenza Virus Pathogenicity: the Hemagglutinin Precursor HA0 of Subtype H16 Has an Alpha-Helix Structure in Its Cleavage Site with Inefficient HA1/HA2 Cleavage.
Authors: Lu, X. / Shi, Y. / Gao, F. / Xiao, H. / Wang, M. / Qi, J. / Gao, G.F.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hemagglutinin
B: hemagglutinin
C: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,8289
Polymers173,8913
Non-polymers1,9376
Water28,2481568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-3 kcal/mol
Surface area63400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.070, 240.783, 69.479
Angle α, β, γ (deg.)90.00, 119.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hemagglutinin /


Mass: 57963.781 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 19-517 / Mutation: V326G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5DL24
#2: 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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1568 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-5 (ADGIQ) AND RESIDUES 505-509 (RLVPR) WERE OBTAINED FROM THE VECTOR.

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Imidazole, 20% (v/v) Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 132280 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→42.498 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 6656 5.04 %RANDOM
Rwork0.1932 ---
all0.1949 132070 --
obs0.1949 132070 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.415 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1039 Å2-0 Å2-2.3858 Å2
2---9.8312 Å2-0 Å2
3---2.7273 Å2
Refinement stepCycle: LAST / Resolution: 1.999→42.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12048 0 126 1568 13742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812450
X-RAY DIFFRACTIONf_angle_d1.18216851
X-RAY DIFFRACTIONf_dihedral_angle_d15.8184620
X-RAY DIFFRACTIONf_chiral_restr0.0791839
X-RAY DIFFRACTIONf_plane_restr0.0042199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9994-2.02210.28112320.2097413299
2.0221-2.04590.25192270.19414205100
2.0459-2.07090.23792010.194171100
2.0709-2.09710.25942070.19524198100
2.0971-2.12470.2412440.18944138100
2.1247-2.15380.23272060.1874236100
2.1538-2.18450.24012250.18824173100
2.1845-2.21710.26922120.19474150100
2.2171-2.25180.25172480.1964178100
2.2518-2.28870.28152310.19674132100
2.2887-2.32820.24932240.1924224100
2.3282-2.37050.23282020.19174171100
2.3705-2.41610.25392270.19384198100
2.4161-2.46540.23342060.19654231100
2.4654-2.5190.23932420.19474111100
2.519-2.57760.22742200.19734250100
2.5776-2.6420.22592220.19124124100
2.642-2.71350.24412030.19094184100
2.7135-2.79330.23592240.19654229100
2.7933-2.88340.23372210.19134199100
2.8834-2.98650.22812210.19634151100
2.9865-3.1060.24422070.19524191100
3.106-3.24730.22922200.18934179100
3.2473-3.41850.21942300.1864171100
3.4185-3.63250.2052500.1824195100
3.6325-3.91280.20642210.17354164100
3.9128-4.30620.2041990.1767421299
4.3062-4.92860.17042300.1801413999
4.9286-6.20640.22952320.2223416899
6.2064-42.50710.23132220.2308421099
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)
1-0.0250.0196-0.01070.0643-0.0254-0.00550.0175-0.06240.00620.00120.02620.12640.0298-0.055800.1782-0.0010.01690.13610.02220.1919-12.793-60.868333.7773
20.0633-0.0213-0.08890.0569-0.00080.1135-0.0085-0.0471-0.03610.2117-0.01110.11440.09410.0168-0.00840.1522-0.00780.0360.11560.00830.104-8.5206-9.631643.8173
30.2685-0.15670.11990.2657-0.20440.20980.0152-0.0819-0.03550.1032-0.0041-0.03710.0294-0.01580.00090.0915-0.00210.00450.1234-0.00040.0719-4.857411.241141.2367
40.11840.1896-0.03140.3208-0.08660.15710.0561-0.0020.0609-0.0187-0.0599-0.05470.00870.0204-0.00450.03860.0097-0.00090.0939-0.00310.05290.867415.072632.7516
5-0.04140.0458-0.04510.1804-0.04090.1896-0.0313-0.0487-0.03350.0839-0.0067-0.02310.09860.0358-0.03790.10560.0070.01360.11260.01090.0963-5.287-8.318741.2388
60.0054-0.0262-0.01480.0608-0.03640.02130.01660.0070.00560.1667-0.03670.1130.01720.005700.149-0.00030.0220.08780.00310.1134-10.0273-42.08832.5557
70.01050.07580.03930.17330.0820.1185-0.0329-0.00090.00650.39480.04290.0446-0.0499-0.0205-0.00680.15330.01320.03490.09560.01250.103-3.7605-48.91438.2865
8-0.01960.05520.08230.1375-0.0932-0.1007-0.0038-0.0006-0.01550.03680.03020.0186-0.0181-0.018-0.00450.11830.01640.01390.11380.00670.1068-2.9954-57.021130.0883
90.0416-0.0481-0.07320.0530.08420.13040.02470.0998-0.0764-0.06070.0533-0.0843-0.008-0.0501-00.13520.01160.0280.15070.01940.1889-4.279-92.375230.4239
100.0472-0.02860.0120.0187-0.00230.0061-0.04670.0011-0.00110.14330.0444-0.21350.0549-0.0023-0.00010.17330.0261-0.01770.1091-0.00420.216118.2176-63.929226.6759
110.04510.2348-0.09650.2204-0.1239-0.0275-0.0077-0.0211-0.0414-0.0082-0.0052-0.14360.0372-0.0102-0.00230.09420.0064-0.00040.10590.00660.135522.5973-9.951216.95
120.3328-0.0922-0.07090.12880.18280.246-0.0706-0.0067-0-0.09910.115-0.1021-0.00290.07220.00760.0555-0.00790.00410.09340.01030.075722.640514.57587.7802
130.4262-0.04020.15340.1115-0.20420.6566-0.08240.0960.098-0.1309-0.1513-0.09690.10770.0554-0.6053-0.1114-0.0182-0.08920.0738-0.0069-0.132113.812314.99168.4586
140.19170.03180.00860.0354-0.02750.0216-0.05350.02650.0505-0.0360.01170.0746-0.0018-0.0017-0.01410.05710.0022-0.0160.10070.00040.06939.253114.470411.6387
150.1683-0.03240.02980.0688-0.02280.1883-0.02940.0031-0.0716-0.05-0.0017-0.14870.0650.0063-0.01210.08280.01020.01310.06970.01270.131520.5945-13.93714.7743
16-0.0054-0.0067-0.00190.0956-0.08140.0959-0.00640.0257-0.02290.008-0.0779-0.27640.02870.0159-0.01630.15680.01420.02550.09510.00520.218418.9262-52.322522.6546
170.03110.0018-0.05930.1343-0.13380.08620.0097-0.010.0257-0.0745-0.0204-0.31290.0024-0.0002-0.01180.10030.00710.01610.08580.01060.154615.9502-47.1715.0887
18-0.07720.0574-0.03870.1968-0.0383-0.04030.00790.0087-0.0026-0.0585-0.0366-0.0346-0.0029-0.0113-0.00040.08590.0010.00290.09110.00120.117410.5122-57.249519.2079
190.13370.01960.09580.08910.05290.07190.0786-0.0216-0.0492-0.02050.0080.01790.0025-0.070400.12250.01380.00120.1385-0.01040.135311.0902-92.76822.0531
200.0304-0.02710.01930.07240.05410.0453-0.05570.07440.028-0.21150.05850.078-0.0107-0.019500.2261-0.0074-0.00970.1189-0.00780.1421-3.6699-61.66352.7907
210.01470.00760.09780.08490.01540.17460.0230.0261-0.0509-0.192-0.04550.1810.0244-0.0558-0.0190.15490.004-0.04170.1225-0.01350.1094-16.8297-11.0494-0.2204
220.07960.087-0.13830.3313-0.04340.20130.01510.0515-0.0456-0.02710.02120.09940.0424-0.01570.01170.08030.0089-0.01090.1121-0.00090.094-16.50115.63675.0621
230.13140.07750.01750.11-0.06390.09010.01370.05850.05340.0020.10320.1979-0.0441-0.01130.03680.11880.0144-0.01950.0911-0.00090.0873-20.099118.63791.7779
240.1096-0.0485-0.11970.1216-0.05190.5440.0134-0.04960.01340.0515-0.06050.0894-0.2053-0.0948-0.07930.03120.0138-0.01050.1084-0.00540.0562-16.576614.449511.4703
250.0777-0.10250.03050.105-0.00640.16320.0266-0.01310.0020.0806-0.0125-0.0174-0.08310.02320.00660.0896-0.0074-0.00570.09920.00160.0614-11.51714.09613.7558
260.0261-0.0192-0.08470.10220.00880.23340.01190.0022-0.0482-0.0389-0.04670.2330.0926-0.0496-0.00640.1176-0.0014-0.0190.10710.00360.1292-17.7814-0.72489.0978
270.0221-0.0040.00380.07890.0580.0226-0.01840.0003-0.0052-0.1465-0.0020.08370.00810.0061-0.01550.1565-0.0022-0.01620.0658-0.00120.107-8.9964-30.79882.4287
280.0630.00290.00650.0904-0.04150.0517-0.07190.0777-0.0316-0.21470.0301-0.01860.03060.0952-0.00220.2137-0.0211-0.04070.1192-0.00580.1312-10.9296-67.71492.4856
290.0706-0.1018-0.05750.12380.0726-0.00230.00080.01570.0642-0.08550.00260.25670.00560.02520.00010.14610.0104-0.01520.1163-0.00380.1014-10.9447-35.649512.7923
30-0.03910.032-0.03720.15380.0567-0.0951-0.01680.0255-0.00070.08230.0312-0.03580.00480.01740.00040.1083-0.0044-0.01250.08240.0040.0801-5.6316-57.571712.9373
310.0569-0.04750.08390.0327-0.07150.1219-0.14090.04-0.14230.03380.0565-0.00210.0825-0.0273-00.1530.00020.01660.1287-0.00450.1263-3.7442-93.107112.7238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:36)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 37:86)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 87:162)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 163:245)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 246:287)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 288:334)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 335:402)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 403:486)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 487:509)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 1:28)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 29:109)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 110:162)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 163:194)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 195:245)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 246:302)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 303:348)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 349:402)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 403:486)
19X-RAY DIFFRACTION19CHAIN B AND (RESSEQ 487:509)
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 1:36)
21X-RAY DIFFRACTION21CHAIN C AND (RESSEQ 37:86)
22X-RAY DIFFRACTION22CHAIN C AND (RESSEQ 87:138)
23X-RAY DIFFRACTION23CHAIN C AND (RESSEQ 139:162)
24X-RAY DIFFRACTION24CHAIN C AND (RESSEQ 163:194)
25X-RAY DIFFRACTION25CHAIN C AND (RESSEQ 195:245)
26X-RAY DIFFRACTION26CHAIN C AND (RESSEQ 246:268)
27X-RAY DIFFRACTION27CHAIN C AND (RESSEQ 269:322)
28X-RAY DIFFRACTION28CHAIN C AND (RESSEQ 323:365)
29X-RAY DIFFRACTION29CHAIN C AND (RESSEQ 366:402)
30X-RAY DIFFRACTION30CHAIN C AND (RESSEQ 403:486)
31X-RAY DIFFRACTION31CHAIN C AND (RESSEQ 487:509)

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