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- PDB-8g2k: Structure of the H3 hemagglutinin of A/California/7/2004 -

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Basic information

Entry
Database: PDB / ID: 8g2k
TitleStructure of the H3 hemagglutinin of A/California/7/2004
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Hemagglutinin / antigen / homotrimer / native
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesAlphainfluenzavirus influenzae
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVenkatramani, L. / Mooers, B.H.M. / Air, G.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)NIH 2P20GM103640
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM145423 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 CA225520 United States
CitationJournal: To Be Published
Title: Structure of the H3 hemagglutinin of A/California/7/2004
Authors: Venkatramani, L. / Mooers, B.H.M. / Air, G.M.
History
DepositionFeb 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,85210
Polymers55,1082
Non-polymers2,7458
Water2,162120
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,55730
Polymers165,3236
Non-polymers8,23424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area43030 Å2
ΔGint-11 kcal/mol
Surface area60400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.199, 101.199, 384.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 35256.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Alphainfluenzavirus influenzae / Strain: A/California/7/2004 / References: UniProt: A4GXY4
#2: Protein Hemagglutinin /


Mass: 19851.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Alphainfluenzavirus influenzae / Strain: A/California/7/2004 / References: UniProt: A3DRV6

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Sugars , 3 types, 8 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAca1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 120 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 310.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Pentaerythritol propoxylate (5/4 PO/OH), 200 mM KCl and 50 mM HEPES (pH 7.5 adjusted with KOH).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→34.25 Å / Num. obs: 31998 / % possible obs: 99.55 % / Observed criterion σ(F): 6 / Redundancy: 9.8 % / Biso Wilson estimate: 48.26 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Rsym value: 0.066 / Net I/av σ(I): 22.4 / Net I/σ(I): 19.94
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9617 / Rpim(I) all: 0.794 / Rrim(I) all: 0.348 / Rsym value: 0.83 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
MOSFLM1.0.7data reduction
SCALA2.1data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→34.25 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1638 5.12 %
Rwork0.197 --
obs0.1988 31992 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 179 120 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044150
X-RAY DIFFRACTIONf_angle_d0.6815641
X-RAY DIFFRACTIONf_dihedral_angle_d13.0171551
X-RAY DIFFRACTIONf_chiral_restr0.046647
X-RAY DIFFRACTIONf_plane_restr0.004726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.420.32191330.26082361X-RAY DIFFRACTION95
2.42-2.50.26111280.24542498X-RAY DIFFRACTION100
2.5-2.590.28661290.23432519X-RAY DIFFRACTION100
2.59-2.690.27391380.23222488X-RAY DIFFRACTION100
2.69-2.810.25161250.24542534X-RAY DIFFRACTION100
2.81-2.960.27611390.23062520X-RAY DIFFRACTION100
2.96-3.150.26921300.21772532X-RAY DIFFRACTION100
3.15-3.390.25451410.21392520X-RAY DIFFRACTION100
3.39-3.730.25671560.19752529X-RAY DIFFRACTION100
3.73-4.270.20061520.16722547X-RAY DIFFRACTION100
4.27-5.370.16931390.15152582X-RAY DIFFRACTION100
5.38-7.430.22181280.19892724X-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)
11.31620.19211.43741.75222.72054.7104-0.00450.01720.1721-0.17290.0510.0854-0.5789-0.56410.06610.40180.05730.07950.27370.02910.5496-5.17917.389106.418
22.213-0.7098-0.07281.4977-0.09323.97970.33460.76240.5436-0.5805-0.0218-0.0893-0.5220.0275-0.23710.7375-0.0090.15790.67460.17230.61066.14825.09856.759
31.31591.6384-0.6472.0098-0.59494.36640.17850.67610.2056-0.52960.0648-0.24670.15831.0932-0.24150.82210.06780.27011.11040.09630.575716.33117.77641.77
42.3987-0.61940.12252.4372-1.03223.0548-0.01330.86620.144-0.68120.1859-0.0891-0.403-0.1772-0.18841.0192-0.00130.18991.13630.02830.49711.02113.60334.401
51.62090.5435-0.24281.86730.25325.22190.00810.53980.0084-0.48440.1795-0.1951-0.10170.5739-0.21750.6798-0.02670.16720.67720.10090.578811.63617.86151.073
61.7761-0.0444-2.23937.3016-4.56067.44660.37310.20450.23470.13670.16280.0988-0.89860.1672-0.37710.4835-0.04480.15640.35120.04580.46972.37121.32675.003
71.2981-0.1124-0.48941.2056-0.282.5849-0.02370.15920.2598-0.0020.05350.0134-0.3903-0.7752-0.12710.35570.07270.05080.3050.03530.5198-4.70315.70392.563
84.7539-4.3271-3.11124.56851.03157.51220.82570.6808-1.55070.1734-0.6762-0.1146-0.1225-0.3849-0.10190.38190.01070.0060.4314-0.03820.6713-6.057.923113.733
97.5501-2.3131-3.5474.77810.30443.3554-0.0317-0.2716-0.35450.4177-0.15410.0972-0.7651-0.35260.00160.44120.03090.02530.3652-0.07810.484-2.35821.277113.937
106.10.0066-1.36635.01923.35629.2685-0.5975-1.04610.14770.4716-0.3570.5505-0.47390.05440.89690.54110.00670.00830.2356-0.10520.4690.34523.003128.405
112.0082-1.1095-2.15911.57552.51015.0575-0.0149-0.07360.12120.1479-0.01960.171-0.32511.0996-0.01180.3701-0.08730.06170.2462-0.06120.55877.0216.575107.406
122.7789-1.9836-0.97892.69090.65880.5390.1965-0.11660.19110.1358-0.49160.12520.92670.61710.14110.7095-0.23620.12160.5406-0.00020.67819.64313.29975.596
130.83390.12621.20240.83211.33447.4424-0.00290.18150.1431-0.11930.04140.0223-0.43350.1663-0.00890.344-0.00330.0320.28270.03260.4831-1.7297.3388.278
142.8210.51690.95235.003-0.98935.81790.1529-0.26970.15070.301-0.1363-0.1824-0.03630.0659-0.05540.423-0.0205-0.00240.3586-0.12180.47484.21712.567134.327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:41 )A8 - 41
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 42:104 OR RESID 401:401 ) )A42 - 104
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 42:104 OR RESID 401:401 ) )A401
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 105:135 OR RESID 402:402 OR RESID 403:403 ) )A105 - 135
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 105:135 OR RESID 402:402 OR RESID 403:403 ) )A402
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 105:135 OR RESID 402:402 OR RESID 403:403 ) )A403
7X-RAY DIFFRACTION4( CHAIN A AND RESID 136:246 )A136 - 246
8X-RAY DIFFRACTION5( CHAIN A AND RESID 247:274 )A247 - 274
9X-RAY DIFFRACTION6( CHAIN A AND RESID 275:304 )A275 - 304
10X-RAY DIFFRACTION7( CHAIN A AND RESID 305:325 )A305 - 325
11X-RAY DIFFRACTION8( CHAIN B AND RESID 1:10 )B1 - 10
12X-RAY DIFFRACTION9( CHAIN B AND RESID 11:22 )B11 - 22
13X-RAY DIFFRACTION10( CHAIN B AND RESID 23:30 )B23 - 30
14X-RAY DIFFRACTION11( CHAIN B AND RESID 31:55 )B31 - 55
15X-RAY DIFFRACTION12( CHAIN B AND RESID 56:65 )B56 - 65
16X-RAY DIFFRACTION13( CHAIN B AND RESID 66:126 )B66 - 126
17X-RAY DIFFRACTION14( CHAIN B AND ( RESID 127:173 OR RESID 201:201 ) )B127 - 173
18X-RAY DIFFRACTION14( CHAIN B AND ( RESID 127:173 OR RESID 201:201 ) )B201

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