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- PDB-4we5: The crystal structure of hemagglutinin from A/Port Chalmers/1/197... -

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Basic information

Entry
Database: PDB / ID: 4we5
TitleThe crystal structure of hemagglutinin from A/Port Chalmers/1/1973 influenza virus
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Hemagglutinin / H3N2 / influenza virus
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 / 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 / Resolution: 2.1 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
CitationJournal: Virology / Year: 2015
Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / database_PDB_caveat / entity / entity_src_gen / 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_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_conn / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.text
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,0077
Polymers56,9672
Non-polymers2,0405
Water6,918384
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)177,02021
Polymers170,9006
Non-polymers6,12015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area38320 Å2
ΔGint-48 kcal/mol
Surface area60480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.128, 153.128, 153.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-551-

HOH

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 36129.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Port Chalmers/1/1973 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1PUD9
#2: Protein Hemagglutinin HA2 chain


Mass: 20837.133 Da / Num. of mol.: 1 / Fragment: unp residues 346-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Port Chalmers/1/1973 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1PUD9

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Sugars , 3 types, 5 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 , 1 types, 384 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5 / Details: 0.1M HEPES, 25% PEG 550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34697 / % possible obs: 99.5 % / Redundancy: 4.9 % / Net I/σ(I): 27.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2.1→30.031 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1743 5.02 %
Rwork0.1818 --
obs0.1842 34697 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→30.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 134 384 4384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074097
X-RAY DIFFRACTIONf_angle_d1.0415559
X-RAY DIFFRACTIONf_dihedral_angle_d19.6361514
X-RAY DIFFRACTIONf_chiral_restr0.068626
X-RAY DIFFRACTIONf_plane_restr0.004714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.1620.29881600.25552662X-RAY DIFFRACTION98
2.162-2.23180.26021450.22532683X-RAY DIFFRACTION98
2.2318-2.31150.27841360.22332723X-RAY DIFFRACTION99
2.3115-2.4040.3191400.20712708X-RAY DIFFRACTION99
2.404-2.51340.29081530.21352738X-RAY DIFFRACTION100
2.5134-2.64580.2731400.20512764X-RAY DIFFRACTION100
2.6458-2.81140.28021300.20862721X-RAY DIFFRACTION100
2.8114-3.02830.26391570.19422770X-RAY DIFFRACTION100
3.0283-3.33270.23471410.19192763X-RAY DIFFRACTION100
3.3327-3.81420.22721390.17012767X-RAY DIFFRACTION100
3.8142-4.80230.16851610.14362776X-RAY DIFFRACTION100
4.8023-30.03390.21141410.17222879X-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)
10.2120.11620.46360.42330.34980.53330.06460.3169-0.2299-0.02180.103-0.04080.12610.07830.00530.29550.00980.03060.2141-0.07940.2818-14.9093-34.3641-42.8768
21.4279-0.95710.67042.564-0.331.2692-0.149-0.06770.25170.18570.1279-0.3088-0.1535-0.0060.00580.2057-0.01190.0130.2167-0.0240.225813.82169.2959-15.0607
30.69250.27890.26731.07470.27590.3787-0.03-0.0604-0.02490.07520.0676-0.01030.0009-0.0142-00.21370.01480.01840.24220.01090.17662.7194-3.006-18.7738
40.20370.05490.07990.05080.01910.3069-0.29180.2709-1.0201-0.57340.3101-0.53740.62930.34080.00180.51060.00230.04970.4157-0.13730.6303-23.8353-46.6632-52.1743
50.3688-0.0890.26980.322-0.41350.4935-0.07520.0815-0.0398-0.2204-0.0557-0.0886-0.4910.02110.00010.482-0.0075-0.04670.3848-0.06950.3942-26.4376-35.1719-53.0355
60.1218-0.0536-0.0660.0590.0160.03540.13780.4111-0.4034-0.2374-0.38080.57880.5478-0.2187-0.00070.4614-0.0376-0.06460.4164-0.09750.4963-10.6085-10.0215-30.4528
7-0.20930.08970.150.35960.32920.83120.0405-0.0403-0.0753-0.003-0.0662-0.0550.0321-0.0823-0.00260.2110.01540.0090.2224-0.05130.207-20.3974-27.8114-30.3606
80.53250.049-0.05370.38510.06390.3962-0.1820.07030.1703-0.04240.0912-0.0833-0.1644-0.10690.00010.3837-0.0149-0.02080.3508-0.03090.3309-42.5809-47.7429-61.5577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 195 )
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 324 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 22 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 65 )
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 132 )
8X-RAY DIFFRACTION8chain 'B' and (resid 133 through 172 )

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