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- PDB-6uig: Crystal structure of human monoclonal antibody H7.200 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6uig
TitleCrystal structure of human monoclonal antibody H7.200 in complex with H7N9 hemagglutinin HA1
Components
  • H7.200 Fab heavy chain
  • H7.200 Fab light chain
  • Hemagglutinin
KeywordsANTIVIRAL PROTEIN / influenza A / monoclonal antibody
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 / metal ion binding
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: 3.2 Å
AuthorsDong, J. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Clin.Invest. / Year: 2020
Title: Anti-influenza H7 human antibody targets antigenic site in hemagglutinin head domain interface.
Authors: Dong, J. / Gilchuk, I. / Li, S. / Irving, R. / Goff, M.T. / Turner, H.L. / Ward, A.B. / Carnahan, R.H. / Crowe Jr., J.E.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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
G: Hemagglutinin
H: H7.200 Fab heavy chain
L: H7.200 Fab light chain
A: Hemagglutinin
B: H7.200 Fab heavy chain
C: H7.200 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2168
Polymers162,7746
Non-polymers4422
Water00
1
G: Hemagglutinin
H: H7.200 Fab heavy chain
L: H7.200 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6084
Polymers81,3873
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-26 kcal/mol
Surface area28880 Å2
MethodPISA
2
A: Hemagglutinin
B: H7.200 Fab heavy chain
C: H7.200 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6084
Polymers81,3873
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-26 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.493, 156.493, 229.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Hemagglutinin


Mass: 33755.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2013(H7N9) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A0A4Y5QYN9, UniProt: R4NN21*PLUS
#2: Antibody H7.200 Fab heavy chain


Mass: 24268.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody H7.200 Fab light chain


Mass: 23362.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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: 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
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: 4.31 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 6.0, 10% isopropanol, 22% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.2→49.821 Å / Num. obs: 47601 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 0.607 / Num. unique obs: 6843

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5J

4n5j


Resolution: 3.2→49.821 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2377 5 %
Rwork0.2072 45125 -
obs0.2085 47502 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.14 Å2 / Biso mean: 88.0847 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→49.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10205 0 28 0 10233
Biso mean--154.54 --
Num. residues----1395
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2001-3.26540.37411530.34862607100
3.2654-3.33640.3381400.31272594100
3.3364-3.4140.34181270.28472628100
3.414-3.49930.28021350.27112613100
3.4993-3.59390.30611390.27122610100
3.5939-3.69960.29651300.26722655100
3.6996-3.8190.32651500.2432609100
3.819-3.95550.26431300.22522644100
3.9555-4.11380.23991370.20472636100
4.1138-4.30090.2091640.18092607100
4.3009-4.52750.18821440.15672639100
4.5275-4.81090.18821410.14872661100
4.8109-5.1820.16541480.14742655100
5.182-5.70290.2231530.17022671100
5.7029-6.52650.23361200.19922731100
6.5265-8.21670.22531360.21892743100
8.2167-49.8210.20051300.2154282297
Refinement TLS params.Method: refined / Origin x: 39.3364 Å / Origin y: -38.6148 Å / Origin z: 29.3136 Å
111213212223313233
T0.5643 Å2-0.0468 Å20.0484 Å2-0.5582 Å20.0735 Å2--0.6118 Å2
L0.3598 °2-0.0036 °20.0306 °2-0.3986 °20.0734 °2--0.6474 °2
S0.0068 Å °-0.0339 Å °-0.028 Å °-0.0444 Å °0.0361 Å °-0.0096 Å °0.0614 Å °0.0304 Å °-0.0415 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allG32 - 300
2X-RAY DIFFRACTION1allG301
3X-RAY DIFFRACTION1allH1 - 221
4X-RAY DIFFRACTION1allL1 - 212
5X-RAY DIFFRACTION1allA32 - 300
6X-RAY DIFFRACTION1allA301
7X-RAY DIFFRACTION1allB1 - 222
8X-RAY DIFFRACTION1allC1 - 210

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