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- PDB-6v44: The crystal structure of hemagglutinin from swine influenza virus... -

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Basic information

Entry
Database: PDB / ID: 6v44
TitleThe crystal structure of hemagglutinin from swine influenza virus A/swine/Missouri/A01727926/2015
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza virus / swine / H4
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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: 2.2 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: Heliyon / Year: 2020
Title: Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins
Authors: Yang, H. / Carney, P.J. / Chang, J. / Stevens, J.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 / citation / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,16412
Polymers174,2816
Non-polymers3,8836
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37960 Å2
ΔGint-95 kcal/mol
Surface area56930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.973, 240.005, 68.953
Angle α, β, γ (deg.)90.000, 119.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
12chain B
22chain D
32chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRPROPROchain AAA3 - 3228 - 327
21TYRTYRPROPROchain CCC3 - 3228 - 327
31TYRTYRPROPROchain EEE3 - 3228 - 327
12GLYGLYILEILEchain BBB1 - 1731 - 173
22GLYGLYILEILEchain DDD1 - 1731 - 173
32GLYGLYILEILEchain FFF1 - 1731 - 173

NCS ensembles :
ID
1
2

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 36651.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Missouri/A01727926/2015(H4N6))
Strain: A/swine/Missouri/A01727926/2015(H4N6) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A140D8S6
#2: Protein Hemagglutinin HA2 chain


Mass: 21442.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Missouri/A01727926/2015(H4N6))
Strain: A/swine/Missouri/A01727926/2015(H4N6) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A140D8S6
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}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.: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.1M Tris-HCl, pH8.5, 30% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 95268 / % possible obs: 98 % / Redundancy: 3.3 % / Rsym value: 0.087 / Net I/σ(I): 29.5
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 8895 / Rsym value: 0.474

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XL2

5xl2


Resolution: 2.2→33.207 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.22
RfactorNum. reflection% reflection
Rfree0.2442 4762 5 %
Rwork0.203 --
obs0.2051 95237 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.88 Å2 / Biso mean: 50.7893 Å2 / Biso min: 25.01 Å2
Refinement stepCycle: final / Resolution: 2.2→33.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11706 0 258 458 12422
Biso mean--67.56 53.06 -
Num. residues----1479
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3081X-RAY DIFFRACTION0.964TORSIONAL
12C3081X-RAY DIFFRACTION0.964TORSIONAL
13E3081X-RAY DIFFRACTION0.964TORSIONAL
21B1566X-RAY DIFFRACTION0.964TORSIONAL
22D1566X-RAY DIFFRACTION0.964TORSIONAL
23F1566X-RAY DIFFRACTION0.964TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2250.34651250.2798235875
2.225-2.25120.37091440.28393043100
2.2512-2.27860.381740.27333042100
2.2786-2.30750.34521540.26553193100
2.3075-2.33780.33051480.2582301699
2.3378-2.36980.33661660.2619311199
2.3698-2.40370.32071600.2662304699
2.4037-2.43950.34991580.2605306599
2.4395-2.47770.31541520.2521308499
2.4777-2.51830.29171540.2546301699
2.5183-2.56170.29821560.2501315899
2.5617-2.60820.3061650.2609297099
2.6082-2.65840.31711710.2512315799
2.6584-2.71260.27711560.2487298798
2.7126-2.77160.3151870.2428307299
2.7716-2.8360.28741490.2451298398
2.836-2.90690.32231500.2324308398
2.9069-2.98540.26331870.2281304898
2.9854-3.07320.28551780.2308295798
3.0732-3.17240.27691580.2174302998
3.1724-3.28560.24691740.212307698
3.2856-3.41710.27771500.2082301598
3.4171-3.57240.21221590.1937297297
3.5724-3.76050.22781630.1806286993
3.7605-3.99580.21221320.1713308298
3.9958-4.30370.18731630.1543307998
4.3037-4.73570.17691610.1491300798
4.7357-5.41840.18211700.1568307398
5.4184-6.81690.19791560.1996308499
6.8169-100.25341420.2129280089
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)
10.0528-0.2027-0.02020.8076-0.07710.01770.0156-0.03780.0310.0529-0.0727-0.1681-0.03040.029-00.3023-0.0078-0.01170.36120.00870.3181102.21920.86679.279
20.06690.33150.07110.37640.16460.14950.08710.0194-0.0310.082-0.1069-0.1417-0.0332-0.00830.00010.3612-0.01-0.01090.32450.0080.403797.89172.18473.285
30.01-0.13010.02550.69150.1190.08160.04930.05340.0394-0.149-0.06350.0381-0.01830.011500.33360.02770.00410.3834-0.01380.33886.70220.86351.268
4-0.01390.0546-0.12480.3131-0.11840.13710.0755-0.02540.0114-0.132-0.1388-0.0966-0.0082-0.01210.00010.4180.0247-0.01260.3520.01790.426383.67872.18858.026
5-0.01010.0111-0.05180.9867-0.08670.08760.0415-0.00430.05840.1027-0.06890.13840.0175-0.0482-00.2998-0.02090.0070.3633-0.01390.268270.26920.85378.725
60.1429-0.27680.03290.5070.304-0.02750.0087-0.0177-0.00830.1378-0.05380.18730.00220.010400.40280.01250.03450.3495-0.01640.448377.6172.20378.006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:322 OR RESID 401:407 ) )A3 - 322
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:322 OR RESID 401:407 ) )A401 - 407
3X-RAY DIFFRACTION2( CHAIN B AND RESID 1:173 )B1 - 173
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:322 OR RESID 401:407 ) )C3 - 322
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:322 OR RESID 401:407 ) )C401 - 407
6X-RAY DIFFRACTION4( CHAIN D AND RESID 1:173 )D1 - 173
7X-RAY DIFFRACTION5( CHAIN E AND ( RESID 3:322 OR RESID 401:407 ) )E3 - 322
8X-RAY DIFFRACTION5( CHAIN E AND ( RESID 3:322 OR RESID 401:407 ) )E401 - 407
9X-RAY DIFFRACTION6( CHAIN F AND RESID 1:173 )F1 - 173

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