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- PDB-6xpr: Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hema... -

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Basic information

Entry
Database: PDB / ID: 6xpr
TitleHuman antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2)
Components
  • (antibody D2 H1-1/H3-1 H3 ...) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / human antibody antigen complex / hemagglutinin / 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 / 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: 4.092 Å
AuthorsMcCarthy, K.R. / Harrison, S.C. / Lee, J.
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 8, 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
B: antibody D2 H1-1/H3-1 H3 heavy chain
C: antibody D2 H1-1/H3-1 H3 light chain
D: Hemagglutinin
E: antibody D2 H1-1/H3-1 H3 heavy chain
F: antibody D2 H1-1/H3-1 H3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,39012
Polymers163,1296
Non-polymers2,2616
Water0
1
A: Hemagglutinin
B: antibody D2 H1-1/H3-1 H3 heavy chain
C: antibody D2 H1-1/H3-1 H3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9596
Polymers81,5643
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin
E: antibody D2 H1-1/H3-1 H3 heavy chain
F: antibody D2 H1-1/H3-1 H3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4316
Polymers81,5643
Non-polymers8673
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.490, 204.490, 132.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Hemagglutinin /


Mass: 32618.846 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/Texas/50/2012(H3N2))
Strain: A/Texas/50/2012(H3N2) / Gene: HA, L998_47834gpHA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4L1D1

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Antibody , 2 types, 4 molecules BECF

#2: Antibody antibody D2 H1-1/H3-1 H3 heavy chain


Mass: 25692.869 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 D2 H1-1/H3-1 H3 light chain


Mass: 23252.756 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 , 3 types, 6 molecules

#4: 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.: 2
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
#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-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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: 4.9 Å3/Da / Density % sol: 74.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M lithium sulfate, 30% v/v PEG400, 0.1 M trisodium citrate, pH 5.6

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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: 4.092→49.12 Å / Num. obs: 25192 / % possible obs: 98.41 % / Redundancy: 3.4 % / Biso Wilson estimate: 97.78 Å2 / CC1/2: 0.965 / CC star: 0.991 / Rmerge(I) obs: 0.3059 / Rpim(I) all: 0.1897 / Rrim(I) all: 0.3614 / Net I/σ(I): 4.53
Reflection shellResolution: 4.092→4.238 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8466 / CC1/2: 0.776 / CC star: 0.935 / Rpim(I) all: 0.5332 / Rrim(I) all: 1.012 / % possible all: 98.07

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5W08, 4Y5V, & 6E4X

5w08

4y5v

6e4x


Resolution: 4.092→49.117 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2981 1236 4.92 %
Rwork0.2518 23910 -
obs0.2541 25146 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 255.6 Å2 / Biso mean: 131.0644 Å2 / Biso min: 26.12 Å2
Refinement stepCycle: final / Resolution: 4.092→49.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10866 0 148 0 11014
Biso mean--168.78 --
Num. residues----1407
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.092-4.25580.38151490.3179260798
4.2558-4.44930.34121290.2804261698
4.4493-4.68370.3031180.2601263899
4.6837-4.97690.26951610.24132656100
4.9769-5.36080.28751370.2395263699
5.3608-5.89940.3251500.2559263998
5.8994-6.75120.30351220.2509268899
6.7512-8.49870.3171300.2494269599
8.4987-49.1170.24581400.2242273597

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