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- PDB-6chx: High Resolution Crystal Structure of the Hemagglutinin H1 Head Do... -

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Basic information

Entry
Database: PDB / ID: 6chx
TitleHigh Resolution Crystal Structure of the Hemagglutinin H1 Head Domain of Influenza A virus Solomon Islands
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / influenza A virus / Solomon Islands
Function / homology
Function and homology information


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
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsDong, J. / Sevy, A.M. / Crowe, J.E.
CitationJournal: To Be Published
Title: High Resolution Crystal Structure of the Hemagglutinin H1 Head Domain of Influenza A virus Solomon Islands
Authors: Dong, J. / Sevy, A.M. / Crowe, J.E.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)48,5862
Polymers48,5862
Non-polymers00
Water9,314517
1
A: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)24,2931
Polymers24,2931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)24,2931
Polymers24,2931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.315, 30.575, 78.718
Angle α, β, γ (deg.)90.00, 114.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin


Mass: 24293.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Escherichia coli (E. coli) / References: UniProt: D1MNG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
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: 1.79 Å3/Da / Density % sol: 31.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M Tris-HCl pH 8.0, 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→42.73 Å / Num. obs: 66743 / % possible obs: 96.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.499 / Num. unique all: 3260

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.4→39.642 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.96
RfactorNum. reflection% reflection
Rfree0.2108 3300 4.95 %
Rwork0.1736 --
obs0.1754 66724 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→39.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 517 3885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013614
X-RAY DIFFRACTIONf_angle_d1.0364943
X-RAY DIFFRACTIONf_dihedral_angle_d7.5292079
X-RAY DIFFRACTIONf_chiral_restr0.098503
X-RAY DIFFRACTIONf_plane_restr0.007655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3988-1.41880.36951180.30682432X-RAY DIFFRACTION91
1.4188-1.43990.31121380.25232568X-RAY DIFFRACTION95
1.4399-1.46250.28341370.22732567X-RAY DIFFRACTION95
1.4625-1.48640.2271380.21892571X-RAY DIFFRACTION95
1.4864-1.51210.26121240.20232600X-RAY DIFFRACTION95
1.5121-1.53960.2451530.20412576X-RAY DIFFRACTION96
1.5396-1.56920.2471440.20352561X-RAY DIFFRACTION95
1.5692-1.60120.24541390.19462569X-RAY DIFFRACTION95
1.6012-1.6360.21311440.18922670X-RAY DIFFRACTION98
1.636-1.67410.2251270.18622586X-RAY DIFFRACTION95
1.6741-1.71590.22331370.17952604X-RAY DIFFRACTION97
1.7159-1.76230.20591310.18472654X-RAY DIFFRACTION97
1.7623-1.81420.20831320.17722616X-RAY DIFFRACTION96
1.8142-1.87280.22251390.18142672X-RAY DIFFRACTION98
1.8728-1.93970.21421640.16972596X-RAY DIFFRACTION96
1.9397-2.01730.19831240.16392694X-RAY DIFFRACTION98
2.0173-2.10910.20661370.16212653X-RAY DIFFRACTION98
2.1091-2.22030.18961400.17072660X-RAY DIFFRACTION97
2.2203-2.35940.20861500.17672711X-RAY DIFFRACTION98
2.3594-2.54160.22521250.17362725X-RAY DIFFRACTION99
2.5416-2.79730.21731580.17332717X-RAY DIFFRACTION99
2.7973-3.20190.19851170.16752742X-RAY DIFFRACTION99
3.2019-4.03340.1711600.14442767X-RAY DIFFRACTION99
4.0334-39.65790.20591240.16222913X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -28.9423 Å / Origin y: 2.9252 Å / Origin z: 16.872 Å
111213212223313233
T0.0879 Å2-0.0023 Å2-0.0141 Å2-0.0812 Å20.0055 Å2--0.1072 Å2
L0.3609 °2-0.1934 °2-0.5782 °2-0.2296 °20.4103 °2--1.3008 °2
S-0.0052 Å °-0.0805 Å °0.0357 Å °0.039 Å °0.0535 Å °-0.0406 Å °0.0124 Å °0.1556 Å °-0.0543 Å °
Refinement TLS groupSelection details: all

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