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- PDB-6xpo: Influenza hemagglutinin A/Bangkok/01/1979(H3N2) -

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Basic information

Entry
Database: PDB / ID: 6xpo
TitleInfluenza hemagglutinin A/Bangkok/01/1979(H3N2)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / fusogen / virus / influenza
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117892 United States
CitationJournal: Mbio / Year: 2021
Title: A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface.
Authors: McCarthy, K.R. / Lee, J. / Watanabe, A. / Kuraoka, M. / Robinson-McCarthy, L.R. / Georgiou, G. / Kelsoe, G. / Harrison, S.C.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)183,92324
Polymers174,0173
Non-polymers9,90621
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24160 Å2
ΔGint101 kcal/mol
Surface area65290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.660, 186.180, 107.400
Angle α, β, γ (deg.)90.000, 110.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin


Mass: 58005.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Bangkok/1/1979 H3N2)
Strain: A/Bangkok/1/1979 H3N2 / Gene: HA / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1K9S3
#2: 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.: 12
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
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}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.: 7
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
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: 5.41 Å3/Da / Density % sol: 77.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 5% (w/v) PEG 400, 0.5M Sodium citrate, pH7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→48.66 Å / Num. obs: 71349 / % possible obs: 96.31 % / Redundancy: 3.9 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1617 / Rpim(I) all: 0.09213 / Rrim(I) all: 0.1867 / Net I/σ(I): 7.88
Reflection shellResolution: 3→3.107 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7168 / CC1/2: 0.751 / CC star: 0.926 / Rpim(I) all: 0.6143 / % possible all: 97.12

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MXU

6mxu


Resolution: 3→48.658 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 3617 5.08 %
Rwork0.2259 67609 -
obs0.2277 71226 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.03 Å2 / Biso mean: 92.9961 Å2 / Biso min: 29.8 Å2
Refinement stepCycle: final / Resolution: 3→48.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11618 0 654 0 12272
Biso mean--147.74 --
Num. residues----1475
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.03940.40521350.3635262897
3.0394-3.0810.36651120.341263297
3.081-3.1250.33271550.325257397
3.125-3.17170.34411360.3244260797
3.1717-3.22120.36321220.3311259196
3.2212-3.2740.36461390.3188257095
3.274-3.33050.37471500.3029250994
3.3305-3.3910.36931020.2821233486
3.391-3.45620.34351360.2687258895
3.4562-3.52670.30111450.2542264598
3.5267-3.60340.26811350.2409266898
3.6034-3.68720.2631560.2394260598
3.6872-3.77940.31991660.2437262898
3.7794-3.88150.26361470.248263398
3.8815-3.99570.29891310.2304265098
3.9957-4.12460.27621380.2186265098
4.1246-4.27190.21711430.2045263398
4.2719-4.44280.27261270.2022264097
4.4428-4.64490.25531340.1961257996
4.6449-4.88960.24471540.1984253693
4.8896-5.19560.23311380.1926242391
5.1956-5.59620.21261560.1977266599
5.5962-6.15840.25291420.2073265599
6.1584-7.04720.26321470.2166267098
7.0472-8.870.19141440.1931265097
8.87-48.6580.18831270.1805264795
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)
10.1965-0.2096-0.45540.02520.05430.1397-0.21670.3215-0.4604-0.0382-0.35490.32350.3428-0.5307-0.00590.6395-0.0060.00120.6558-0.05590.5415.247762.758724.311
20.4977-0.267-0.71390.8042-0.26631.12850.01770.1625-0.0743-0.2817-0.1697-0.07410.35460.032-0.00070.72490.19940.05330.52740.00140.392544.556853.36480.654
31.9575-1.1684-1.18950.7350.43491.8175-0.05470.2928-0.137-0.1526-0.00080.1420.0741-0.2765-0.17270.4552-0.0977-0.04940.5163-0.04030.63281.787169.515943.4599
40.12180.0455-0.10790.14110.21560.22730.06510.5931-0.0874-0.293-0.2263-0.07830.1317-0.1175-00.72020.09-0.01250.6310.02440.585520.2668.483931.5278
50.14450.28090.10790.8716-0.33170.62840.0714-0.08590.11140.02660.02850.0707-0.1077-0.048400.21960.0203-0.13150.2826-0.02150.3854.063378.336154.5329
60.3192-0.2143-0.05410.86790.07920.1367-0.0709-0.17360.0239-0.0080.0613-0.14140.04670.1304-0.00010.57820.01360.01010.48610.04750.533841.415539.521143.1504
70.71-0.9076-0.51881.33140.71670.47430.0728-0.07720.0195-0.2993-0.1251-0.1269-0.05070.0081-0.02030.71790.08980.10390.5080.07220.570346.249837.909330.1339
80.3996-0.1396-0.12970.6932-0.01730.185-0.0681-0.32350.01740.19890.15050.10920.00650.1907-00.46040.0379-0.01980.48140.01540.362515.406266.682265.1213
90.75770.57070.25391.05460.30171.43530.3693-0.28840.4137-0.64650.0022-0.2654-0.68010.26560.04670.70050.11810.05070.426-0.00150.593416.689793.778154.5228
101.06640.0721-0.24180.5243-0.07650.75160.0686-0.08540.2223-0.22330.092-0.37830.03170.510900.62120.11350.11650.745-0.01170.754664.250163.538325.7182
110.015-0.0746-0.13451.08670.20110.45430.030.00720.1002-0.07890.0356-0.0276-0.12910.2099-0.00140.48570.0302-0.06210.4237-0.02940.476225.947383.017252.084
120.2762-0.0128-0.07030.09930.06870.1413-0.1486-0.69190.14470.6362-0.013-0.03870.30680.1515-0.00060.8847-0.13340.09980.6406-0.1570.67226.618297.849677.861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 89 )A8 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 288 )A90 - 288
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 366 )A289 - 366
4X-RAY DIFFRACTION4chain 'A' and (resid 367 through 404 )A367 - 404
5X-RAY DIFFRACTION5chain 'A' and (resid 405 through 502 )A405 - 502
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 146 )B7 - 146
7X-RAY DIFFRACTION7chain 'B' and (resid 147 through 337 )B147 - 337
8X-RAY DIFFRACTION8chain 'B' and (resid 338 through 502 )B338 - 502
9X-RAY DIFFRACTION9chain 'C' and (resid 4 through 41 )C4 - 41
10X-RAY DIFFRACTION10chain 'C' and (resid 42 through 322 )C42 - 322
11X-RAY DIFFRACTION11chain 'C' and (resid 323 through 461 )C323 - 461
12X-RAY DIFFRACTION12chain 'C' and (resid 462 through 502 )C462 - 502

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