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- PDB-4lcx: The structure of hemagglutinin from avian-origin H7N9 influenza v... -

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Basic information

Entry
Database: PDB / ID: 4lcx
TitleThe structure of hemagglutinin from avian-origin H7N9 influenza virus (A/Shanghai/1/2013)
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN / homotrimer / virus attachment and membrane fusion
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 B / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.094 Å
AuthorsShi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses.
Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0249
Polymers162,3616
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33050 Å2
ΔGint-138 kcal/mol
Surface area55990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.880, 225.982, 75.336
Angle α, β, γ (deg.)90.00, 117.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin HA1


Mass: 34485.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/1/2013 (H7N9) / Description: baculovirus expressing system / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: V5IRV0*PLUS
#2: Protein Hemagglutinin HA2


Mass: 19634.502 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/1/2013 (H7N9) / Description: baculovirus expressing system / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: V5IRU7*PLUS
#3: 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.: 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
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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 8000, 18% Ethylene glycol, 0.12 M Di-Ethyleneglycol, 0.12 M Tri-Ethyleneglycol, 0.12 M TetraEthyleneglycol, 0.12 M Penta-Ethyleneglycol, 0.1 M Tris, 0.1 M Bicine, pH 8.5, VAPOR ...Details: 18% PEG 8000, 18% Ethylene glycol, 0.12 M Di-Ethyleneglycol, 0.12 M Tri-Ethyleneglycol, 0.12 M TetraEthyleneglycol, 0.12 M Penta-Ethyleneglycol, 0.1 M Tris, 0.1 M Bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.094→50 Å / Num. all: 39528 / Num. obs: 39468 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.1→3.21 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.094→49.882 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1972 5 %RANDOM
Rwork0.2263 ---
all0.2283 39528 --
obs0.2283 39468 98.12 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.826 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.9817 Å2-0 Å21.2916 Å2
2---29.5169 Å2-0 Å2
3---12.5353 Å2
Refinement stepCycle: LAST / Resolution: 3.094→49.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11379 0 42 0 11421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111649
X-RAY DIFFRACTIONf_angle_d1.34315699
X-RAY DIFFRACTIONf_dihedral_angle_d19.094302
X-RAY DIFFRACTIONf_chiral_restr0.0931689
X-RAY DIFFRACTIONf_plane_restr0.0042082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0936-3.1710.4391980.35392163X-RAY DIFFRACTION80
3.171-3.25670.44311400.34142745X-RAY DIFFRACTION100
3.2567-3.35250.381370.3042701X-RAY DIFFRACTION100
3.3525-3.46070.30391510.29462690X-RAY DIFFRACTION100
3.4607-3.58430.29761520.26382759X-RAY DIFFRACTION100
3.5843-3.72780.29951470.24632683X-RAY DIFFRACTION100
3.7278-3.89740.30251540.23472710X-RAY DIFFRACTION99
3.8974-4.10280.26171430.21962721X-RAY DIFFRACTION100
4.1028-4.35970.24611540.20112694X-RAY DIFFRACTION100
4.3597-4.69610.20621260.1842755X-RAY DIFFRACTION100
4.6961-5.16820.20921240.19512727X-RAY DIFFRACTION100
5.1682-5.91510.25561550.22712721X-RAY DIFFRACTION100
5.9151-7.44840.24091420.21142747X-RAY DIFFRACTION100
7.4484-49.8880.25461490.2092680X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -19.0408 Å / Origin y: -10.0818 Å / Origin z: 10.5644 Å
111213212223313233
T0.4859 Å20.0332 Å20.0076 Å2-0.6453 Å20.0009 Å2--0.5638 Å2
L0.2169 °20.0205 °20.0398 °2-1.8498 °2-0.0335 °2--0.3898 °2
S-0.0037 Å °0.0602 Å °0.0691 Å °0.1335 Å °-0.016 Å °0.1498 Å °-0.0972 Å °-0.0485 Å °-0 Å °
Refinement TLS groupSelection details: all

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