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- PDB-8txm: Crystal structure of 05.GC.w13.02 Fab in complex with H1 HA from ... -

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Basic information

Entry
Database: PDB / ID: 8txm
TitleCrystal structure of 05.GC.w13.02 Fab in complex with H1 HA from A/California/04/2009(H1N1)
Components
  • (GC_w13_B, Fab ...) x 2
  • (Hemagglutinin) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / H1N1 / Antibody / Hemagglutinin / 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 / 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 speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsLin, T.H. / Moore, N. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: J.Exp.Med. / Year: 2024
Title: Maturation of germinal center B cells after influenza virus vaccination in humans.
Authors: McIntire, K.M. / Meng, H. / Lin, T.H. / Kim, W. / Moore, N.E. / Han, J. / McMahon, M. / Wang, M. / Malladi, S.K. / Mohammed, B.M. / Zhou, J.Q. / Schmitz, A.J. / Hoehn, K.B. / Carreno, J.M. / ...Authors: McIntire, K.M. / Meng, H. / Lin, T.H. / Kim, W. / Moore, N.E. / Han, J. / McMahon, M. / Wang, M. / Malladi, S.K. / Mohammed, B.M. / Zhou, J.Q. / Schmitz, A.J. / Hoehn, K.B. / Carreno, J.M. / Yellin, T. / Suessen, T. / Middleton, W.D. / Teefey, S.A. / Presti, R.M. / Krammer, F. / Turner, J.S. / Ward, A.B. / Wilson, I.A. / Kleinstein, S.H. / Ellebedy, A.H.
History
DepositionAug 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 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

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_B, Fab heavy chain
L: GC_w13_B, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1499
Polymers103,2344
Non-polymers9155
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_B, Fab heavy chain
L: GC_w13_B, Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_B, Fab heavy chain
L: GC_w13_B, Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_B, Fab heavy chain
L: GC_w13_B, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,44727
Polymers309,70112
Non-polymers2,74615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area47670 Å2
ΔGint-269 kcal/mol
Surface area117830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.531, 167.531, 167.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 36357.000 Da / Num. of mol.: 1 / Fragment: HA1 subdomain (UNP residues 18-344)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: C3W5S1
#2: Protein Hemagglutinin


Mass: 19789.908 Da / Num. of mol.: 1 / Fragment: HA2 subdomain (UNP residues 326-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A1D5AKA4

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Antibody , 2 types, 2 molecules HL

#3: Antibody GC_w13_B, Fab heavy chain


Mass: 23728.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody GC_w13_B, Fab light chain


Mass: 23357.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 3 molecules

#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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: obtained synthetically / 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 , 1 types, 2 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.76 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, pH 6.2, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.25→44.77 Å / Num. obs: 24917 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 1 / Net I/σ(I): 12
Reflection shellResolution: 3.25→3.31 Å / Num. unique obs: 1320 / CC1/2: 0.67 / Rpim(I) all: 0.053 / Rsym value: 0.189 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M4Y

4m4y


Resolution: 3.25→44.77 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 1320 5.3 %
Rwork0.2752 --
obs0.2759 24915 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7242 0 58 0 7300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027462
X-RAY DIFFRACTIONf_angle_d0.44110125
X-RAY DIFFRACTIONf_dihedral_angle_d3.7961027
X-RAY DIFFRACTIONf_chiral_restr0.0461133
X-RAY DIFFRACTIONf_plane_restr0.0041297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.380.39591530.35132589X-RAY DIFFRACTION100
3.38-3.540.35121300.32252639X-RAY DIFFRACTION100
3.54-3.720.37051370.33592571X-RAY DIFFRACTION100
3.72-3.960.29631390.30112609X-RAY DIFFRACTION100
3.96-4.260.31321240.28392611X-RAY DIFFRACTION100
4.26-4.690.23321410.26122624X-RAY DIFFRACTION100
4.69-5.360.25531730.2492589X-RAY DIFFRACTION100
5.37-6.750.28771630.27472629X-RAY DIFFRACTION100
6.76-44.770.27241600.24572734X-RAY DIFFRACTION100

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