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- PDB-6uyn: Crystal structure of influenza A virus hemagglutinin from A/Ohio/... -

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Basic information

Entry
Database: PDB / ID: 6uyn
TitleCrystal structure of influenza A virus hemagglutinin from A/Ohio/09/2015 bound to the stalk-binding CR6261 antibody Fab
Components
  • CR6261 Fab heavy chain
  • CR6261 Fab light chain
  • Hemagglutinin HA1 chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / vaccine design / antibody / Fab / flu / influenza / H1N1 / structural genomics / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of influenza A virus hemagglutinin from A/Ohio/09/2015 bound to the stalk-binding CR6261 antibody Fab
Authors: Edwards, T.E. / Fox III, D. / Horanyi, P.S. / Lorimer, D.D. / Calhoun, B. / Conrady, D.G. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionNov 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 HA1 chain
H: CR6261 Fab heavy chain
L: CR6261 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4188
Polymers174,5164
Non-polymers9024
Water68538
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
H: CR6261 Fab heavy chain
L: CR6261 Fab light chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
H: CR6261 Fab heavy chain
L: CR6261 Fab light chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
H: CR6261 Fab heavy chain
L: CR6261 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,25524
Polymers523,54812
Non-polymers2,70712
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area41900 Å2
ΔGint-260 kcal/mol
Surface area102600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.590, 205.590, 205.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 63224.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Ohio/09/2015 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6C0TB04

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Antibody , 2 types, 2 molecules HL

#2: Antibody CR6261 Fab heavy chain


Mass: 24810.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): 293
#3: Antibody CR6261 Fab light chain


Mass: 23257.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): 293

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Sugars , 2 types, 3 molecules

#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: 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

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Non-polymers , 2 types, 39 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: InvbR.18715.a.KN11.PD38335/CR6261 Fab PD38376 at 10.3 mg/mL against Morpheus screen condition C6: 10% PEG 8000, 20% ethylene glycol, 0.1 M MOPS/HEPES pH 7.5, 0.03 M each sodium nitrate, ...Details: InvbR.18715.a.KN11.PD38335/CR6261 Fab PD38376 at 10.3 mg/mL against Morpheus screen condition C6: 10% PEG 8000, 20% ethylene glycol, 0.1 M MOPS/HEPES pH 7.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate, crystal tracking ID 311368c6, unique puck ID dai6-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→35.26 Å / Num. obs: 33765 / % possible obs: 99.9 % / Redundancy: 6.928 % / Biso Wilson estimate: 73.976 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Χ2: 1.016 / Net I/σ(I): 15.52 / Num. measured all: 233927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.85-2.927.0550.892.1717596249424940.740.962100
2.92-37.030.6992.7916964241324130.8340.755100
3-3.097.0340.5013.8316551235323530.9150.542100
3.09-3.197.0350.3825.0716068228422840.9420.413100
3.19-3.297.0320.2936.4815584221622160.9690.317100
3.29-3.417.0070.2188.4714876212321230.9780.236100
3.41-3.547.0240.16211.1514568207420740.9870.175100
3.54-3.686.9970.12214.1914000200120010.9930.132100
3.68-3.846.980.10516.1113310190719070.9940.113100
3.84-4.036.9850.08220.1712839183818380.9960.089100
4.03-4.256.9570.07222.5212056173517330.9960.07899.9
4.25-4.516.9010.06425.6111379165016490.9960.06999.9
4.51-4.826.8790.05827.3210738156115610.9970.063100
4.82-5.26.8360.05627.749905144914490.9970.06100
5.2-5.76.850.05528.699159133713370.9970.06100
5.7-6.376.7720.05428.918269122112210.9970.058100
6.37-7.366.7250.0530.767229107510750.9980.054100
7.36-9.016.6460.04433.8361019209180.9990.04899.8
9.01-12.756.3960.04235.5846187237220.9970.04699.9
12.75-35.265.3320.04430.2921174233970.9970.04993.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBN

3gbn


Resolution: 2.85→35.26 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1613 4.78 %
Rwork0.2086 32115 -
obs0.2104 33728 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 260.63 Å2 / Biso mean: 94.4453 Å2 / Biso min: 31.13 Å2
Refinement stepCycle: final / Resolution: 2.85→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5864 0 57 38 5959
Biso mean--117.44 59.14 -
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056066
X-RAY DIFFRACTIONf_angle_d0.7028273
X-RAY DIFFRACTIONf_dihedral_angle_d18.6222094
X-RAY DIFFRACTIONf_chiral_restr0.047938
X-RAY DIFFRACTIONf_plane_restr0.0061069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.930.3261540.29426652819100
2.93-3.030.33281270.26426392766100
3.03-3.140.28481120.246426652777100
3.14-3.260.25911600.235526452805100
3.26-3.410.30941250.25126622787100
3.41-3.590.27441180.241326802798100
3.59-3.820.24531330.209326722805100
3.82-4.110.23741160.190526952811100
4.11-4.520.21591640.166926322796100
4.52-5.170.20781460.173226822828100
5.18-6.510.26311240.210227232847100
6.51-35.260.23881340.21182755288999
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)
12.2988-2.11912.12892.654-2.40483.82380.10760.17820.3634-0.1117-0.3323-0.68870.34470.64020.21450.3987-0.0120.0490.6012-0.02930.5737-46.1549-34.701125.0569
22.3018-1.49142.01981.5047-2.82395.99670.45980.8251-0.1822-0.0455-0.4671-0.88380.8921.49750.31370.7930.1879-0.13771.14190.01251.2255-26.9636-51.223744.7355
30.3037-0.7695-0.24432.5277-0.14363.3009-0.0244-1.2943-0.37920.1941-0.2156-1.11650.28221.3260.27260.68980.0404-0.24141.82610.31541.3042-17.28-53.015155.825
45.5459-0.72210.74274.6008-0.91415.3548-0.2859-1.2045-0.81740.8303-0.5175-0.81341.17341.59490.41621.13980.5194-0.13671.55040.30221.1896-22.8759-58.09362.8146
53.6213-1.70472.7563.1498-3.09634.0973-0.16270.13970.9514-0.0151-0.4279-0.74060.07471.42980.79680.60340.0518-0.04930.98020.04430.9433-31.4006-40.052139.829
64.1838-3.63943.4774.025-4.07994.0274-0.02240.14610.40260.0186-0.2365-0.43760.00960.55110.13190.33970.03040.05310.4832-0.03410.5428-51.5571-34.360125.5266
73.9178-0.1174-1.37534.8577-2.87055.9661-0.25190.6573-0.2216-0.67220.066-0.02040.6128-0.13540.1870.40770.00270.10930.409-0.09480.4259-69.9639-19.13510.2759
82.6187-2.45362.21544.8736-2.71244.2986-0.29420.00340.23510.29980.1816-0.2301-0.6504-0.34810.08780.3088-0.10280.08430.4442-0.07030.4438-64.5786-12.97316.354
90.2684-1.18850.9315.5304-4.14923.2258-0.2319-1.24130.97981.77350.4084-1.6448-1.37170.45560.41471.52980.2555-0.09681.3686-0.16240.8545-49.8735-31.767938.8415
100.9672-1.65181.5535.2187-4.174.2876-0.1822-0.1552-0.00030.2240.1839-0.1410.0247-0.183-0.05970.4645-0.04850.01980.4279-0.07520.4269-63.2121-33.386829.2982
112.4412-0.58032.40947.2811-3.21158.35180.38691.22670.677-0.70980.10780.0334-0.5487-0.7121-0.5850.55710.09280.06930.74310.09520.6182-79.803-5.91161.6805
122.67370.5563-2.92173.7249-5.37479.5160.70940.26891.1820.4635-0.1584-1.1916-1.73920.1346-0.08770.81090.0420.10370.56060.03220.7089-71.6380.39217.4683
133.91920.058-2.35748.7294-0.02664.57460.34830.24880.9247-0.16280.8181.0069-2.0993-1.6555-0.83681.05480.44160.13810.93620.10130.8775-82.82224.52136.8309
143.96584.29090.10156.9629-2.00247.3064-0.0278-0.6385-1.00940.2696-0.2132-0.44730.06021.16310.11980.3867-0.0411-0.08680.76060.0360.5774-34.0127-10.008324.8201
156.32991.7666-0.98074.0597-1.00332.1047-0.1010.0904-0.45-0.2390.0463-0.2645-0.01580.24830.0590.3789-0.03850.07750.4598-0.15190.5367-43.7426-10.610119.1078
167.13583.3993-0.05214.4874-0.79784.5135-0.2001-0.10730.22060.07030.0938-0.2198-0.25270.58560.04950.4235-0.07490.02240.4061-0.11310.4424-38.6945-4.45520.6368
179.9371-0.29751.37992.56592.43532.6047-0.16890.19280.11471.80650.80460.7660.802-0.1956-0.43311.0399-0.11120.18371.8355-0.36421.2662-12.6996-3.488927.2003
187.8779-4.52280.48135.2403-0.66681.4956-0.64030.35530.67741.5529-1.91830.81721.8648-0.65072.21911.3064-0.53680.191.8849-0.4181.2838-14.51942.731724.2282
197.42471.4632-2.04543.30591.9762.92310.31240.8931.1419-1.2833-0.02530.269-1.5963-1.0624-0.34251.0892-0.15150.16590.73410.11471.2284-48.123516.005517.1522
207.1904-1.09640.18858.02730.3755.28730.2188-0.47471.19620.23730.0326-0.0248-0.5658-0.2377-0.15440.5371-0.00560.10680.5299-0.15170.9343-49.915511.177624.9724
213.1815-3.2228-3.75445.55975.11825.18180.06881.37010.8007-3.59310.55-0.2817-2.3401-0.1192-0.60511.0805-0.10820.0670.7955-0.07330.7229-45.71413.816211.1429
224.6405-0.7497-0.68783.7187-0.83252.39570.89771.0002-1.51330.6213-0.4817-0.54010.34871.0072-0.39550.8998-0.1659-0.58181.4137-0.55191.8035-17.930411.457127.3674
234.9426-5.05362.6085.1686-2.84753.42790.0348-0.0979-0.3746-0.6768-0.0157-1.99040.2980.9120.12210.8636-0.11930.30051.7975-0.76032.4943-7.952113.137326.3276
240.6215-1.4850.72094.1738-1.74720.83250.33520.00570.2132-0.3451-0.0125-1.47970.00760.7008-0.85361.22430.1033-0.3581.6898-0.753.1359-16.573213.733428.074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 87 )A16 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 114 )A88 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 177 )A115 - 177
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 269 )A178 - 269
5X-RAY DIFFRACTION5chain 'A' and (resid 270 through 299 )A270 - 299
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 341 )A300 - 341
7X-RAY DIFFRACTION7chain 'B' and (resid 345 through 366 )B345 - 366
8X-RAY DIFFRACTION8chain 'B' and (resid 367 through 402 )B367 - 402
9X-RAY DIFFRACTION9chain 'B' and (resid 403 through 407 )B403 - 407
10X-RAY DIFFRACTION10chain 'B' and (resid 408 through 476 )B408 - 476
11X-RAY DIFFRACTION11chain 'B' and (resid 477 through 489 )B477 - 489
12X-RAY DIFFRACTION12chain 'B' and (resid 490 through 498 )B490 - 498
13X-RAY DIFFRACTION13chain 'B' and (resid 499 through 511 )B499 - 511
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 17 )H1 - 17
15X-RAY DIFFRACTION15chain 'H' and (resid 18 through 83 )H18 - 83
16X-RAY DIFFRACTION16chain 'H' and (resid 84 through 124 )H84 - 124
17X-RAY DIFFRACTION17chain 'H' and (resid 125 through 156 )H125 - 156
18X-RAY DIFFRACTION18chain 'H' and (resid 157 through 188 )H157 - 188
19X-RAY DIFFRACTION19chain 'L' and (resid 3 through 33 )L3 - 33
20X-RAY DIFFRACTION20chain 'L' and (resid 34 through 93 )L34 - 93
21X-RAY DIFFRACTION21chain 'L' and (resid 94 through 106 )L94 - 106
22X-RAY DIFFRACTION22chain 'L' and (resid 107 through 131 )L107 - 131
23X-RAY DIFFRACTION23chain 'L' and (resid 132 through 162 )L132 - 162
24X-RAY DIFFRACTION24chain 'L' and (resid 163 through 183 )L163 - 183

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