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- PDB-8txp: Crystal structure of 05.GC.w13.01 Fab in complex with H1 HA from ... -

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Basic information

Entry
Database: PDB / ID: 8txp
TitleCrystal structure of 05.GC.w13.01 Fab in complex with H1 HA from A/California/04/2009(H1N1)
Components
  • (GC_w13_A, 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: 2.75 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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5049
Polymers103,8954
Non-polymers2,6085
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,51127
Polymers311,68612
Non-polymers7,82515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area55160 Å2
ΔGint-138 kcal/mol
Surface area120360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.350, 128.350, 155.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 36729.402 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 / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: C3W5S1
#2: Protein Hemagglutinin


Mass: 20206.320 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 / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: I1ZFF9

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Antibody , 2 types, 2 molecules HL

#3: Antibody GC_w13_A, Fab heavy chain


Mass: 23561.643 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_A, Fab light chain


Mass: 23397.830 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, 5 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.: 2
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: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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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: 3.56 Å3/Da / Density % sol: 65.49 %
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: 2.75→45.24 Å / Num. obs: 38915 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 0.99 / Rpim(I) all: 0.035 / Rsym value: 0.137 / Net I/σ(I): 21.6
Reflection shellResolution: 2.76→2.8 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1962 / CC1/2: 0.56 / Rpim(I) all: 0.423 / Rsym value: 1 / % possible all: 100

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Processing

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

4m4y


Resolution: 2.75→45.24 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 1962 5.05 %
Rwork0.2496 --
obs0.2517 38860 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7231 0 173 0 7404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037567
X-RAY DIFFRACTIONf_angle_d0.62110271
X-RAY DIFFRACTIONf_dihedral_angle_d7.991092
X-RAY DIFFRACTIONf_chiral_restr0.0441181
X-RAY DIFFRACTIONf_plane_restr0.0051301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.44491010.39552623X-RAY DIFFRACTION100
2.82-2.90.39811610.34712584X-RAY DIFFRACTION100
2.9-2.990.38371330.31972625X-RAY DIFFRACTION100
2.99-3.080.32931370.28772599X-RAY DIFFRACTION100
3.08-3.190.3391630.28842596X-RAY DIFFRACTION100
3.19-3.320.35181570.29852597X-RAY DIFFRACTION100
3.32-3.470.40741110.31492639X-RAY DIFFRACTION100
3.47-3.650.33341490.27252571X-RAY DIFFRACTION99
3.65-3.880.40111340.28092631X-RAY DIFFRACTION99
3.88-4.180.32061230.22922631X-RAY DIFFRACTION100
4.18-4.60.22941330.20992678X-RAY DIFFRACTION100
4.6-5.270.22361570.2012630X-RAY DIFFRACTION100
5.27-6.630.23561530.23692686X-RAY DIFFRACTION100
6.63-45.240.26271500.22942808X-RAY DIFFRACTION100

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