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- PDB-6mxu: Crystal structure of hemagglutinin from influenza virus A/Texas/1... -

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Basic information

Entry
Database: PDB / ID: 6mxu
TitleCrystal structure of hemagglutinin from influenza virus A/Texas/1/1977 (H3N2)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 (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 / molecular replacement / Resolution: 1.85 Å
AuthorsDai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of hemagglutinin from influenza virus A/Texas/1/1977 (H3N2)
Authors: Dai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_struct_special_symmetry / 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 / _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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,42720
Polymers167,1483
Non-polymers6,27917
Water23,7981321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20310 Å2
ΔGint56 kcal/mol
Surface area59830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.890, 186.240, 106.960
Angle α, β, γ (deg.)90.000, 110.090, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1222-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 324 or resid 334 through 502 or resid 701 through 708 or resid 703))
21(chain B and (resid 9 through 324 or resid 334 through 502 or resid 703 through 709 or resid 700))
31(chain C and (resid 9 through 324 or resid 334 through 502 or resid 701 through 705 or resid 708))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 324 or resid 334 through 502 or resid 701 through 708 or resid 703))A9 - 324
121(chain A and (resid 9 through 324 or resid 334 through 502 or resid 701 through 708 or resid 703))A334 - 502
131(chain A and (resid 9 through 324 or resid 334 through 502 or resid 701 through 708 or resid 703))A701 - 708
141(chain A and (resid 9 through 324 or resid 334 through 502 or resid 701 through 708 or resid 703))A703
211(chain B and (resid 9 through 324 or resid 334 through 502 or resid 703 through 709 or resid 700))B9 - 324
221(chain B and (resid 9 through 324 or resid 334 through 502 or resid 703 through 709 or resid 700))B334 - 502
231(chain B and (resid 9 through 324 or resid 334 through 502 or resid 703 through 709 or resid 700))B703 - 709
241(chain B and (resid 9 through 324 or resid 334 through 502 or resid 703 through 709 or resid 700))B700
311(chain C and (resid 9 through 324 or resid 334 through 502 or resid 701 through 705 or resid 708))C9 - 324
321(chain C and (resid 9 through 324 or resid 334 through 502 or resid 701 through 705 or resid 708))C334 - 502
331(chain C and (resid 9 through 324 or resid 334 through 502 or resid 701 through 705 or resid 708))C701 - 705
341(chain C and (resid 9 through 324 or resid 334 through 502 or resid 701 through 705 or resid 708))C708

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Components

#1: Protein Hemagglutinin /


Mass: 55716.148 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Texas/1/1977(H3N2))
Strain: A/Texas/1/1977 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H9XIU5
#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.: 7 / Source method: isolated from a natural 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: 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.: 3 / Source method: isolated from a natural 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: 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.: 7 / Source method: isolated from a natural 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.: 1321 / Source method: isolated from a natural source / Formula: H2O

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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: 5.54 Å3/Da / Density % sol: 77.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.056M sodium phosphate monobasic, 1.4M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 19, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.85→48.55 Å / Num. obs: 308174 / % possible obs: 99.9 % / Redundancy: 17.6 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.274 / Rpim(I) all: 0.097 / Rrim(I) all: 0.291 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 16.1 % / Rmerge(I) obs: 7.594 / Num. unique obs: 15279 / CC1/2: 0.433 / Rpim(I) all: 2.794 / Rrim(I) all: 8.116 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP5

2yp5


Resolution: 1.85→46.373 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2123 15260 4.98 %
Rwork0.1925 --
obs0.1935 306376 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.2 Å2 / Biso mean: 41.1706 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 1.85→46.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11522 0 411 1321 13254
Biso mean--65.73 46.18 -
Num. residues----1462
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7243X-RAY DIFFRACTION7.699TORSIONAL
12B7243X-RAY DIFFRACTION7.699TORSIONAL
13C7243X-RAY DIFFRACTION7.699TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8710.36824570.37478983944092
1.871-1.8930.35014730.35029197967094
1.893-1.91610.35064920.335596201011298
1.9161-1.94040.31794680.304597401020899
1.9404-1.96590.29914950.283968210177100
1.9659-1.99280.29645040.271972010224100
1.9928-2.02130.28225220.2569975910281100
2.0213-2.05150.2715100.2512974610256100
2.0515-2.08350.26055040.249976010264100
2.0835-2.11770.24075270.2267975410281100
2.1177-2.15420.2485450.217964010185100
2.1542-2.19340.23495330.2128977210305100
2.1934-2.23560.23275180.2097971010228100
2.2356-2.28120.23845340.2179974210276100
2.2812-2.33080.23614900.2034975010240100
2.3308-2.3850.24215130.2036978610299100
2.385-2.44470.23195510.1945965810209100
2.4447-2.51080.22595310.1978976610297100
2.5108-2.58460.22174880.1976973110219100
2.5846-2.66810.21875040.1937978510289100
2.6681-2.76340.23835110.1994975610267100
2.7634-2.8740.21525290.1954976710296100
2.874-3.00480.21684940.1879979110285100
3.0048-3.16320.21235370.1834976210299100
3.1632-3.36130.19995580.1745970810266100
3.3613-3.62080.17494950.1626979910294100
3.6208-3.9850.16654820.156985910341100
3.985-4.56120.15245150.1382980010315100
4.5612-5.74490.17144870.154983310320100
5.7449-46.38770.2154930.205497401023398
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)
12.9949-1.9133-4.59421.39812.81946.43680.00890.5125-0.1773-0.0915-0.32940.18610.0852-0.69660.32420.21060.0151-0.06050.3621-0.02360.2318-23.730862.3988127.2491
21.9075-0.067-1.72880.52770.17082.72620.02830.2474-0.0364-0.2586-0.1048-0.08910.1546-0.02340.06480.3710.11610.01280.24640.04790.19753.578554.4081104.3625
33.884-3.1677-2.68272.55341.9421.83140.0660.15710.023-0.0733-0.06350.0214-0.0263-0.1244-0.0080.157-0.0179-0.05450.201-0.01410.2182-32.166275.3394149.2463
42.5297-3.281-2.96274.20723.98333.7712-0.4416-0.4091-0.13550.5260.35250.00080.55380.3750.06070.41920.08560.03330.29160.07190.2426-3.682149.5228156.5793
50.9148-0.8535-0.67032.05211.22871.3121-0.0434-0.0001-0.0803-0.1538-0.0386-0.1730.19540.07860.07940.36570.07030.07070.18880.0860.279411.420732.6594126.7949
63.8114-1.5026-4.15310.75171.6384.2492-0.1947-0.1671-0.08220.17050.08840.02170.2650.17270.11360.27570.0692-0.02040.29480.04830.181-21.253466.6888166.0136
74.5254-2.3395-2.90471.69321.44342.38710.4037-0.11650.5642-0.20840.0718-0.4516-0.37550.2334-0.47020.3169-0.08480.03260.2046-0.06110.3475-7.001688.6873148.2322
83.1525-1.5773-1.57531.81630.87461.99510.1181-0.13220.2761-0.10910.071-0.5675-0.02070.5338-0.19320.2233-0.00770.02520.3653-0.00580.399228.77160.9307124.2656
92.4782-2.8076-3.17553.10383.91064.5734-0.0209-0.24210.220.03190.1677-0.194-0.0060.3216-0.15530.3222-0.02340.0220.17850.00260.2441-10.85582.7292152.1219
105.49792.4527-0.94163.89390.07045.93510.2549-0.5610.54290.09130.0978-0.0336-0.41080.3873-0.30790.3213-0.0532-0.00810.238-0.11760.2679-31.029997.8441177.8043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 79 )A9 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 314 )A80 - 314
3X-RAY DIFFRACTION3chain 'A' and (resid 315 through 502 )A315 - 502
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 79 )B8 - 79
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 314 )B80 - 314
6X-RAY DIFFRACTION6chain 'B' and (resid 315 through 503 )B315 - 503
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 57 )C8 - 57
8X-RAY DIFFRACTION8chain 'C' and (resid 58 through 314 )C58 - 314
9X-RAY DIFFRACTION9chain 'C' and (resid 315 through 461 )C315 - 461
10X-RAY DIFFRACTION10chain 'C' and (resid 462 through 503 )C462 - 503

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