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- PDB-6xpz: Human antibody S1V2-83 in complex with the influenza hemagglutini... -

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Basic information

Entry
Database: PDB / ID: 6xpz
TitleHuman antibody S1V2-83 in complex with the influenza hemagglutinin head domain of A/Moscow/10/1999(H3N2)
Components
  • (antibody S1V2-83 ...) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody antigen complex / hemagglutinin / virus / influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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
D: Hemagglutinin
B: antibody S1V2-83 heavy chain
C: antibody S1V2-83 light chain
E: antibody S1V2-83 heavy chain
F: antibody S1V2-83 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,79812
Polymers164,1716
Non-polymers2,6266
Water0
1
A: Hemagglutinin
B: antibody S1V2-83 heavy chain
C: antibody S1V2-83 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3186
Polymers82,0863
Non-polymers1,2323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin
E: antibody S1V2-83 heavy chain
F: antibody S1V2-83 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4806
Polymers82,0863
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.790, 103.710, 220.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Hemagglutinin /


Mass: 32319.330 Da / Num. of mol.: 2 / Fragment: head domain (UNP residues 53-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Moscow/10/1999(H3N2))
Strain: A/Moscow/10/1999(H3N2) / Gene: HA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1NZ37

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Antibody , 2 types, 4 molecules BECF

#2: Antibody antibody S1V2-83 heavy chain


Mass: 26269.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody antibody S1V2-83 light chain


Mass: 23496.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Sugars , 4 types, 6 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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-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
DManpb1-4DGlcpNAcb1-6DGlcpNAcb1-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/a6-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 1
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
#7: 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.: 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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Details

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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 5% w/v PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2018
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.45→49.1 Å / Num. obs: 26508 / % possible obs: 99.49 % / Redundancy: 9 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.07339 / Rrim(I) all: 0.2248 / Net I/σ(I): 10.01
Reflection shellResolution: 3.45→3.573 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2582 / CC1/2: 0.837 / CC star: 0.955 / Rpim(I) all: 0.3951 / Rrim(I) all: 1.216 / % possible all: 99.08

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5W08,6DC3, 5SX4, & 6E4X

5w08

6dc3

5sx4

6e4x


Resolution: 3.45→49.1 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3068 1325 5.01 %
Rwork0.2505 25126 -
obs0.2533 26451 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 444.85 Å2 / Biso mean: 140.073 Å2 / Biso min: 59.56 Å2
Refinement stepCycle: final / Resolution: 3.45→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11009 0 173 0 11182
Biso mean--156.53 --
Num. residues----1425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.45-3.590.38671310.34472730286199
3.59-3.750.39521590.321627372896100
3.75-3.950.41061520.297327282880100
3.95-4.20.32521600.269127442904100
4.2-4.520.31570.242127802937100
4.52-4.970.27921130.223428112924100
4.98-5.690.27011440.227727952939100
5.69-7.170.33251590.261928392998100
7.17-49.10.24521500.21362962311299
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)
11.70921.41080.13611.15560.1466-0.01670.05350.2373-0.3849-0.1509-0.0554-0.6879-0.02850.1953-0.09841.44460.1458-0.23481.19750.09460.6623-14.976-9.684-4.262
20.457-0.315-0.11850.20970.19310.47010.24730.0562-0.0165-0.0399-0.098-0.0586-0.1820.61201.08150.056-0.08280.93450.17871.179-19.747.40910.434
30.71740.6615-0.30920.606-0.28960.13510.1730.27160.617-0.2701-0.16560.7059-0.23690.25710.01460.93040.2095-0.110.7935-0.15260.7073-25.2276.39620.058
41.50521.07510.22991.25190.49710.30480.04170.19360.55240.0214-0.25090.43590.3835-0.1492-0.0511.61430.1232-0.32931.18270.04880.5992-21.482-15.031-6.687
50.50480.2031-0.36340.4878-0.2070.2223-0.04250.01910.259-0.1061-0.0921-0.18550.06810.4253-00.80450.07150.02990.7771-0.00751.0167-46.0852.534.83
60.7556-0.2741-0.06350.36560.40420.5324-0.13250.14570.28430.14230.19940.4415-0.48630.2792-0.00020.87870.02060.07030.82390.02631.2801-59.32212.56444.402
70.210.14220.06290.09810.0520.0071-0.2356-0.2850.0072-0.3961-0.4585-0.54420.20090.5157-0.00021.1770.270.05631.03440.13710.8154-46.736-4.80824.74
80.11430.07870.11970.28120.01990.1292-0.1817-0.4170.0721-0.1410.10710.87050.6225-0.36860.01291.14370.07-0.15760.9016-0.3660.7327-48.001-21.97520.873
90.0941-0.0566-0.22620.4611-0.0090.55980.14480.22140.03270.0971-0.03430.05410.0693-0.1996-0.00010.79290.0719-0.13650.8465-0.12831.5705-20.626-26.60432.003
100.34090.35430.29710.35020.30240.23880.3276-0.06930.0144-0.5447-0.4589-0.20570.27910.05450.00030.85470.0435-0.11751.08220.11521.2864-16.425-20.93730.569
110.76830.7063-0.10242.4220.86470.52450.07090.4679-0.0559-0.42640.0227-0.4340.06630.01360.55771.2139-0.1645-0.9341.10720.05422.26612.625-49.40258.76
121.576-1.0307-1.50720.76130.90061.48750.7416-0.5112-0.58810.8248-0.7874-0.09360.351-0.6061-0.00621.0008-0.6071-0.38310.83350.21471.3872-4.772-44.63959.465
130.56460.49930.19760.4310.0730.7356-0.0444-0.0460.22360.03820.2893-0.2871-0.29360.2947-00.6573-0.01080.01940.70670.00511.4322-0.234-16.08634.757
140.0509-0.00070.0634-0.00210.00020.07840.0313-0.4013-0.2024-0.2059-0.0277-0.5149-0.00580.38370.00060.7090.0443-0.23091.1950.29881.547712.152-27.46348.942
150.453-0.6691-0.88231.05981.34321.7405-0.1074-0.49780.2143-0.04260.9372-0.20520.1969-0.52770.92621.6024-0.1784-1.111.38890.28292.43182.442-55.3155.803
160.19180.2173-0.64730.4083-0.94842.50170.0850.5506-1.13620.24690.4971-0.3065-0.1995-0.23710.32540.98120.0679-0.58091.0687-0.32132.14638.663-42.83547.934
170.80380.1645-0.26010.05640.02730.36440.373-0.0674-0.3636-0.56320.50270.49820.8241-0.1742.69881.54340.0969-1.26710.825-0.20583.34811.265-53.66248.998
180.43230.23780.3930.4940.24290.3460.21060.0989-0.14150.11960.15220.18920.0582-0.262900.8205-0.0351-0.03880.7819-0.08051.2097-59.504-22.47260.004
190.0121-0.21250.05992.1185-0.45170.06990.156-0.1283-0.2395-0.456-0.35620.39460.3544-0.0459-0.66030.6197-0.09230.24480.98920.26161.2029-52.534-26.83372.396
200.0027-0.08290.06731.5102-1.24861.01610.3574-0.7627-0.0299-0.3802-0.3427-0.44460.8917-0.03090.08390.765-0.35110.1211.37860.28091.3724-52.484-38.10389.56
211.28181.4555-0.22281.6362-0.26050.03780.16750.3810.1053-0.50780.90960.50790.2664-0.8950.43581.2497-0.6358-0.18332.01090.09890.6387-59.309-43.04694.201
220.2333-0.1563-0.02130.21640.00830.6868-0.0586-0.09880.0445-0.0377-0.2726-0.8462-0.16360.21930.00040.69780.0346-0.16190.77770.09730.9842-41.182-12.10771.286
230.3108-0.039-0.23791.60071.03540.81030.4166-0.9371-0.6055-0.38580.1874-1.01340.608-0.15790.17551.3465-0.0848-0.25191.06220.47631.1661-38.369-43.62487.878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 41:89 )A41 - 89
2X-RAY DIFFRACTION2( CHAIN A AND RESID 90:184 )A90 - 184
3X-RAY DIFFRACTION3( CHAIN A AND RESID 185:251 )A185 - 251
4X-RAY DIFFRACTION4( CHAIN A AND RESID 252:308 )A252 - 308
5X-RAY DIFFRACTION5( CHAIN D AND RESID 44:146 )D44 - 146
6X-RAY DIFFRACTION6( CHAIN D AND RESID 147:255 )D147 - 255
7X-RAY DIFFRACTION7( CHAIN D AND RESID 256:280 )D256 - 280
8X-RAY DIFFRACTION8( CHAIN D AND RESID 281:312 )D281 - 312
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1:94 )B1 - 94
10X-RAY DIFFRACTION10( CHAIN B AND RESID 95:134 )B95 - 134
11X-RAY DIFFRACTION11( CHAIN B AND RESID 135:160 )B135 - 160
12X-RAY DIFFRACTION12( CHAIN B AND RESID 161:229 )B161 - 229
13X-RAY DIFFRACTION13( CHAIN C AND RESID 1:102 )C1 - 102
14X-RAY DIFFRACTION14( CHAIN C AND RESID 103:113 )C103 - 113
15X-RAY DIFFRACTION15( CHAIN C AND RESID 114:128 )C114 - 128
16X-RAY DIFFRACTION16( CHAIN C AND RESID 129:174 )C129 - 174
17X-RAY DIFFRACTION17( CHAIN C AND RESID 175:211 )C175 - 211
18X-RAY DIFFRACTION18( CHAIN E AND RESID 1:94 )E1 - 94
19X-RAY DIFFRACTION19( CHAIN E AND RESID 95:160 )E95 - 160
20X-RAY DIFFRACTION20( CHAIN E AND RESID 161:205 )E161 - 205
21X-RAY DIFFRACTION21( CHAIN E AND RESID 206:229 )E206 - 229
22X-RAY DIFFRACTION22( CHAIN F AND RESID 1:110 )F1 - 110
23X-RAY DIFFRACTION23( CHAIN F AND RESID 111:211 )F111 - 211

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